bims-histon 2020-06-28 papers

bims-histon

Biomed News

on Histones

Issue of 2020–06–28
28 papers selected by
Benjamin Weekley, University of Southern California

OsHDA710-mediated Histone Deacetylation Regulates Callus Formation of Rice Mature Embryo.
Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA.
Structural Basis of Nucleosome Recognition and Modulation.
Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats.
Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin.
Nucleosome Binding by the Lysine Specific Demethylase 1 (LSD1) Enzyme Enables Histone H3 Demethylation.
circEgg regulates histone H3K9me3 by sponging bmo-miR-3391-5p and encoding circEgg-P122 protein in the silkworm, Bombyx mori.
The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence-associated epigenomic remodeling.
Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis.
Cooperative binding of transcription factors in the human genome.
The hypomethylation of imprinted genes in IVF/ICSI placenta samples is associated with concomitant changes in histone modifications.
Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis.
Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.
Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase.
Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity.
Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.
Single-molecule regulatory architectures captured by chromatin fiber sequencing.
SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.
Bromodomain Protein BRD4 Accelerates Glucocorticoid Dysregulation of Bone Mass and Marrow Adiposis by Modulating H3K9 and Foxp1.
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.
Maternal inheritance of centromeres through the germline.
Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor.
SPANX control of Lamin A/C modulates nuclear architecture and promotes melanoma growth.
DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner.
TET1 Deficiency Impairs Morphogen-free Differentiation of Human Embryonic Stem Cells to Neuroectoderm.
Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development.
Post-transcriptional gene regulation regulates germline stem cell to oocyte transition during Drosophila oogenesis.
Six1 Overexpression Promotes Glucose Metabolism and Invasion Through Regulation of GLUT3, MMP2 and Snail in Thyroid Cancer Cells.

Plant Cell Physiol. 2020 Jun 27. pii: pcaa086. [Epub ahead of print]

OsHDA710-mediated Histone Deacetylation Regulates Callus Formation of Rice Mature Embryo.

Haidao Zhang, Fu Guo, Peipei Qi, Yizi Huang, Yongyao Xie, Lei Xu, Ning Han, Lin Xu, Hongwu Bian.

  Histone deacetylases (HDACs) play important roles in the regulation of eukaryotic gene expression. The role of HDACs in specialized transcriptional regulation and biological processes is poorly understood. In this study, we evaluated the global expression patterns of genes related to epigenetic modifications during callus initiation in rice. We found that the repression of HDAC activity by trichostatin A (TSA) or by OsHDA710 mutation (hda710) results in impaired callus formation of rice mature embryo and increased global histone H3 acetylation levels. The HDAC inhibition decreased auxin response and cell proliferation in callus formation. Meanwhile, the transcriptional repressors OsARF18 and OsARF22 were upregulated in the callus of hda710. The ChIP-qPCR analysis demonstrated that the callus of hda710 exhibited enhanced histone H3 acetylation levels at the chromatin regions of OsARF18 and OsARF22. Furthermore, we found that OsARF18 and OsARF22 were regulated through the OsHDA710 recruitment to their target loci. Additionally, overexpression of OsARF18 decreased the transcription of downstream genes PLT1 and PLT2, and inhibited callus formation of mature embryo. These results demonstrate that OsHDA710 regulates callus formation by suppressing repressive OsARFs via histone deacetylation during callus formation of rice mature embryo. This indicates that OsHDA710-mediated histone deacetylation is an epigenetic regulation pathway for maintaining auxin response during cell dedifferentiation.

Keywords:   OsARF18 ; OsHDA710 ; auxin; callus formation; histone deacetylase; mature embryo; rice; trichostatin A

DOI:  https://doi.org/10.1093/pcp/pcaa086
Mol Cell. 2020 Jun 16. pii: S1097-2765(20)30386-5. [Epub ahead of print]

Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA.

Ke Zhang, Dan-Ya Wu, Hui Zheng, Yao Wang, Qiao-Ran Sun, Xin Liu, Li-Yan Wang, Wen-Jing Xiong, Qiujun Wang, James D P Rhodes, Kai Xu, Lijia Li, Zili Lin, Guang Yu, Weikun Xia, Bo Huang, Zhenhai Du, Yao Yao, Kim A Nasmyth, Robert J Klose, Yi-Liang Miao, Wei Xie.

  Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of 3D chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that, during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger topologically associating domains (TADs) at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell-specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.

Keywords:  Hi-C; SCNT; TAD; chromatin reprogramming; cohesin; early embryo; minor ZGA; somatic cell nuclear transfer; three-dimensional chromatin structure

DOI:  https://doi.org/10.1016/j.molcel.2020.06.001
Bioessays. 2020 Jun 22. e1900234

Structural Basis of Nucleosome Recognition and Modulation.

Rajivgandhi Sundaram, Dileep Vasudevan.

  Chromatin structure and dynamics regulate key cellular processes such as DNA replication, transcription, repair, remodeling, and gene expression, wherein different protein factors interact with the nucleosomes. In these events, DNA and RNA polymerases, chromatin remodeling enzymes and transcription factors interact with nucleosomes, either in a DNA-sequence-specific manner and/or by recognizing different structural features on the nucleosome. The molecular details of the recognition of a nucleosome by different viral proteins, remodeling enzymes, histone post-translational modifiers, and RNA polymerase II, have been explored in the recent past. The present review puts forth critical insights into the basic mechanisms of nucleosome recognition by the various protein factors and the role of distinct surface epitopes on a nucleosome. These determinants of the underlying specificity include features such as the acidic patch, arginine anchor, histone post-translational modifications, core DNA, DNA lesions, and linker DNA.

