bims-histon 2020-06-14 papers

bims-histon

Biomed News

on Histones

Issue of 2020–06–14
38 papers selected by
Benjamin Weekley, University of Southern California

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction.
Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions.
NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis.
Linker histone variant H1T functions as a chromatin de-condenser on genic regions.
Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency.
Spt6 is a maintenance factor for centromeric CENP-A.
Linker histone epitopes are hidden by in situ higher-order chromatin structure.
Roles of OCT4 in pathways of embryonic development and cancer progression.
HDAC3 is required for XPC recruitment and nucleotide excision repair of DNA damage induced by UV irradiation.
ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype.
Histone chaperone FACT is essential to overcome replication stress in mammalian cells.
Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi.
Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model.
The Emerging Roles of Heterochromatin in Cell Migration.
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue.
EZH2-inhibitor DZNep enhances apoptosis of renal tubular epithelial cells in presence and absence of cisplatin.
Epigenetic strategies synergize with PD-L1/PD-1 targeted cancer immunotherapies to enhance antitumor responses.
Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection.
CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.
Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early- and late-replicating euchromatin.
The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle.
Acetylation/methylation at lysine 9 in histone H3 as a mark of nucleosome asymmetry in human somatic breast cells.
CTCF-mediated genome organization and leukemogenesis.
CRISPR-tools for physiology & cell state changes - potential of transcriptional engineering and epigenome editing.
Overexpression of H3K36 methyltransferase NSD in glial cells affects brain development in Drosophila.
The Ras-ERK1/2 signaling pathway regulates H3K9ac through PCAF to promote the development of pancreatic cancer.
Evidence for NAD+-dependent histone dynamics and tunneling associated conformational transitions in circadian deacetylase SIRT1.
The Expression and Localization of Histone Acetyltransferases HAT1 and PCAF in Neurons and Astrocytes of the Photothrombotic Stroke-Induced Penumbra in the Rat Brain Cortex.
Nuclear Receptor Binding Protein 2 Is Downregulated in Medulloblastoma, and Reduces Tumor Cell Survival upon Overexpression.
Maternal H3K27me3-dependent autosomal and X chromosome imprinting.
Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code.
Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.
p300-mediated acetylation of histone demethylase JMJD1A prevents its degradation by ubiquitin ligase STUB1 and enhances its activity in prostate cancer.
Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.
Prognostic role of H3K27M mutation, histone H3K27 methylation status, and EZH2 expression in diffuse spinal cord gliomas.
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation.
Epigenetic and transcriptional regulation of osteoclast differentiation.
The cell adhesion molecule L1 interacts with nuclear proteins via its intracellular domain.

Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 201920725. [Epub ahead of print]

H1 linker histones silence repetitive elements by promoting both histone H3K9 methylation and chromatin compaction.

Sean E Healton, Hugo D Pinto, Laxmi N Mishra, Gregory A Hamilton, Justin C Wheat, Kalina Swist-Rosowska, Nicholas Shukeir, Yali Dou, Ulrich Steidl, Thomas Jenuwein, Matthew J Gamble, Arthur I Skoultchi.

  Nearly 50% of mouse and human genomes are composed of repetitive sequences. Transcription of these sequences is tightly controlled during development to prevent genomic instability, inappropriate gene activation and other maladaptive processes. Here, we demonstrate an integral role for H1 linker histones in silencing repetitive elements in mouse embryonic stem cells. Strong H1 depletion causes a profound de-repression of several classes of repetitive sequences, including major satellite, LINE-1, and ERV. Activation of repetitive sequence transcription is accompanied by decreased H3K9 trimethylation of repetitive sequence chromatin. H1 linker histones interact directly with Suv39h1, Suv39h2, and SETDB1, the histone methyltransferases responsible for H3K9 trimethylation of chromatin within these regions, and stimulate their activity toward chromatin in vitro. However, we also implicate chromatin compaction mediated by H1 as an additional, dominant repressive mechanism for silencing of repetitive major satellite sequences. Our findings elucidate two distinct, H1-mediated pathways for silencing heterochromatin.

Keywords:  chromatin; epigenetics; linker histones; repetitive elements

DOI:  https://doi.org/10.1073/pnas.1920725117
Cell Rep. 2020 Jun 09. pii: S2211-1247(20)30731-2. [Epub ahead of print]31(10): 107751

Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions.

Julia V DiFiore, Travis S Ptacek, Yi Wang, Bing Li, Jeremy M Simon, Brian D Strahl.

  Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. Although H3K36me1/2 and H3K36me3 are functionally redundant in many SET2 deletion phenotypes, we found that H3K36me3 has a unique function related to Bur1 kinase activity and FACT (facilitates chromatin transcription) complex function. Further, during nutrient stress, either H3K36me1/2 or H3K36me3 represses high levels of histone acetylation and cryptic transcription that arises from within genes. Our findings uncover the potential for the regulation of diverse chromatin functions by different H3K36 methylation states.

Keywords:  H3K36 methylation; RNA Polymerase II; Set2; chromatin; cryptic transcription; epigenetics; histone; nutrient stress; transcriptional regulation

DOI:  https://doi.org/10.1016/j.celrep.2020.107751
Nat Commun. 2020 Jun 08. 11(1): 2887

NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis.

Yafei Wang, Zhenhui Zhong, Yaxin Zhang, Linhao Xu, Suhua Feng, Shima Rayatpisheh, James A Wohlschlegel, Zonghua Wang, Steven E Jacobsen, Israel Ausin.

In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.

DOI: https://doi.org/10.1038/s41467-020-16691-x
Biochem Biophys Res Commun. 2020 Jun 05. pii: S0006-291X(20)31041-X. [Epub ahead of print]

Linker histone variant H1T functions as a chromatin de-condenser on genic regions.

Koji Hayakawa, Ruiko Tani, Kenta Nishitani, Satoshi Tanaka.

  Linker histone H1 is mainly localized in the linker DNA region, between two nucleosome cores, and regulates chromatin structures linking gene expression. There are 11 variants in histone H1, and each variant has unique functions. Our previous study demonstrates that one of the H1 variants, H1T is mainly localized in the nucleolus and targets the rDNA repeat region. Moreover, H1T condenses the chromatin structures on rDNA to repress pre-rRNA expression. Although H1T is partially localized in the nucleoplasm area, the functions of H1T in the non-repeat genic region are unclear. In this study, we aimed to identify the target loci and the role of H1T in the genic region. Chromatin immunoprecipitation sequencing analysis showed that H1T is localized around the transcriptional start site and the chromatin structures of the region were relaxed. H1T knockdown and overexpression experiments revealed that H1T induced chromatin de-condensation and was associated with the increased expression of target genes. Moreover, we observed H1T co-localization with transcriptional factor SPZ1 on the genic region. Collectively, H1T has opposing roles in the genic region and in rDNA repeats; H1T functions to facilitate chromatin relaxation linked gene activation.

Keywords:  Chromatin; De-condensation; Genic region; Linker histone; Testis-specific

DOI:  https://doi.org/10.1016/j.bbrc.2020.05.119
Front Microbiol. 2020 ;11 850

Epigenetic Regulation of Kaposi's Sarcoma-Associated Herpesvirus Latency.