Keywords:  acidic patch; chromatin factors; chromatin remodelers; linker histones; nucleosome; post-translational modifications; viral proteins

DOI:  https://doi.org/10.1002/bies.201900234
Genes (Basel). 2020 Jun 18. pii: E663. [Epub ahead of print]11(6):

Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats.

Isidoro Feliciello, Antonio Sermek, Željka Pezer, Maja Matulić, Đurđica Ugarković.

  Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of "silent" H3K9me3 and "active" H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1-2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.

Keywords:  alpha satellite DNA; epigenetics; euchromatin; gene silencing; heat stress; heterochromatin; histone modification; transcription

DOI:  https://doi.org/10.3390/genes11060663
Mol Cell. 2020 Jun 22. pii: S1097-2765(20)30357-9. [Epub ahead of print]

Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin.

Jonathan Lerner, Pablo Aurelio Gomez-Garcia, Ryan L McCarthy, Zhe Liu, Melike Lakadamyali, Kenneth S Zaret.

Enzymatic probes of chromatin structure reveal accessible versus inaccessible chromatin states, while super-resolution microscopy reveals a continuum of chromatin compaction states. Characterizing histone H2B movements by single-molecule tracking (SMT), we resolved chromatin domains ranging from low to high mobility and displaying different subnuclear localizations patterns. Heterochromatin constituents correlated with the lowest mobility chromatin, whereas transcription factors varied widely with regard to their respective mobility with low- or high-mobility chromatin. Pioneer transcription factors, which bind nucleosomes, can access the low-mobility chromatin domains, whereas weak or non-nucleosome binding factors are excluded from the domains and enriched in higher mobility domains. Nonspecific DNA and nucleosome binding accounted for most of the low mobility of strong nucleosome interactor FOXA1. Our analysis shows how the parameters of the mobility of chromatin-bound factors, but not their diffusion behaviors or SMT-residence times within chromatin, distinguish functional characteristics of different chromatin-interacting proteins.

DOI: https://doi.org/10.1016/j.molcel.2020.05.036
Biochemistry. 2020 Jun 26.

Nucleosome Binding by the Lysine Specific Demethylase 1 (LSD1) Enzyme Enables Histone H3 Demethylation.

Abhinav Dhall, Patrick M M Shelton, Aurore M-F Delachat, Calvin J A Leonen, Beat Fierz, Champak Chatterjee.

The essential human enzyme lysine specific demethylase 1 (LSD1) silences genes by demethylating mono- and dimethylated lysine 4 in histone H3 (H3K4me1/2). Studies of the minimal requirements for LSD1 activity are complicated by the heterogeneity of histone modification states in cells. We overcame this challenge by generating homogeneous mononucleosome substrates containing semisynthetic H3K4me2. Biophysical and biochemical assays with full-length LSD1 revealed its ability to bind and demethylate nucleosomes. Consistent with a requirement for nucleosome binding prior to demethylation, a competing nucleosome-binding peptide from the high-mobility group protein effectively inhibited LSD1 activity. Thus, our studies provide the first glimpse of nucleosome demethylation by LSD1 in the absence of other scaffolding proteins.

DOI: https://doi.org/10.1021/acs.biochem.0c00412
Insect Biochem Mol Biol. 2020 Jun 22. pii: S0965-1748(20)30119-3. [Epub ahead of print] 103430

circEgg regulates histone H3K9me3 by sponging bmo-miR-3391-5p and encoding circEgg-P122 protein in the silkworm, Bombyx mori.

Zhangyan Wang, Yunshan Zhang, Kun Dai, Zi Liang, Min Zhu, Mingtian Zhang, Jun Pan, Xiaolong Hu, Xing Zhang, Renyu Xue, Guangli Cao, Chengliang Gong.

  A large number of circular RNAs (circRNAs) have been found in different organisms; however, their function in the regulation of histone modification remains unknown. In this study, we found that the circRNA circEgg, cyclized by the 9th-13th exon of Bombyx mori histone-lysine N-methyltransferase eggless (BmEgg) gene, mainly distributes in the cytoplasm, its expression levels changed with silkworm developmental stages, and the linear transcript level of the BmEgg gene was decreased when circEgg was overexpressed. Moreover, circEgg was found to repress histone H3 lysine 9 methylation (H3K9me3), promote histone H3 lysine 9 acetylation (H3K9ac), and positively regulate histone deacetylase (HDAC) Rpd3 (BmHDAC Rpd3) gene expression by sponging the microRNA bmo-miR-3391-5p. Furthermore, circEgg encodes a circEgg-P122 protein which appears to inhibit H3K9me3. These results suggest that circEgg regulates histone modification by sponging bmo-miR-3391-5p and encoding circEgg-P122 protein. To our knowledge, this is the first report showing that a circRNA produced by BmEgg plays an important role in histone epigenetic modification.