Mel Campbell, Wan-Shan Yang, Wayne W Yeh, Chen-Hsuan Kao, Pei-Ching Chang.

  Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic γ-herpesvirus that infects humans and exhibits a biphasic life cycle consisting of latent and lytic phases. Following entry into host cells, the KSHV genome undergoes circularization and chromatinization into an extrachromosomal episome ultimately leading to the establishment of latency. The KSHV episome is organized into distinct chromatin domains marked by variations in repressive or activating epigenetic modifications, including DNA methylation, histone methylation, and histone acetylation. Thus, the development of KSHV latency is believed to be governed by epigenetic regulation. In the past decade, interrogation of the KSHV epitome by genome-wide approaches has revealed a complex epigenetic mark landscape across KSHV genome and has uncovered the important regulatory roles of epigenetic modifications in governing the development of KSHV latency. Here, we highlight many of the findings regarding the role of DNA methylation, histone modification, post-translational modification (PTM) of chromatin remodeling proteins, the contribution of long non-coding RNAs (lncRNAs) in regulating KSHV latency development, and the role of higher-order episomal chromatin architecture in the maintenance of latency and the latent-to-lytic switch.

Keywords:  DNA methylation; Kaposi’s sarcoma-associated herpesvirus (KSHV); epigenetic; histone modification; long non-coding RNAs (lncRNAs); post-translational modification (PTM)

DOI:  https://doi.org/10.3389/fmicb.2020.00850
Nat Commun. 2020 Jun 10. 11(1): 2919

Spt6 is a maintenance factor for centromeric CENP-A.

Georg O M Bobkov, Anming Huang, Sebastiaan J W van den Berg, Sreyoshi Mitra, Eduard Anselm, Vasiliki Lazou, Sarah Schunter, Regina Feederle, Axel Imhof, Alexandra Lusser, Lars E T Jansen, Patrick Heun.

Replication and transcription of genomic DNA requires partial disassembly of nucleosomes to allow progression of polymerases. This presents both an opportunity to remodel the underlying chromatin and a danger of losing epigenetic information. Centromeric transcription is required for stable incorporation of the centromere-specific histone dCENP-A in M/G1 phase, which depends on the eviction of previously deposited H3/H3.3-placeholder nucleosomes. Here we demonstrate that the histone chaperone and transcription elongation factor Spt6 spatially and temporarily coincides with centromeric transcription and prevents the loss of old CENP-A nucleosomes in both Drosophila and human cells. Spt6 binds directly to dCENP-A and dCENP-A mutants carrying phosphomimetic residues alleviate this association. Retention of phosphomimetic dCENP-A mutants is reduced relative to wildtype, while non-phosphorylatable dCENP-A retention is increased and accumulates at the centromere. We conclude that Spt6 acts as a conserved CENP-A maintenance factor that ensures long-term stability of epigenetic centromere identity during transcription-mediated chromatin remodeling.

DOI: https://doi.org/10.1038/s41467-020-16695-7
Epigenetics Chromatin. 2020 Jun 06. 13(1): 26

Linker histone epitopes are hidden by in situ higher-order chromatin structure.

Vladimir B Teif, Travis J Gould, Christopher T Clarkson, Logan Boyd, Enoch B Antwi, Naveed Ishaque, Ada L Olins, Donald E Olins.

BACKGROUND: Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements.
RESULTS: We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde.
CONCLUSION: Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized higher-order structure with hidden H1 epitopes. However, the H1 xChIP-seq comparison cannot define their differences. Application of the xxChIP-seq versus H1 xChIP-seq method is particularly relevant to chromatin-associated proteins, such as linker histones, that play dynamic roles in establishing chromatin higher-order structure.

DOI: https://doi.org/10.1186/s13072-020-00345-9
Mech Ageing Dev. 2020 Jun 09. pii: S0047-6374(20)30082-8. [Epub ahead of print] 111286

Roles of OCT4 in pathways of embryonic development and cancer progression.

Samir Kumar Patra.

  Somatic cells may be reprogrammed to pluripotent state by ectopic expression of certain transcription factors; namely, OCT4, SOX2, KLF4 and c-MYC. However, the molecular and cellular mechanisms are not adequately understood, especially for human embryonic development. Studies during the last five years implicated importance of OCT4 in human zygotic genome activation (ZGA), patterns of OCT4 protein folding and role of specialized sequences in binding to DNA for modulation of gene expression during development. Epigenetic modulation of OCT4 gene and post translational modifications of OCT4 protein activity in the context of multiple cancers are important issues. A consensus is emerging that chromatin organization and epigenetic landscape play crucial roles for the interactions of transcription factors, including OCT4 with the promoters and/or regulatory sequences of genes associated with human embryonic development (ZGA through lineage specification) and that when the epigenome niche is deregulated OCT4 helps in cancer progression, and how OCT4 silencing in somatic cells of adult organisms may impact ageing.

Keywords:  OCT4; Zygote; breast cancer; cancers; embryonic development; epigenetic modifications; epigenome; pluripotency; pluripotency inducing factors; prostate cancer; totipotency

DOI:  https://doi.org/10.1016/j.mad.2020.111286
Mol Cancer Res. 2020 Jun 11. pii: molcanres.0214.2020. [Epub ahead of print]

HDAC3 is required for XPC recruitment and nucleotide excision repair of DNA damage induced by UV irradiation.

Koji Nishimoto, Hiroyuki Niida, Chiharu Uchida, Tatsuya Ohhata, Kyoko Kitagawa, Akira Motegi, Takafumi Suda, Masatoshi Kitagawa.

Recent studies have demonstrated that lysine acetylation of histones is crucial for nucleotide excision repair (NER) by relaxing the chromatin structure, which facilitates the recruitment of repair factors. However, few studies have focused on the contribution of histone deacetylases (HDACs) to NER. Here, we found that histone H3 Lys14 (H3K14) was deacetylated by HDAC3 after UV irradiation. Depletion of HDAC3 caused defects in cyclobutene pyrimidine dimer excision and sensitized cells to UV irradiation. HDAC3-depleted cells had impaired unscheduled DNA synthesis, but not recovery of RNA synthesis, which indicates that HDAC3 was required for global genome NER. Moreover, Xeroderma pigmentosum, complementation group C (XPC) accumulation at the local UV-irradiated area was attenuated in HDAC3-depleted cells. In addition to the delay of XPC accumulation at DNA damage sites, XPC ubiquitylation was inhibited in HDAC3-depleted cells. These results suggest that the deacetylation of histone H3K14 by HDAC3 after UV irradiation contributes to XPC recruitment to DNA lesions to promote global genome NER. Implications: Involvement of histone deacetylation for XPC accumulation after UV irradiation indicates conversion of chromatin structure is essential for nucleotide excision repair in human cancer cells.

DOI: https://doi.org/10.1158/1541-7786.MCR-20-0214
Oncogene. 2020 Jun 07.

ZSCAN4 facilitates chromatin remodeling and promotes the cancer stem cell phenotype.