Keywords:  Bmo-miR-3391–5p; Histone-lysine N-Methyltransferase; circEgg; circEgg-P122; circRNA

DOI:  https://doi.org/10.1016/j.ibmb.2020.103430
Aging Cell. 2020 Jun 22.

The NSD2/WHSC1/MMSET methyltransferase prevents cellular senescence-associated epigenomic remodeling.

Hiroshi Tanaka, Tomoka Igata, Kan Etoh, Tomoaki Koga, Shin-Ichiro Takebayashi, Mitsuyoshi Nakao.

  Senescent cells may possess the intrinsic programs of metabolic and epigenomic remodeling, but the molecular mechanism remains to be clarified. Using an RNAi-based screen of chromatin regulators, we found that knockdown of the NSD2/WHSC1/MMSET methyltransferase induced cellular senescence that augmented mitochondrial mass and oxidative phosphorylation in primary human fibroblasts. Transcriptome analysis showed that loss of NSD2 downregulated the expression of cell cycle-related genes in a retinoblastoma protein (RB)-mediated manner. Chromatin immunoprecipitation analyses further revealed that NSD2 was enriched at the gene bodies of actively transcribed genes, including cell cycle-related genes, and that loss of NSD2 decreased the levels of histone H3 lysine 36 trimethylation (H3K36me3) at these gene loci. Consistent with these findings, oncogene-induced or replicative senescent cells showed reduced NSD2 expression together with lower H3K36me3 levels at NSD2-enriched genes. In addition, we found that NSD2 gene was upregulated by serum stimulation and required for the induction of cell cycle-related genes. Indeed, in both mouse and human tissues and human cancer cell lines, the expression levels of NSD2 were positively correlated with those of cell cycle-related genes. These data reveal that NSD2 plays a pivotal role in epigenomic maintenance and cell cycle control to prevent cellular senescence.

Keywords:  H3K36 methylation; NSD2/WHSC1/MMSET; cell cycle control; retinoblastoma; senescence-associated epigenomic remodeling; senescence-associated metabolic remodeling

DOI:  https://doi.org/10.1111/acel.13173
J Cell Sci. 2020 Jun 23. pii: jcs.243444. [Epub ahead of print]

Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis.

Yoko Hayashi-Takanaka, Yuto Kina, Fumiaki Nakamura, Leontine E Becking, Yoichi Nakao, Takahiro Nagase, Naohito Nozaki, Hiroshi Kimura.

  Post-translational modifications on histones can be stable epigenetic marks and transient signals that can occur in response to internal and external stimuli. Levels of histone modifications fluctuate during the cell cycle and vary among different cell types. Here we describe a simple system to monitor the levels of multiple histone modifications in single cells by multicolor immunofluorescence using directly labeled modification-specific antibodies. We analyzed histone H3 and H4 modifications during the cell cycle. Levels of active marks, such as acetylation and H3K4 methylation, were increased during the S phase, in association with chromatin duplication. By contrast, levels of some repressive modifications gradually increased during the G2 and the next G1 phases. We applied this method to validate the target modifications of various histone demethylases in cells using a transient overexpression system. We also screened chemical compounds in marine organism extracts that affect histone modifications and identified psammaplin A, which was previously reported to inhibit histone deacetylases. Thus, the method presented here is a powerful and convenient tool for analyzing the changes in histone modifications.

Keywords:  Chemical biology; Chromatin; Epigenetics; Histone modification; Monoclonal antibody

DOI:  https://doi.org/10.1242/jcs.243444
Genomics. 2020 Jun 20. pii: S0888-7543(19)30258-7. [Epub ahead of print]

Cooperative binding of transcription factors in the human genome.

Yumin Nie, Chuanjun Shu, Xiao Sun.

  Transcription factors (TFs) cooperatively bind to specific DNA sequences to control chromatin and gene transcription in eukaryotes. Here, we searched canonical binding, co-binding and tethered binding regions of a TF within ChIP-seq peaks, and investigated the effect of TF-TF cooperation in human GM12878 and K562 cells. We found that TFs except for CTCF and SPI1 showed a large proportion of co-binding and tethered binding regions, and TFs frequently co-binding with other TFs would also frequently tether other TFs to their binding positions. We further observed lower in vivo nucleosome occupancy, higher in vitro nucleosome occupancy and higher levels of H2A.Z, H3K27ac, H3K9ac, H3K4me1, H3K4me2 and H3K4me3 within distal co-binding regions where other TFs were recruited. In addition, target genes for proximal co-binding regions where other TFs were recruited showed significantly higher expression levels. These results indicated that TF-TF cooperation directly associate with the chromatin structure and gene transcription.

Keywords:  Chromatin; Co-binding; Tethered binding; Transcription factor

DOI:  https://doi.org/10.1016/j.ygeno.2020.06.029
Epigenetics. 2020 Jun 23. 1-10

The hypomethylation of imprinted genes in IVF/ICSI placenta samples is associated with concomitant changes in histone modifications.

Cécile Choux, Paolo Petazzi, Marta Sanchez-Delgado, José R Hernandez Mora, Ana Monteagudo, Paul Sagot, David Monk, Patricia Fauque.

  Although more and more children are born by Assisted Reproductive Technologies (ART), ART safety has not fully been demonstrated. Notably, ART could disturb the delicate step of implantation, and trigger placenta-related adverse outcomes with potential long-term effects, through disrupted epigenetic regulation. We have previously demonstrated that placental DNA methylation was significantly lower after IVF/ICSI than following natural conception at two differentially methylated regions (DMRs) associated with imprinted genes (IGs): H19/IGF2 and KCNQ1OT1. As histone modifications are critical for placental physiology, the aim of this study was to profile permissive and repressive histone marks in placenta biopsies to reveal a better understanding of the epigenetic changes in the context of ART. Utilizing chromatin immunoprecipitation (ChIP) coupled with quantitative PCR, permissive (H3K4me3, H3K4me2, and H3K9ac) and repressive (H3K9me3 and H3K9me2) post-translational histone modifications were quantified. The analyses revealed a significantly higher quantity of H3K4me2 precipitation in the IVF/ICSI group than in the natural conception group for H19/IGF2 and KCNQ1OT1 DMRs (P = 0.016 and 0.003, respectively). Conversely, the quantity of both repressive marks at H19/IGF2 and SNURF DMRs was significantly lower in the IVF/ICSI group than in the natural conception group (P = 0.011 and 0.027 for H19/IGF2; and P = 0.010 and 0.035 for SNURF). These novel findings highlight that DNA hypomethylation at imprinted DMRs following ART is linked with increased permissive/decreased repressive histone marks, altogether promoting a more permissive chromatin conformation. This concomitant change in epigenetic state at IGs at birth might be an important developmental event because of ART manipulations.

Keywords:   in vitro fertilization; Assisted reproductive technologies; DNA methylation; epigenetics; histone modifications; placenta

DOI:  https://doi.org/10.1080/15592294.2020.1783168
Nat Plants. 2020 Jun 22.

Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis.

Jun Wang, Chaoyi Yu, Shuaibing Zhang, Juanying Ye, Hang Dai, Hongkuan Wang, Jiyue Huang, Xiaofeng Cao, Jinbiao Ma, Hong Ma, Yingxiang Wang.

Histone demethylation is crucial for proper chromatin structure and to ensure normal development, and requires the large family of Jumonji C (JmjC)-containing demethylases; however, the molecular mechanisms that regulate the substrate specificity of these JmjC-containing demethylases remain largely unknown. Here, we show that the substrate specificity of the Arabidopsis histone demethylase JMJ16 is broadened from Lys 4 of histone H3 (H3K4) alone in somatic cells to both H3K4 and H3K9 when it binds to the meiocyte-specific histone reader MMD1. Consistent with this, the JMJ16 catalytic domain exhibits both H3K4 and H3K9 demethylation activities. Moreover, the JMJ16 C-terminal FYR domain interacts with the JMJ16 catalytic domain and probably restricts its substrate specificity. By contrast, MMD1 can compete with the N-terminal catalytic domain of JMJ16 for binding to the FYR-C domain, thereby expanding the substrate specificity of JMJ16 by preventing the FYR domain from binding to the catalytic domain. We propose that MMD1 and JMJ16 together in male meiocytes promote gene expression in an H3K9me3-dependent manner and thereby contribute to meiotic chromosome condensation.

DOI: https://doi.org/10.1038/s41477-020-0697-0
Nat Commun. 2020 Jun 26. 11(1): 3241

Protein arginine deiminase 4 antagonizes methylglyoxal-induced histone glycation.

Qingfei Zheng, Adewola Osunsade, Yael David.

Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it has been shown to associate with general chromatin decompaction and compete with arginine methylation. Recently, we found that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications, as well as changing the overall biophysical properties of the fiber. Here, we report that PAD4 antagonizes histone MGO-glycation by protecting the reactive arginine sites, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4's oncogenic properties.

DOI: https://doi.org/10.1038/s41467-020-17066-y
PLoS Genet. 2020 Jun 22. 16(6): e1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase.

Richard Cardoso da Silva, María Ascensión Villar-Fernández, Gerben Vader.

Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific 'licensing' of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1, and Rec8). Inactivating RNAPII-dependent transcription/Orc1 does not lead to effects on the chromosomal abundance of Hop1, a known chromosomal client of Pch2, suggesting a complex relationship between SC formation, Pch2 recruitment and Hop1 chromosomal association. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription.

DOI: https://doi.org/10.1371/journal.pgen.1008905
Nat Immunol. 2020 Jun 22.

Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity.

Shinya Tanaka, Wataru Ise, Takeshi Inoue, Ayako Ito, Chisato Ono, Yoshihito Shima, Shuhei Sakakibara, Manabu Nakayama, Kentaro Fujii, Ikuo Miura, Jafar Sharif, Haruhiko Koseki, Pandelakis A Koni, Indu Raman, Quan-Zhen Li, Masato Kubo, Katsunori Fujiki, Ryuichiro Nakato, Katsuhiko Shirahige, Hiromitsu Araki, Fumihito Miura, Takashi Ito, Eiryo Kawakami, Yoshihiro Baba, Tomohiro Kurosaki.