Benjamin A Portney, Michal Arad, Aditi Gupta, Robert A Brown, Raju Khatri, Phyo Nay Lin, Andrea M Hebert, Kristen H Angster, Lorna E Silipino, W Alex Meltzer, Rodney J Taylor, Michal Zalzman.

Cancer stem cells (CSCs) are cells within tumors that maintain the ability to self-renew, drive tumor growth, and contribute to therapeutic resistance and cancer recurrence. In this study, we investigate the role of Zinc finger and SCAN domain containing 4 (ZSCAN4) in human head and neck squamous cell carcinoma (HNSCC). The murine Zscan4 is involved in telomere maintenance and genomic stability of mouse embryonic stem cells. Our data indicate that the human ZSCAN4 is enriched for, marks and is co-expressed with CSC markers in HNSCC. We show that transient ZSCAN4 induction for just 2 days increases CSC frequency both in vitro and in vivo and leads to upregulation of pluripotency and CSC factors. Importantly, we define for the first time the role of ZSCAN4 in altering the epigenetic profile and regulating the chromatin state. Our data show that ZSCAN4 leads to a functional histone 3 hyperacetylation at the promoters of OCT3/4 and NANOG, leading to an upregulation of CSC factors. Consistently, ZSCAN4 depletion leads to downregulation of CSC markers, decreased ability to form tumorspheres and severely affects tumor growth. Our study suggests that ZSCAN4 plays an important role in the maintenance of the CSC phenotype, indicating it is a potential therapeutic target in HNSCC.

DOI: https://doi.org/10.1038/s41388-020-1333-1
Oncogene. 2020 Jun 12.

Histone chaperone FACT is essential to overcome replication stress in mammalian cells.

Laura Prendergast, Erin Hong, Alfiya Safina, Dante Poe, Katerina Gurova.

The histone chaperone FACT is upregulated during mammary tumorigenesis and necessary for the viability and growth of breast tumor cells. We established that only proliferating tumor cells are sensitive to FACT knockdown, suggesting that FACT functions during DNA replication in tumor cells but not in normal cells. We hypothesized that the basal level of replication stress defines the FACT dependence of cells. Using genetic and chemical tools, we demonstrated that FACT is needed to overcome replication stress. In the absence of FACT during replication stress, the MCM2-7 helicase dissociates from chromatin, resulting in the absence of ssDNA accumulation, RPA binding, and activation of the ATR/CHK1 checkpoint response. Without this response, stalled replication forks are not stabilized, and new origin firing cannot be prevented, leading to the accumulation of DNA damage and cell death. Thus, we propose a novel role for FACT as a factor preventing helicase dissociation from chromatin during replication stress.

DOI: https://doi.org/10.1038/s41388-020-1346-9
Genes (Basel). 2020 Jun 09. pii: E638. [Epub ahead of print]11(6):

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi.

John B Ridenour, Mareike Möller, Michael Freitag.

  Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.

Keywords:  Cryptococcus; Fusarium; Neurospora; PRC2; Zymoseptoria; fungi; histones; lysine methylation; polycomb repressive complex

DOI:  https://doi.org/10.3390/genes11060638
F1000Res. 2020 ;pii: F1000 Faculty Rev-299. [Epub ahead of print]9

Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model.

Bagdeser Akdogan-Ozdilek, Katherine L Duval, Mary G Goll.

  Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.

Keywords:  DNA methylation; chromatin; histones; maternal-to-zygotic transition; transcription; zebrafish

DOI:  https://doi.org/10.12688/f1000research.21809.1
Front Cell Dev Biol. 2020 ;8 394

The Emerging Roles of Heterochromatin in Cell Migration.

Gabi Gerlitz.

  Cell migration is a key process in health and disease. In the last decade an increasing attention is given to chromatin organization in migrating cells. In various types of cells induction of migration leads to a global increase in heterochromatin levels. Heterochromatin is required for optimal cell migration capabilities, since various interventions with heterochromatin formation impeded the migration rate of numerous cell types. Heterochromatin supports the migration process by affecting both the mechanical properties of the nucleus as well as the genetic processes taking place within it. Increased heterochromatin levels elevate nuclear rigidity in a manner that allows faster cell migration in 3D environments. Condensed chromatin and a more rigid nucleus may increase nuclear durability to shear stress and prevent DNA damage during the migration process. In addition, heterochromatin reorganization in migrating cells is important for induction of migration-specific transcriptional plan together with inhibition of many other unnecessary transcriptional changes. Thus, chromatin organization appears to have a key role in the cellular migration process.

Keywords:  cancer metastasis; cell nucleus; chromatin; genome organization; histones

DOI:  https://doi.org/10.3389/fcell.2020.00394
Nat Commun. 2020 Jun 09. 11(1): 2907

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue.

Miao Liu, Yanfang Lu, Bing Yang, Yanbo Chen, Jonathan S D Radda, Mengwei Hu, Samuel G Katz, Siyuan Wang.

The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and lamina- and nucleolus-associated regions, have been discovered. However, how these structures are arranged in the same cell and how they are mutually correlated in different cell types in mammalian tissue are largely unknown. Here, we develop Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We apply this method in mouse fetal liver, and identify de novo cell-type-specific chromatin architectures associated with gene expression, as well as cell-type-independent principles of chromatin organization. Polymer simulation shows that both intra-chromosomal self-associating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our results illustrate a multi-faceted picture and physical principles of chromatin organization.

DOI: https://doi.org/10.1038/s41467-020-16732-5
Cell Div. 2020 ;15 8

EZH2-inhibitor DZNep enhances apoptosis of renal tubular epithelial cells in presence and absence of cisplatin.

Si-Qi Chen, Jia-Qi Li, Xiao-Qiao Wang, Wen-Jing Lei, Hao Li, Jiao Wan, Zheng Hu, Yao-Wei Zou, Xiao-Yu Wu, Hong-Xin Niu.

   Background: The enhancer of zeste homolog 2 (EZH2) is a histone methyltransferase and induces the trimethylation of histone H3 lysine 27 (H3K27me3) in the promoter of many key genes; EZH2 acts as a transcriptional repressor and is an epigenetic regulator for several cancers. However, the role of EZH2 in nonneoplastic diseases, such as kidney diseases, is unknown and has been investigated.
Materials and method: NRK-52E cells were treated with DZNep, a potent inhibitor of EZH2, with different concentrations and for different times to evaluate the apoptosis level of NRK-52E cells by Western blot and Flow cytometry analysis. The binding of EZH2 to the Deptor promoter was determined by ChIP assay.
Results: The inhibition of EZH2 with 3-deazaneplanocin A (DZNep), a specific inhibitor of EZH2, led to the apoptosis of NRK-52E cells and the inhibition of mTORC1 and mTORC2 activity. A ChIP assay demonstrated that EZH2 bound the promoter region of Deptor, an endogenous inhibitor of mTORC1 and mTORC2, and regulated the transcription of Deptor by modulating H3K27me3 in its promoter region. Further experiments were performed to examine the effects of EZH2 inhibition on cisplatin-induced injured cells. Cisplatin induced the activation of mTORC1 and mTORC2 and apoptosis in NRK-52E cells, and DZNep inhibited mTORC1 and mTORC2 activity and aggravated cell apoptosis.
Conclusions: These data suggested that EZH2 inhibition increased the transcription of Deptor by modifying H3K27me3 in its promoter region, subsequently inhibited mTORC1 and mTORC2 activities, downregulated the expression of apoptosis suppressor genes, and finally led to apoptosis in renal tubular cells. The inhibition of EZH2 aggravated the cisplatin-induced injury in renal tubular cells by inactivating the mTOR complexes. The present study provides new insight into renal protection and suggests that EZH2 might be a target.

Keywords:  Apoptosis; Deptor; EZH2; Renal tubular cells

DOI:  https://doi.org/10.1186/s13008-020-00064-3
Acta Pharm Sin B. 2020 May;10(5): 723-733

Epigenetic strategies synergize with PD-L1/PD-1 targeted cancer immunotherapies to enhance antitumor responses.

Xi Chen, Xiaohui Pan, Wenxin Zhang, Hongjie Guo, Shuyuan Cheng, Qiaojun He, Bo Yang, Ling Ding.

  Immunotherapy strategies targeting the programmed cell death ligand 1 (PD-L1)/programmed cell death 1 (PD-1) pathway in clinical treatments have achieved remarkable success in treating multiple types of cancer. However, owing to the heterogeneity of tumors and individual immune systems, PD-L1/PD-1 blockade still shows slow response rates in controlling malignancies in many patients. Accumulating evidence has shown that an effective response to anti-PD-L1/anti-PD-1 therapy requires establishing an integrated immune cycle. Damage in any step of the immune cycle is one of the most important causes of immunotherapy failure. Impairments in the immune cycle can be restored by epigenetic modification, including reprogramming the environment of tumor-associated immunity, eliciting an immune response by increasing the presentation of tumor antigens, and by regulating T cell trafficking and reactivation. Thus, a rational combination of PD-L1/PD-1 blockade and epigenetic agents may offer great potential to retrain the immune system and to improve clinical outcomes of checkpoint blockade therapy.

Keywords:  5-AzaC, 5-azacitidine; ACE1, angiotensin converting enzyme; ACP1, human red cell acid phosphatase; APC, antigen-presenting cell; BETi, bromodomain and extra-terminal motif inhibitors; CCL22 (MDC), macrophage-derived chemokine; CLL, chronic lymphocytic leukemia; CTA, cancer testis antigen; CTLA-4, cytotoxic T lymphocyte antigen 4; CTLs, cytotoxic T lymphocytes; CX3CL1, C-X3-C motif chemokine ligand 1; CXCL, CXC chemokine ligand; Cancer; DC, dendritic cell; DNMT1, DNA methyltransferase 1; DNMTi, DNA methyltransferase inhibitors; EZH2, enhancer of zeste homolog 2; Epigenetic regulation; FDA, U. S. Food and Drug Administration; FOXP3, forkhead box P3; H3K27me3, tri-methylation of lysine 27 on histone H3; HDACi, histone deacetylase inhibitor; IDO, indoleamine 2,3-dioxygenase; IFN-γ, interferon-gamma; Immune cycle; Immunotherapy; LAG-3, lymphocyte activation gene-3; MDSCs, myeloid-derived suppressor cells; MHC, major histocompatibility complex; OS, overall survival; PD-1, programmed cell death 1; PD-L1, programmed cell death ligand 1; PD-L1/PD-1 blockade; PRC2, polycomb repressive complex 2; TAA, tumor-associated antigen; TET2, ten-eleven translocation 2; TH-1, T helper type 1; TIL, tumor infiltrating lymphocytes; TIM-3, T cell immunoglobulin and mucin domain 3; Tregs, regulatory T cells; UHRF1, ubiquitin-like PHD and RING finger domain-containing 1

DOI:  https://doi.org/10.1016/j.apsb.2019.09.006
PLoS Pathog. 2020 Jun 08. 16(6): e1008633

Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection.

Xiangshuo Kong, Guisheng Wei, Nan Chen, Shudi Zhao, Yunwang Shen, Jianjia Zhang, Yang Li, Xiaoqun Zeng, Xiaofeng Wu.

DNA viruses can hijack and manipulate the host chromatin state to facilitate their infection. Multiple lines of evidences reveal that DNA virus infection results in the host chromatin relocation, yet there is little known about the effects of viral infection on the architecture of host chromatin. Here, a combination of epigenomic, transcriptomic and biochemical assays were conducted to investigate the temporal dynamics of chromatin accessibility in response to Bombyx mori nucleopolyhedrovirus (BmNPV) infection. The high-quality ATAC-seq data indicated that progressive chromatin remodeling took place following BmNPV infection. Viral infection resulted in a more open chromatin architecture, along with the marginalization of host genome and nucleosome disassembly. Moreover, our results revealed that chromatin accessibility in uninfected cells was regulated by euchromatic modifications, whereas the viral-induced highly accessible chromatin regions were originally associated with facultative heterochromatic modification. Overall, our findings illustrate for the first time the organization and accessibility of host chromatin in BmNPV-infected cells, which lay the foundation for future studies on epigenomic regulation mediated by DNA viruses.

DOI: https://doi.org/10.1371/journal.ppat.1008633
Nat Genet. 2020 Jun 08.

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.

Grégoire Stik, Enrique Vidal, Mercedes Barrero, Sergi Cuartero, Maria Vila-Casadesús, Julen Mendieta-Esteban, Tian V Tian, Jinmi Choi, Clara Berenguer, Amaya Abad, Beatrice Borsari, François le Dily, Patrick Cramer, Marc A Marti-Renom, Ralph Stadhouders, Thomas Graf.

Three-dimensional organization of the genome is important for transcriptional regulation1-7. In mammals, CTCF and the cohesin complex create submegabase structures with elevated internal chromatin contact frequencies, called topologically associating domains (TADs)8-12. Although TADs can contribute to transcriptional regulation, ablation of TAD organization by disrupting CTCF or the cohesin complex causes modest gene expression changes13-16. In contrast, CTCF is required for cell cycle regulation17, embryonic development and formation of various adult cell types18. To uncouple the role of CTCF in cell-state transitions and cell proliferation, we studied the effect of CTCF depletion during the conversion of human leukemic B cells into macrophages with minimal cell division. CTCF depletion disrupts TAD organization but not cell transdifferentiation. In contrast, CTCF depletion in induced macrophages impairs the full-blown upregulation of inflammatory genes after exposure to endotoxin. Our results demonstrate that CTCF-dependent genome topology is not strictly required for a functional cell-fate conversion but facilitates a rapid and efficient response to an external stimulus.

DOI: https://doi.org/10.1038/s41588-020-0643-0
Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 202004664. [Epub ahead of print]

Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early- and late-replicating euchromatin.

Timothy Hoggard, Carolin A Müller, Conrad A Nieduszynski, Michael Weinreich, Catherine A Fox.