A contribution of epigenetic modifications to B cell tolerance has been proposed but not directly tested. Here we report that deficiency of ten-eleven translocation (Tet) DNA demethylase family members Tet2 and Tet3 in B cells led to hyperactivation of B and T cells, autoantibody production and lupus-like disease in mice. Mechanistically, in the absence of Tet2 and Tet3, downregulation of CD86, which normally occurs following chronic exposure of self-reactive B cells to self-antigen, did not take place. The importance of dysregulated CD86 expression in Tet2- and Tet3-deficient B cells was further demonstrated by the restriction, albeit not complete, on aberrant T and B cell activation following anti-CD86 blockade. Tet2- and Tet3-deficient B cells had decreased accumulation of histone deacetylase 1 (HDAC1) and HDAC2 at the Cd86 locus. Thus, our findings suggest that Tet2- and Tet3-mediated chromatin modification participates in repression of CD86 on chronically stimulated self-reactive B cells, which contributes, at least in part, to preventing autoimmunity.

DOI: https://doi.org/10.1038/s41590-020-0700-y
Nat Genet. 2020 Jun 22.

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.

Jennifer M Luppino, Daniel S Park, Son C Nguyen, Yemin Lan, Zhuxuan Xu, Rebecca Yunker, Eric F Joyce.

The human genome can be segmented into topologically associating domains (TADs), which have been proposed to spatially sequester genes and regulatory elements through chromatin looping. Interactions between TADs have also been suggested, presumably because of variable boundary positions across individual cells. However, the nature, extent and consequence of these dynamic boundaries remain unclear. Here, we combine high-resolution imaging with Oligopaint technology to quantify the interaction frequencies across both weak and strong boundaries. We find that chromatin intermingling across population-defined boundaries is widespread but that the extent of permissibility is locus-specific. Cohesin depletion, which abolishes domain formation at the population level, does not induce ectopic interactions but instead reduces interactions across all boundaries tested. In contrast, WAPL or CTCF depletion increases inter-domain contacts in a cohesin-dependent manner. Reduced chromatin intermingling due to cohesin loss affects the topology and transcriptional bursting frequencies of genes near boundaries. We propose that cohesin occasionally bypasses boundaries to promote incorporation of boundary-proximal genes into neighboring domains.

DOI: https://doi.org/10.1038/s41588-020-0647-9
Science. 2020 Jun 26. 368(6498): 1449-1454

Single-molecule regulatory architectures captured by chromatin fiber sequencing.

Andrew B Stergachis, Brian M Debo, Eric Haugen, L Stirling Churchman, John A Stamatoyannopoulos.

Gene regulation is chiefly determined at the level of individual linear chromatin molecules, yet our current understanding of cis-regulatory architectures derives from fragmented sampling of large numbers of disparate molecules. We developed an approach for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using nonspecific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing of chromatin stencils enabled nucleotide-resolution readout of the primary architecture of multikilobase chromatin fibers (Fiber-seq). Fiber-seq exposed widespread plasticity in the linear organization of individual chromatin fibers and illuminated principles guiding regulatory DNA actuation, the coordinated actuation of neighboring regulatory elements, single-molecule nucleosome positioning, and single-molecule transcription factor occupancy. Our approach and results open new vistas on the primary architecture of gene regulation.

DOI: https://doi.org/10.1126/science.aaz1646
Aging (Albany NY). 2020 Jun 25. 12

SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.

Sarallah Rezazadeh, David Yang, Seyed Ali Biashad, Denis Firsanov, Masaki Takasugi, Michael Gilbert, Gregory Tombline, Natarajan V Bhanu, Benjamin A Garcia, Andrei Seluanov, Vera Gorbunova.

  When transcribed DNA is damaged, the transcription and DNA repair machineries must interact to ensure successful DNA repair. The mechanisms of this interaction in the context of chromatin are still being elucidated. Here we show that the SIRT6 protein enhances non-homologous end joining (NHEJ) DNA repair by transiently repressing transcription. Specifically, SIRT6 mono-ADP ribosylates the lysine demethylase JHDM1A/KDM2A leading to rapid displacement of KDM2A from chromatin, resulting in increased H3K36me2 levels. Furthermore, we found that through HP1α binding, H3K36me2 promotes subsequent H3K9 tri-methylation. This results in transient suppression of transcription initiation by RNA polymerase II and recruitment of NHEJ factors to DNA double-stranded breaks (DSBs). These data reveal a mechanism where SIRT6 mediates a crosstalk between transcription and DNA repair machineries to promote DNA repair. SIRT6 functions in multiple pathways related to aging, and its novel function coordinating DNA repair and transcription is yet another way by which SIRT6 promotes genome stability and longevity.

Keywords:  DNA repair; SIRT6; genome stability; longevity; transcription

DOI:  https://doi.org/10.18632/aging.103567
Cells. 2020 Jun 19. pii: E1500. [Epub ahead of print]9(6):

Bromodomain Protein BRD4 Accelerates Glucocorticoid Dysregulation of Bone Mass and Marrow Adiposis by Modulating H3K9 and Foxp1.

Feng-Sheng Wang, Yu-Shan Chen, Jih-Yang Ko, Chung-Wen Kuo, Huei-Jing Ke, Chin-Kuei Hsieh, Shao-Yu Wang, Pei-Chen Kuo, Holger Jahr, Wei-Shiung Lian.