  A eukaryotic chromosome relies on the function of multiple spatially distributed DNA replication origins for its stable inheritance. The spatial location of an origin is determined by the chromosomal position of an MCM complex, the inactive form of the DNA replicative helicase that is assembled onto DNA in G1-phase (also known as origin licensing). While the biochemistry of origin licensing is understood, the mechanisms that promote an adequate spatial distribution of MCM complexes across chromosomes are not. We have elucidated a role for the Sir2 histone deacetylase in establishing the normal distribution of MCM complexes across Saccharomyces cerevisiae chromosomes. In the absence of Sir2, MCM complexes accumulated within both early-replicating euchromatin and telomeric heterochromatin, and replication activity within these regions was enhanced. Concomitantly, the duplication of several regions of late-replicating euchromatin were delayed. Thus, Sir2-mediated attenuation of origin licensing within both euchromatin and telomeric heterochromatin established the normal spatial distribution of origins across yeast chromosomes important for normal genome duplication.

Keywords:  Sir; chromatin; chromosomes; origin licensing; yeast

DOI:  https://doi.org/10.1073/pnas.2004664117
Open Biol. 2020 Jun;10(6): 200051

The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle.

Kathryn Kixmoeller, Praveen Kumar Allu, Ben E Black.

  Eukaryotic chromosome segregation relies upon specific connections from DNA to the microtubule-based spindle that forms at cell division. The chromosomal locus that directs this process is the centromere, where a structure called the kinetochore forms upon entry into mitosis. Recent crystallography and single-particle electron microscopy have provided unprecedented high-resolution views of the molecular complexes involved in this process. The centromere is epigenetically specified by nucleosomes harbouring a histone H3 variant, CENP-A, and we review recent progress on how it differentiates centromeric chromatin from the rest of the chromosome, the biochemical pathway that mediates its assembly and how two non-histone components of the centromere specifically recognize CENP-A nucleosomes. The core centromeric nucleosome complex (CCNC) is required to recruit a 16-subunit complex termed the constitutive centromere associated network (CCAN), and we highlight recent structures reported of the budding yeast CCAN. Finally, the structures of multiple modular sub-complexes of the kinetochore have been solved at near-atomic resolution, providing insight into how connections are made to the CCAN on one end and to the spindle microtubules on the other. One can now build molecular models from the DNA through to the physical connections to microtubules.

Keywords:  centromere; chromatin; epigenetics; kinetochore; mitosis; nucleosome

DOI:  https://doi.org/10.1098/rsob.200051
Cell Death Discov. 2020 ;6 39

Acetylation/methylation at lysine 9 in histone H3 as a mark of nucleosome asymmetry in human somatic breast cells.

Bruno Perillo, Annalisa Di Santi, Gustavo Cernera, Giovanni Galasso, Gabriella Pocsfalvi, Gabriella Castoria, Antimo Migliaccio.



Keywords:  Epigenetics; Histone post-translational modifications

DOI:  https://doi.org/10.1038/s41420-020-0278-z
Leukemia. 2020 Jun 09.

CTCF-mediated genome organization and leukemogenesis.

Yi Qiu, Suming Huang.

Recent technological advancements and genome-wide studies provide compelling evidence that dynamic chromatin interaction and three-dimensional genome organization in nuclei play an important role in regulating gene expression. Mammalian genomes consist of many small functional domains termed topologically associated domains (TADs), many of them organized by CCCTC-binding factor (CTCF) and the cohesion complex. Changes in genome TADs might result in inappropriate promoter/enhancer communications leading to activation of oncogenes or suppression of tumor suppressors. During normal hematopoiesis and leukemogenesis, genome structure alters considerably to facilitate normal and malignant hematopoiesis, respectively. Delineating theses normal and abnormal processes will evolve our understanding of disease pathogenesis and development of potential treatment strategies. This review highlights the role of CTCF and its associated protein complexes in three-dimensional genome organization in development and leukemogenesis, as well as the roles of CTCF boundary defined TAD in transcription regulation. We further explore the function of chromatin modulators, such as CTCF, cohesin, and long noncoding RNAs (lncRNAs) in chromosomal interactions and hematopoietic genome organization. Finally, we focus on the implication of 3D genome alteration in the pathogenesis of leukemia and provide a scientific basis for targeted intervention.

DOI: https://doi.org/10.1038/s41375-020-0906-x
Physiol Rev. 2020 Jun 11.

CRISPR-tools for physiology & cell state changes - potential of transcriptional engineering and epigenome editing.

Christopher Breunig, Anna Köferle, Andrea Neuner, Maximilian Wiesbeck, Valentin Baumann, Stefan H Stricker.

  Given the large amount of genome-wide data that has been collected during the last decades a good understanding of how and why cells change during development, homeostasis and disease might be expected. Unfortunately, the opposite is true; Triggers that cause cellular state changes remain elusive and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools: namely, activation and/or repression of master transcription factors in their endogenous chromatin context, targeting transcription factors to endogenous, alternative or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.

Keywords:  CRISPR; Epigenome editing; Transcriptional engineering; cell states; dCas9

DOI:  https://doi.org/10.1152/physrev.00034.2019
Glia. 2020 Jun 12.

Overexpression of H3K36 methyltransferase NSD in glial cells affects brain development in Drosophila.

Taejoon Kim, Hyewon Shin, Bokyeong Song, Chihyun Won, Hideki Yoshida, Masamitsu Yamaguchi, Kyoung Sang Cho, Im-Soon Lee.

  NSD1 is a histone methyltransferase that methylates the lysine 36 at histone H3. NSD duplication is associated with short stature, microcephaly, intellectual disability, and behavioral defects in humans. Ectopic overexpression of NSD, an NSD1 homolog in Drosophila, was shown to induce developmental abnormalities via apoptosis. In this study, to investigate the effects of NSD overexpression on Drosophila brain development, we first examined the typical NSD expression pattern in larval brains and found that endogenous NSD promoter activity was detected only in subsets of glial cells. Pan-glial, but not pan-neuronal, NSD overexpression induced apoptosis in larval brain cells. However, pan-glial NSD overexpression also induced caspase-3 cleavage in neuronal cells. Among the various glial cell types, NSD overexpression in only astrocytic glia induced apoptosis and abnormal learning defects in the larval stage. Furthermore, NSD overexpression downregulated the expression of various astrocyte-specific genes, including draper (drpr), possibly owing to an indirect effect of NSD overexpression-induced astrocytic apoptosis. Since drpr plays a role in axon pruning during mushroom body (MB) formation in Drosophila astrocytes, we examined the effect of astrocytic NSD overexpression on this process and found that it disrupted the clearance of γ-neurons in the MB, subsequently inducing arrhythmic locomotor activity of the fly. Thus, these results suggest that aberrant NSD overexpression may cause neurodevelopmental disorders by interfering with crucial functions of astrocytes in the brain, underlining the importance of the tightly controlled astrocytic NSD expression for proper neurodevelopment.

Keywords:  Drosophila; NSD; NSD1; apoptosis; astrocyte; draper

DOI:  https://doi.org/10.1002/glia.23867
Life Sci. 2020 Jun 09. pii: S0024-3205(20)30686-X. [Epub ahead of print] 117936

The Ras-ERK1/2 signaling pathway regulates H3K9ac through PCAF to promote the development of pancreatic cancer.