  Glucocorticoid provokes bone mass loss and fatty marrow, accelerating osteoporosis development. Bromodomain protein BRD4, an acetyl-histone-binding chromatin reader, regulates stem cell and tissue homeostasis. We uncovered that glucocorticoid inhibited acetyl Lys-9 at the histone 3 (H3K9ac)-binding Runx2 promoter and decreased osteogenic differentiation, whereas bromodomain protein 4 (BRD4) and adipocyte formation were upregulated in bone-marrow mesenchymal progenitor cells. BRD4 knockdown improved H3K9ac occupation at the Runx2 promoter and osteogenesis, but attenuated glucocorticoid-mediated adipocyte formation together with the unaffected H3K9ac-binding PPARγ2 promoter. BRD4 regulated epigenome related to fatty acid metabolism and the forkhead box P1 (Foxp1) pathway, which occupied the PPARγ2 promoter to modulate glucocorticoid-induced adipocytic activity. In vivo, BRD4 inhibitor JQ-1 treatment mitigated methylprednisolone-induced suppression of bone mass, trabecular microstructure, mineral acquisition, and osteogenic differentiation. Foxp1 signaling, marrow fat, and adipocyte formation in glucocorticoid-treated skeleton were reversed upon JQ-1 treatment. Taken together, glucocorticoid-induced H3K9 hypoacetylation augmented BRD4 action to Foxp1, which steered mesenchymal progenitor cells toward adipocytes at the cost of osteogenic differentiation in osteoporotic skeletons. BRD4 inhibition slowed bone mass loss and marrow adiposity. Collective investigations convey a new epigenetic insight into acetyl histone reader BRD4 control of osteogenesis and adipogenesis in skeleton, and highlight the remedial effects of the BRD4 inhibitor on glucocorticoid-induced osteoporosis.

Keywords:  BRD4; Foxp1; H3K9; JQ-1; acetylation; glucocorticoid

DOI:  https://doi.org/10.3390/cells9061500
Brief Bioinform. 2020 Jun 24. pii: bbaa120. [Epub ahead of print]

Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.

Kangning Dong, Shihua Zhang.

  The rapid accumulation of single-cell chromatin accessibility data offers a unique opportunity to investigate common and specific regulatory mechanisms across different cell types. However, existing methods for cis-regulatory network reconstruction using single-cell chromatin accessibility data were only designed for cells belonging to one cell type, and resulting networks may be incomparable directly due to diverse cell numbers of different cell types. Here, we adopt a computational method to jointly reconstruct cis-regulatory interaction maps (JRIM) of multiple cell populations based on patterns of co-accessibility in single-cell data. We applied JRIM to explore common and specific regulatory interactions across multiple tissues from single-cell ATAC-seq dataset containing ~80 000 cells across 13 mouse tissues. Reconstructed common interactions among 13 tissues indeed relate to basic biological functions, and individual cis-regulatory networks show strong tissue specificity and functional relevance. More importantly, tissue-specific regulatory interactions are mediated by coordination of histone modifications and tissue-related TFs, and many of them may reveal novel regulatory mechanisms.

Keywords:   cis-regulatory interaction networks; Gaussian graphical LASSO; single-cell ATAC-seq

DOI:  https://doi.org/10.1093/bib/bbaa120
Curr Top Dev Biol. 2020 ;pii: S0070-2153(20)30062-4. [Epub ahead of print]140 35-54

Maternal inheritance of centromeres through the germline.

Arunika Das, Ben E Black, Michael A Lampson.

  The centromere directs chromosome segregation but is not itself genetically encoded. In most species, centromeres are epigenetically defined by the presence of a histone H3 variant CENP-A, independent of the underlying DNA sequence. Therefore, to maintain centromeres and ensure accurate chromosome segregation, CENP-A nucleosomes must be inherited across generations through the germline. In this chapter we discuss three aspects of maternal centromere inheritance. First, we propose mechanisms for maintaining CENP-A nucleosomes through the prolonged prophase arrest in mammalian oocytes. Second, we review mechanisms by which selfish centromeres bias their transmission through female meiosis. Third, we discuss regulation of centromere size through early embryonic development.

Keywords:  CENP-A; Centromeres; Female germline; Inheritance

DOI:  https://doi.org/10.1016/bs.ctdb.2020.03.004
Cell Rep. 2020 Jun 23. pii: S2211-1247(20)30784-1. [Epub ahead of print]31(12): 107803

Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor.

Mei Yang, Ji Hoon Lee, Zhao Zhang, Richard De La Rosa, Mingjun Bi, Yuliang Tan, Yiji Liao, Juyeong Hong, Baowen Du, Yanming Wu, Jessica Scheirer, Tao Hong, Wei Li, Teng Fei, Chen-Lin Hsieh, Zhijie Liu, Wenbo Li, Michael G Rosenfeld, Kexin Xu.

  The function of enhancer RNAs (eRNAs) in transcriptional regulation remains obscure. By analyzing the genome-wide nascent transcript profiles in breast cancer cells, we identify a special group of eRNAs that are essential for estrogen-induced transcriptional repression. Using eRNAs of TM4SF1 and EFEMP1 as the paradigms, we find that these RNA molecules not only stabilize promoter-enhancer interactions but also recruit liganded estrogen receptor α (ERα) to particular enhancer regions, facilitate the formation of a functional transcriptional complex, and cause gene silencing. Interestingly, ERα is shown to directly bind with eRNAs by its DNA-binding domain. These eRNAs help with the formation of a specific ERα-centered transcriptional complex and promote the association of the histone demethylase KDM2A, which dismisses RNA polymerase II from designated enhancers and suppresses the transcription of target genes. Our work demonstrates a complete mechanism underlying the action of eRNAs in modulating and refining the locus-specific transcriptional program.