Yu-Hong Li, Ying-Xue Li, Mu Li, Shao-Wei Song, Yang Ge, Jun-Yi Jin, Xiao-Ying Li, Xiao-Dong Tan, Jing Ye.

   AIMS: The regulation of the Ras-ERK pathway is the crucial point in pancreatic carcinogenesis, and the Ras kinase is an essential regulatory upstream signal molecule of the ERK1/2 pathway. H3K9ac is a vital histone modification, but its specific role in pancreatic cancer remains unclear. This research aims to study whether the modification level of H3K9ac can regulate the characteristic phenotype of the pancreatic cancer cells by affecting the downstream expression, proliferation, migration, and other related genes.
MAIN METHODS: The RasG12V/T35S were used to transfect pancreatic cancer cells, and the levels of phosphorylated ERK1/2 and H3K9ac were detected by western blotting. The colony formation assay, transwell assay, and chromatin immunoprecipitation assay were used to study cell viability, migration, and the downstream genes of the ERK1/2 pathway.
KEY FINDINGS: The results showed that Ras ERK1/2 reduced H3K9ac expression in ASPC-1 cells, and H3K9ac significantly repressed the viability of cells, colony formation, and ASPC-1 cell movement induced by Ras ERK1/2. Besides, HDAC1 silencing increased H3K9ac expression, and changed the effect of Ras ERK1/2 on ASPC-1 cells proliferation, its movement, and mRNAs of ERK1/2 downstream genes. Moreover, Ras ERK1/2 inhibited H3K9ac expression by the degradation of PCAF via MDM2.
SIGNIFICANCE: Ras ERK1/2 promotes pancreatic carcinogenesis cell movement, through down-regulating H3K9ac via MDM2 mediated PCAF degradation.

Keywords:  ASPC-1 cell; H3K9ac; HDAC1; PCAF; Ras-ERK pathway

DOI:  https://doi.org/10.1016/j.lfs.2020.117936
J Mol Graph Model. 2020 May 18. pii: S1093-3263(20)30435-6. [Epub ahead of print]99 107646

Evidence for NAD+-dependent histone dynamics and tunneling associated conformational transitions in circadian deacetylase SIRT1.

Najumuddin, Muhammad Fakhar, Sajid Rashid.

  Circadian rhythm is a biological cycle that is involved in all processes over 24 h day and night period. Sirtuin 1 (SIRT1) is a 747 amino acid-long class III Nicotinamide adenine dinucleotide (NAD+)-dependent histone that acts as a circadian deacetylase. Here we present a detailed in-silico analysis to address comparative structure-function relationship and interaction pattern of SIRT1-NAD+/Zn+2 and SIRT1NAD+/Zn+2-acetylated histone H4 (H4KAC16) complexes. MD-based ensemble analysis suggested an overall loss of helical content (21.144-17.230%) in H4KAC16-bound SIRT1NAD+/Zn+2 due to conformational readjustments of 32 residues, as compared to SIRT1NAD+/Zn+2. Due to increased flexibility, SIRT1-specific SER275, SER442 and ARG466 residues involved in NAD+ association facilitated in the formation of a transient tunnel (17.77 Å) that was further elongated to 19.25 Å upon SIRT1NAD+/Zn+2 binding to H4KAC16. A close conformation of SIRT1NAD+/Zn+2 was achieved due to binding of H4KAC16 that results in the movement of helical module towards Zn+2 binding module together with Rossmann fold at NAD+ binding region. Furthermore, a 2-fold increase (4.31-8.82 Å) in the measured inter-atomic distance between imidazole nitrogen of conserved HIS363 and NAD+-specific 2'-hydroxyl group of ribose ring was evident in SIRT1NAD+/Zn+2-H4KAC16 complex. At 90 ns time scale, the distance between C6A of adenine ring and C2N of nicotinamide ring was more extended (19.32 Å) in SIRT1NAD+/Zn+2-H4KAC16 as compared to SIRT1NAD+/Zn+2 (11.54 Å). These data suggest that H4KAC16 binding to SIRT1 may coordinate an unusual conformational readjustment of nicotinamide ring at site-b and reposition of HIS363 to facilitate SIRT1-dependent deacetylase activity. Taken together, our findings will help in understanding the precise structural changes occurring in response to SIRT1 deacetylase activity of core histone.

Keywords:  Circadian deacetylase SIRT1; Circadian rhythm; Deacetylation; Energy metabolism

DOI:  https://doi.org/10.1016/j.jmgm.2020.107646
Mol Neurobiol. 2020 Jun 06.

The Expression and Localization of Histone Acetyltransferases HAT1 and PCAF in Neurons and Astrocytes of the Photothrombotic Stroke-Induced Penumbra in the Rat Brain Cortex.

S V Demyanenko, V A Dzreyan, A B Uzdensky.

  Stroke is one of the leading reasons of human death. Ischemic penumbra that surrounds the stroke-induced infarction core is potentially salvageable, but molecular mechanisms of its formation are poorly known. Histone acetylation induces chromatin decondensation and stimulates gene expression. We studied the changes in the levels and localization of histone acetyltransferases HAT1 and PCAF in penumbra after photothrombotic stroke (PTS, a stroke model). In PTS, laser irradiation induces local occlusion of cerebral vessels after photosensitization by Rose Bengal. HAT1 and PCAF are poorly expressed in normal cortical neurons and astrocytes, but they are overexpressed 4-24 h after PTS. Their predominant localization in neuronal nuclei did not change after PTS, but their levels in the astrocyte nuclei significantly increased. Western blotting showed the increase of HAT1 and PCAF levels in the cytoplasmic fraction of the PTS-induced penumbra. In the nuclear fraction, PCAF level did not change, and HAT1 was overexpressed only at 24 h post-PTS. PTS-induced upregulation of HAT1 and PCAF in the penumbra was mainly associated with overexpression in the cytoplasm of neurons and especially astrocytes. HAT1 and PCAF did not co-localize with TUNEL-positive cells that indicated their nonparticipation in PTS-induced apoptosis.

Keywords:  Epigenetics; Histone acetyltransferase, HAT1, PCAF; Penumbra; Photothrombotic stroke

DOI:  https://doi.org/10.1007/s12035-020-01959-6
Cancers (Basel). 2020 Jun 06. pii: E1483. [Epub ahead of print]12(6):

Nuclear Receptor Binding Protein 2 Is Downregulated in Medulloblastoma, and Reduces Tumor Cell Survival upon Overexpression.

Anqi Xiong, Ananya Roy, Argyris Spyrou, Holger Weishaupt, Voichita D Marinescu, Tommie Olofsson, Ola Hermanson, Fredrik J Swartling, Karin Forsberg-Nilsson.