Keywords:  ERα signaling; enhancer RNA; enhancer activity regulation; transcriptional repression

DOI:  https://doi.org/10.1016/j.celrep.2020.107803
Mol Cancer Res. 2020 Jun 22. pii: molcanres.0291.2020. [Epub ahead of print]

SPANX control of Lamin A/C modulates nuclear architecture and promotes melanoma growth.

Ikrame Lazar, Bertrand Fabre, Yongmei Feng, Ali Khateb, Patrick Turko, Maria Julia Martinez-Gomez, Dennie T Frederick, Mitchell P Levesque, Lea Feld, Gao Zhang, Tongwu Zhang, Brian James, Jeny Shklover, Emily Avitan Hersh, Ido Livneh, Marzia Scortegagna, Kevin Brown, Ola Larsson, Ivan Topisirovic, Haguy Wolfenson, Meenhard Herlyn, Keith Flaherty, Reinhard Dummer, Ze'ev A Ronai.

Mechanisms regulating nuclear organization control fundamental cellular processes, including the cell and chromatin organization. Their disorganization, including aberrant nuclear architecture, has been often implicated in cellular transformation. Here, we identify Lamin A, among proteins essential for nuclear architecture, as SPANX, a cancer testis antigen previously linked to invasive tumor phenotypes, interacting protein in melanoma. SPANX interaction with Lamin A was mapped to the immunoglobulin fold-like domain, a region critical for Lamin A function, which is often mutated in laminopathies. SPANX down-regulation in melanoma cell lines perturbed nuclear organization, decreased cell viability and promoted senescence-associated phenotypes. Moreover, SPANX knockdown in melanoma cells promoted proliferation arrest, a phenotype mediated in part by IRF3/IL1A signaling. SPANX-knockdown in melanoma cells also prompted the secretion of IL1A, which attenuated the proliferation of naive melanoma cells. Identification of SPANX as a nuclear architecture complex component provides an unexpected insight into the regulation of Lamin A and its importance in melanoma. Implications: SPANX, a testis protein, interacts with LAMNA and controls nuclear architecture and melanoma growth.

DOI: https://doi.org/10.1158/1541-7786.MCR-20-0291
Nat Commun. 2020 Jun 22. 11(1): 3158

DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner.

Patrick L Collins, Caitlin Purman, Sofia I Porter, Vincent Nganga, Ankita Saini, Katharina E Hayer, Greer L Gurewitz, Barry P Sleckman, Jeffrey J Bednarski, Craig H Bassing, Eugene M Oltz.

Efficient repair of DNA double-strand breaks (DSBs) requires a coordinated DNA Damage Response (DDR), which includes phosphorylation of histone H2Ax, forming γH2Ax. This histone modification spreads beyond the DSB into neighboring chromatin, generating a DDR platform that protects against end disassociation and degradation, minimizing chromosomal rearrangements. However, mechanisms that determine the breadth and intensity of γH2Ax domains remain unclear. Here, we show that chromosomal contacts of a DSB site are the primary determinants for γH2Ax landscapes. DSBs that disrupt a topological border permit extension of γH2Ax domains into both adjacent compartments. In contrast, DSBs near a border produce highly asymmetric DDR platforms, with γH2Ax nearly absent from one broken end. Collectively, our findings lend insights into a basic DNA repair mechanism and how the precise location of a DSB may influence genome integrity.

DOI: https://doi.org/10.1038/s41467-020-16926-x
Sci Rep. 2020 Jun 25. 10(1): 10343

TET1 Deficiency Impairs Morphogen-free Differentiation of Human Embryonic Stem Cells to Neuroectoderm.

Hanqin Li, Zhixing Hu, Houbo Jiang, Jiali Pu, Ilana Selli, Jingxin Qiu, Baorong Zhang, Jian Feng.

The TET family of 5-methylcytosine (5mC) dioxygenases plays critical roles in development by modifying DNA methylation. Using CRISPR, we inactivated the TET1 gene in H9 human embryonic stem cells (hESCs). Mutant H9 hESCs remained pluripotent, even though the level of hydroxymethylcytosine (5hmC) decreased to 30% of that in wild-type cells. Neural differentiation induced by dual SMAD inhibitors was not significantly affected by loss of TET1 activity. However, in a morphogen-free condition, TET1 deficiency significantly reduced the generation of NESTIN+SOX1+ neuroectoderm cells from 70% in wild-type cells to 20% in mutant cells. This was accompanied by a 20-fold reduction in the expression level of PAX6 and a significant decrease in the amount of 5hmC on the PAX6 promoter. Overexpression of the TET1 catalytic domain in TET1-deficient hESCs significantly increased 5hmC levels and elevated PAX6 expression during differentiation. Consistent with these in vitro data, PAX6 expression was significantly decreased in teratomas formed by TET1-deficient hESCs. However, TET1 deficiency did not prevent the formation of neural tube-like structures in teratomas. Our results suggest that TET1 deficiency impairs the intrinsic ability of hESCs to differentiate to neuroectoderm, presumably by decreasing the expression of PAX6, a key regulator in the development of human neuroectoderm.

DOI: https://doi.org/10.1038/s41598-020-67143-x
Nat Struct Mol Biol. 2020 Jun 22.

Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development.

Kristjan H Gretarsson, Jamie A Hackett.

Early mammalian development entails genome-wide epigenome remodeling, including DNA methylation erasure and reacquisition, which facilitates developmental competence. To uncover the mechanisms that orchestrate DNA methylation dynamics, we coupled a single-cell ratiometric DNA methylation reporter with unbiased CRISPR screening in murine embryonic stem cells (ESCs). We identify key genes and regulatory pathways that drive global DNA hypomethylation, and characterize roles for Cop1 and Dusp6. We also identify Dppa2 and Dppa4 as essential safeguards of focal epigenetic states. In their absence, developmental genes and evolutionarily young LINE1 elements, which are specifically bound by DPPA2, lose H3K4me3 and gain ectopic de novo DNA methylation in pluripotent cells. Consequently, lineage-associated genes and LINE1 acquire a repressive epigenetic memory, which renders them incompetent for activation during future lineage specification. Dppa2/4 thereby sculpt the pluripotent epigenome by facilitating H3K4me3 and bivalency to counteract de novo methylation, a function co-opted by evolutionarily young LINE1 to evade epigenetic decommissioning.

DOI: https://doi.org/10.1038/s41594-020-0445-1
Curr Top Dev Biol. 2020 ;pii: S0070-2153(19)30078-X. [Epub ahead of print]140 3-34

Post-transcriptional gene regulation regulates germline stem cell to oocyte transition during Drosophila oogenesis.

Patrick Blatt, Elliot T Martin, Shane M Breznak, Prashanth Rangan.

  During oogenesis, several developmental processes must be traversed to ensure effective completion of gametogenesis including, stem cell maintenance and asymmetric division, differentiation, mitosis and meiosis, and production of maternally contributed mRNAs, making the germline a salient model for understanding how cell fate transitions are mediated. Due to silencing of the genome during meiotic divisions, there is little instructive transcription, barring a few examples, to mediate these critical transitions. In Drosophila, several layers of post-transcriptional regulation ensure that the mRNAs required for these processes are expressed in a timely manner and as needed during germline differentiation. These layers of regulation include alternative splicing, RNA modification, ribosome production, and translational repression. Many of the molecules and pathways involved in these regulatory activities are conserved from Drosophila to humans making the Drosophila germline an elegant model for studying the role of post-transcriptional regulation during stem cell differentiation and meiosis.

Keywords:  Drosophila; Gametogenesis; Germline differentiation; Germline stem cell; Oogenesis; RNA binding proteins; RNA modifications; RNA regulation; Ribosome biogenesis; Splicing; Translation control

DOI:  https://doi.org/10.1016/bs.ctdb.2019.10.003
Onco Targets Ther. 2020 ;13 4855-4863

Six1 Overexpression Promotes Glucose Metabolism and Invasion Through Regulation of GLUT3, MMP2 and Snail in Thyroid Cancer Cells.

Chuanjia Yang, Weixue Xu, Jian Gong, Fang Chai, Dongxu Cui, Zhen Liu.

   Introduction: Sineoculis homeobox homolog 1 (Six1) overexpression has been implicated in several human cancers. To date, its clinical significance and potential function in human thyroid cancer remain unclear.
Methods: Immunohistochemistry was used to examine the protein expression of BCAT1 in 89 cases of thyroid cancer tissues. We overexpressed and knockdown Six1 in TPC-1 and B-CPAP thyroid cancer cell lines. Biological roles and potential mechanisms of Six1 were examined using CCK-8, colony formation assay, Matrigel invasion assay, Western blot, PCR, ATP assay, and 2-NBDG uptake assay.
Results: We showed that Six1 protein was upregulated in thyroid cancers and was associated with tumor size and nodal metastasis. Analysis of TCGA dataset indicated that Six1 mRNA was higher in thyroid cancers compared with normal thyroid. CCK-8, colony formation and Matrigel invasion assays demonstrated that Six1 overexpression promoted proliferation, colony number and invasion while Six1 siRNA knockdown inhibited the growth rate, colony formation ability and invasive ability in both cell lines. Notably, Six1 upregulated glucose consumption, lactate production level and ATP level. 2-NBDG uptake analysis showed that Six1 overexpression upregulated glucose uptake while Six1 knockdown inhibited glucose uptake. Further analysis revealed that Six1 overexpression upregulated Snail, MMP2 and GLUT3 at both mRNA and protein levels. TCGA analysis demonstrated positive associations between Six1 and Snail, MMP2 and GLUT3 at the mRNA levels.
Conclusion: Taken together, our data demonstrated that Six1 was upregulated in human thyroid cancers and promoted cell proliferation and invasion. Our data also revealed new roles of Six1 in thyroid cancer development by modulating glucose metabolism and invasion, possibly through regulation of Snail, MMP2 and GLUT3.

Keywords:  GLUT3; Six1; glucose metabolism; thyroid cancer

DOI:  https://doi.org/10.2147/OTT.S227291