  Pseudokinases, comprising 10% of the human kinome, are emerging as regulators of canonical kinases and their functions are starting to be defined. We previously identified the pseudokinase Nuclear Receptor Binding Protein 2 (NRBP2) in a screen for genes regulated during neural differentiation. During mouse brain development, NRBP2 is expressed in the cerebellum, and in the adult brain, mainly confined to specific neuronal populations. To study the role of NRBP2 in brain tumors, we stained a brain tumor tissue array for NRPB2, and find its expression to be low, or absent, in a majority of the tumors. This includes medulloblastoma (MB), a pediatric tumor of the cerebellum. Using database mining of published MB data sets, we also find that NRBP2 is expressed at a lower level in MB than in the normal cerebellum. Recent studies indicate that MB exhibits frequent epigenetic alternations and we therefore treated MB cell lines with drugs inhibiting DNA methylation or histone deacetylation, which leads to an upregulation of NRBP2 mRNA expression, showing that it is under epigenetic regulation in cultured MB cells. Furthermore, forced overexpression of NRBP2 in MB cell lines causes a dramatic decrease in cell numbers, increased cell death, impaired cell migration and inhibited cell invasion in vitro. Taken together, our data indicate that downregulation of NRBP2 may be a feature by which MB cells escape growth regulation.

Keywords:  NRBP; apoptosis; brain tumor; pediatric cancer; pseudokinase

DOI:  https://doi.org/10.3390/cancers12061483
Nat Rev Genet. 2020 Jun 08.

Maternal H3K27me3-dependent autosomal and X chromosome imprinting.

Zhiyuan Chen, Yi Zhang.

Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele. Germline-derived differential DNA methylation is the best-studied epigenetic mark that initiates imprinting, but evidence indicates that other mechanisms exist. Recent studies have revealed that maternal trimethylation of H3 on lysine 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role in imprinted XCI through repression of maternal Xist. Furthermore, loss of H3K27me3-mediated imprinting contributes to the developmental defects observed in cloned embryos. This novel maternal H3K27me3-mediated non-canonical imprinting mechanism further emphasizes the important role of parental chromatin in development and could provide the basis for improving the efficiency of embryo cloning.

DOI: https://doi.org/10.1038/s41576-020-0245-9
J Biol Chem. 2020 Jun 09. pii: jbc.REV120.011666. [Epub ahead of print]

Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code.

Nitika, Corey M Porter, Andrew W Truman, Matthias C Truttmann.

  Cells must be able to cope with the challenge of folding newly synthesized proteins and refolding those that have become misfolded in the context of a crowded cytosol. One such coping mechanism that has appeared during evolution is the expression of well-conserved molecular chaperones, such as those that are part of the heat shock protein 70 (Hsp70) family of proteins that bind and fold a large proportion of the proteome. Although Hsp70 family chaperones have been extensively examined for the last 50 years, most studies have focused on regulation of Hsp70 activities by altered transcription, co-chaperone "helper" proteins, and ATP binding and hydrolysis. The rise of modern proteomics has uncovered a vast array of post-translational modifications (PTMs) on Hsp70 family proteins that include phosphorylation, acetylation, ubiquitination, AMPylation, and ADP-ribosylation. Similarly to the pattern of histone modifications, the histone code, this complex pattern of chaperone PTMs is now known as the "Chaperone Code." In this review, we discuss the history of the Hsp70 chaperone code, its currently understood regulation and functions, as well as thoughts on what the future of research into the chaperone code may entail.

Keywords:  70 kilodalton heat shock protein (Hsp70); acetylation; molecular chaperone; post-translational modification (PTM); protein AMPylation; protein methylation; protein phosphorylation

DOI:  https://doi.org/10.1074/jbc.REV120.011666
Genome Biol. 2020 Jun 08. 21(1): 135

Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.

Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B Fraser, Thomas Quertermous.

   BACKGROUND: To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells (HCASMCs).
RESULTS: We use a pooling approach with HCASMC lines to map regulatory variants that mediate binding of the CAD-associated transcription factor TCF21 with ChIPseq studies (bQTLs), variants that regulate chromatin accessibility with ATACseq studies (caQTLs), and chromosomal looping with Hi-C methods (clQTLs). We examine the overlap of these QTLs and their relationship to smooth muscle-specific genes and transcription factors. Further, we use multiple analyses to show that these QTLs are highly associated with CAD GWAS loci and correlate to lead SNPs where they show allelic effects. By utilizing genome editing, we verify that identified functional variants can regulate both chromatin accessibility and chromosomal looping, providing new insights into functional mechanisms regulating chromatin state and chromosomal structure. Finally, we directly link the disease-associated TGFB1-SMAD3 pathway to the CAD-associated FN1 gene through a response QTL that modulates both chromatin accessibility and chromosomal looping.
CONCLUSIONS: Together, these studies represent the most thorough mapping of multiple QTL types in a highly disease-relevant primary cultured cell type and provide novel insights into their functional overlap and mechanisms that underlie these genomic features and their relationship to disease risk.

Keywords:  Chromatin accessibility; Chromosomal looping; Coronary artery disease; Quantitative trait locus; Smooth muscle cells; TCF21

DOI:  https://doi.org/10.1186/s13059-020-02049-5
Cancer Res. 2020 Jun 10. pii: canres.0233.2020. [Epub ahead of print]

p300-mediated acetylation of histone demethylase JMJD1A prevents its degradation by ubiquitin ligase STUB1 and enhances its activity in prostate cancer.

Songhui Xu, Lingling Fan, Hee-Young Jeon, Fengbo Zhang, Xiaolu Cui, McKayla B Mickle, Guihong Peng, Arif Hussain, Ladan Fazli, Martin E Gleave, Xuesen Dong, Jianfei Qi.

The androgen receptor (AR) pathway plays a central role in the development of castration-resistant prostate cancer (CRPC). The histone demethylase JMJD1A has been shown to regulate activities of AR and c-Myc transcription factors and promote prostate cancer progression. Here we report that JMJD1A protein stability is controlled by the ubiquitin ligase STUB1. High levels of JMJD1A were strongly correlated with low STUB1 levels in human CRPC specimens. STUB1 inhibited AR activity, AR-V7 levels, and prostate cancer cell growth partly through degradation of JMJD1A. Furthermore, the acetyltransferase p300 acetylated JMJD1A at lysine (K) 421, a modification that recruits the BET family member BRD4 to block JMJD1A degradation and promote JMJD1A recruitment to AR targets. Increased levels of both total and K421-acetylated JMJD1A were observed in prostate cancer cells as they developed resistance to the AR antagonist enzalutamide. Treatment of prostate cancer cells with either p300 or BET inhibitors destabilized JMJD1A and enzalutamide-resistant prostate cancer cells were more sensitive than parental cells to these inhibitors. Together, our findings identify a critical role for acetylation of JMJD1A in regulating JMJD1A stability and AR activity in CRPC. These newly identified mechanisms controlling JMJD1A protein stability provide potential druggable targets to encourage the development of additional therapies for advanced prostate cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-0233
Nucleic Acids Res. 2020 Jun 08. pii: gkaa482. [Epub ahead of print]

Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.

Xiang Sun, Zhijun Ren, Yixian Cun, Cai Zhao, Xianglin Huang, Jiajian Zhou, Rong Hu, Xiaoxi Su, Lu Ji, Peng Li, King Lun Kingston Mak, Feng Gao, Yi Yang, He Xu, Junjun Ding, Nan Cao, Shuo Li, Wensheng Zhang, Ping Lan, Hao Sun, Jinkai Wang, Ping Yuan.

Hippo-YAP signaling pathway functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. We found that knockout (KO) of Mst1 and Mst2, two key components of the Hippo signaling in mouse embryonic stem cells (ESCs), resulted in a disruption of differentiation into mesendoderm lineage. To further uncover the underlying regulatory mechanisms, we performed a series of ChIP-seq experiments with antibodies against YAP, ESC master transcription factors and some characterized histone modification markers as well as RNA-seq assays using wild type and Mst KO samples at ES and day 4 embryoid body stage respectively. We demonstrate that YAP is preferentially co-localized with super-enhancer (SE) markers such as Nanog, Sox2, Oct4 and H3K27ac in ESCs. The hyper-activation of nuclear YAP in Mst KO ESCs facilitates the binding of Nanog, Sox2 and Oct4 as well as H3K27ac modification at the loci where YAP binds. Moreover, Mst depletion results in novel SE formation and enhanced liquid-liquid phase-separated Med1 condensates on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Our study reveals a novel mechanism on how Hippo-YAP signaling pathway dictates ESC lineage differentiation.

DOI: https://doi.org/10.1093/nar/gkaa482
Brain Tumor Pathol. 2020 Jun 11.

Prognostic role of H3K27M mutation, histone H3K27 methylation status, and EZH2 expression in diffuse spinal cord gliomas.

Yukitomo Ishi, Soichiro Takamiya, Toshitaka Seki, Kazuyoshi Yamazaki, Kazutoshi Hida, Kanako C Hatanaka, Yusuke Ishida, Yoshitaka Oda, Shinya Tanaka, Shigeru Yamaguchi.

  The objective of this study is to clarify clinical significance of the H3F3A K27M mutation (H3K27M) and analyze the correlation between H3K27M, H3K27me3 status, and EZH2 expression and prognosis in spinal cord gliomas. Patients with spinal cord diffuse glioma regardless of World Health Organization (WHO) grade underwent genetic analysis for H3F3A, HIST1H3B, TERT promoter, IDH1/2, and BRAF. H3K27me3 status and EZH2 expression were analyzed through immunohistochemistry. Thereafter, the association between H3K27M, H3K27me3 status, and EZH2 expression and prognosis was retrospectively analyzed using the log-rank test. A total of 26 cases, 5 with WHO grade 4, 9 with grade 3, and 12 with grade 2 glioma, were analyzed. Although WHO grade 2 cases tended to present favorable overall survival, the difference was not statistically significant. H3K27M, which was detected in four grade 4 cases (80%) and three grade 3 cases (33%), was not associated with prognosis among grade 3 and 4 cases. Among WHO grade 2-4 cases, the combination of retained H3K27me3 and negative EZH2 expression was correlated with favorable overall survival (p = 0.03). The combination of H3K27me3 status and EZH2 expression was considered as a potential prognostic marker in WHO grade 2-4 diffuse spinal cord gliomas.

Keywords:  EZH2; Glioma; H3F3A; H3K27me3; Spinal cord

DOI:  https://doi.org/10.1007/s10014-020-00369-9
Dev Biol. 2020 Jun 03. pii: S0012-1606(20)30152-4. [Epub ahead of print]

The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation.

Jeannine M Basta, Ajeet Singh, Lynn Robbins, Lisa Stout, Michelle Pherson, Michael Rauchman.

Chromatin-remodeling complexes play critical roles in establishing gene expression patterns in response to developmental signals. How these epigenetic regulators determine the fate of progenitor cells during development of specific organs is not well understood. We found that genetic deletion of Brg1 (Smarca4), the core enzymatic protein in SWI/SNF, in nephron progenitor cells leads to severe renal hypoplasia. Nephron progenitor cells were depleted in Six2-Cre, Brg1flx/flx mice due to reduced cell proliferation. This defect in self-renewal, together with impaired differentiation resulted in a profound nephron deficit in Brg1 mutant kidneys. Sall1, a transcription factor that is required for expansion and maintenance of nephron progenitors, associates with SWI/SNF. Brg1 and Sall1 bind promoters of many progenitor cell genes and regulate expression of key targets that promote their proliferation.

DOI: https://doi.org/10.1016/j.ydbio.2020.05.008
Bone. 2020 Jun 08. pii: S8756-3282(20)30251-9. [Epub ahead of print] 115471

Epigenetic and transcriptional regulation of osteoclast differentiation.

Daisuke Kurotaki, Haruka Yoshida, Tomohiko Tamura.

  Osteoclasts are derived from mononuclear phagocyte lineage cells and are indispensable for bone resorption. Recent findings suggest that fetal yolk sac macrophage progenitors give rise to neonatal osteoclasts, while hematopoietic stem cell-derived cells, such as monocytes, contribute to maintaining osteoclast syncytia in vivo. Osteoclast differentiation is dependent on macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-κB ligand (RANKL) signaling that mediates global epigenetic and transcriptional changes. PU.1 is a transcription factor that establishes cell type-specific enhancer landscapes in osteoclast precursors and mature osteoclasts by collaborating with interferon regulatory factor-8 (IRF8) and nuclear factor of activated T-cells (NFATc1), respectively. Irf8 and Nfatc1 genes are tightly controlled by epigenetic mechanisms such as DNA methylation and histone modifications during osteoclastogenesis. Thus, key transcription factors orchestrate osteoclast-specific transcription regulatory networks through epigenetic modifications. In this review, we discuss recent advances in our understanding of the molecular mechanisms involved in osteoclast development.

Keywords:  Epigenome; IRF8; NFATc1; Osteoclast differentiation; PU.1; Transcription factor

DOI:  https://doi.org/10.1016/j.bone.2020.115471
FASEB J. 2020 Jun 13.

The cell adhesion molecule L1 interacts with nuclear proteins via its intracellular domain.

Maria Girbes Minguez, Gerrit Wolters-Eisfeld, David Lutz, Friedrich Buck, Melitta Schachner, Ralf Kleene.

  Proteolytic cleavage of the cell adhesion molecule L1 (L1) in brain tissue and in cultured cerebellar neurons results in the generation and nuclear import of a 30 kDa fragment comprising most of L1's C-terminal, intracellular domain. In search of molecules that interact with this domain, we performed affinity chromatography with the recombinant intracellular L1 domain and a nuclear extract from mouse brains, and identified potential nuclear L1 binding partners involved in transcriptional regulation, RNA processing and transport, DNA repair, chromatin remodeling, and nucleocytoplasmic transport. By co-immunoprecipitation and enzyme-linked immunosorbent assay using recombinant proteins, we verified the direct interaction between L1 and the nuclear binding partners non-POU domain containing octamer-binding protein and splicing factor proline/glutamine-rich. The proximity ligation assay confirmed this close interaction in cultures of cerebellar granule cells. Our findings suggest that L1 fragments regulate multiple nuclear functions in the nervous system. We discuss possible physiological and pathological roles of these interactions in regulation of chromatin structure, gene expression, RNA processing, and DNA repair.

Keywords:  DNA/RNA-binding proteins; Drosophila behavior/human splicing (DBHS) proteins; cell adhesion molecule L1; nuclear import; proteolytic processing

DOI:  https://doi.org/10.1096/fj.201902242R