bims-crepig 2022-01-23 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022–01–23
twenty-two papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit

Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos.
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis.
The role of DNA methylation in genome-wide gene regulation during development.
Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.
Domain adaptive neural networks improve cross-species prediction of transcription factor binding.
Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs.
Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites.
Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration.
TAF4b transcription networks regulating early oocyte differentiation.
Expression of Lineage Transcription Factors Identifies Differences in Transition States of Induced Human Oligodendrocyte Differentiation.
Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.
Thyroid hormone dependent transcriptional programming by TRβ requires SWI/SNF chromatin remodelers.
The isoquinoline PRL-295 increases the thermostability of Keap1 and disrupts its interaction with Nrf2.
ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export.
E2F and STAT3 provide transcriptional synergy for histone variant H2AZ activation to sustain glioblastoma chromatin accessibility and tumorigenicity.
Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve.
Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro.
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.
53BP1 regulates heterochromatin through liquid phase separation.
YAP1 regulates the self-organized fate patterning of hESC-derived gastruloids.
Recruitment of MLL1 complex is essential for SETBP1 to induce myeloid transformation.
Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation.

Nat Commun. 2022 Jan 17. 13(1): 346

Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos.

Chen C Li, Guangyu Zhang, Junjie Du, Di Liu, Zongcheng Li, Yanli Ni, Jie Zhou, Yunqiao Li, Siyuan Hou, Xiaona Zheng, Yu Lan, Bing Liu, Aibin He.

The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.

DOI: https://doi.org/10.1038/s41467-022-28018-z
Genome Res. 2022 Jan 19. pii: gr.275864.121. [Epub ahead of print]

Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis.

Paola Cornejo-Paramo, Kathrein Roper, Sandie Degnan, Bernard Degnan, Emily S Wong.

The chromatin environment plays a central role in regulating developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica These profiles are reproducible within stages, reflect histone modifications, and identify transcription factor (TF) binding sequence motifs predictive of cis-regulatory elements operating during embryogenesis in other metazoans, but not the unicellular relative Capsaspora Motif analysis of chromatin accessibility profiles across Amphimedon embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (silencers) are prominent during late embryogenesis. They coincide with an increase in cis-regulatory regions harbouring metazoan TF binding motifs, and an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced chromatin, and TF-DNA binding specificity in animal embryogenesis.

DOI: https://doi.org/10.1101/gr.275864.121
Development. 2022 Jan 15. pii: dev200118. [Epub ahead of print]149(2):

The role of DNA methylation in genome-wide gene regulation during development.

Howard Cedar, Ofra Sabag, Yitzhak Reizel.

  Although it is well known that DNA methylation serves to repress gene expression, precisely how it functions during the process of development remains unclear. Here, we propose that the overall pattern of DNA methylation established in the early embryo serves as a sophisticated mechanism for maintaining a genome-wide network of gene regulatory elements in an inaccessible chromatin structure throughout the body. As development progresses, programmed demethylation in each cell type then provides the specificity for maintaining select elements in an open structure. This allows these regulatory elements to interact with a large range of transcription factors and thereby regulate the gene expression profiles that define cell identity.

Keywords:  Chromatin; Development; Enhancers; Epigenetics; Global repression; Pioneer factors

DOI:  https://doi.org/10.1242/dev.200118
Mol Omics. 2022 Jan 19.

Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.

Yekaterina Kori, Peder J Lund, Matteo Trovato, Simone Sidoli, Zuo-Fei Yuan, Kyung-Min Noh, Benjamin A Garcia.

Histone variants, such as histone H3.3, replace canonical histones within the nucleosome to alter chromatin accessibility and gene expression. Although the biological roles of selected histone post-translational modifications (PTMs) have been extensively characterized, the potential differences in the function of a given PTM on different histone variants is almost always elusive. By applying proteomics and genomics techniques, we investigate the role of lysine 27 tri-methylation specifically on the histone variant H3.3 (H3.3K27me3) in the context of mouse embryonic stem cell pluripotency and differentiation as a model system for development. We demonstrate that while the steady state overall levels of methylation on both H3K27 and H3.3K27 decrease during differentiation, methylation dynamics studies indicate that methylation on H3.3K27 is maintained more than on H3K27. Using a custom-made antibody, we identify a unique enrichment of H3.3K27me3 at lineage-specific genes, such as olfactory receptor genes, and at binding motifs for the transcription factors FOXJ2/3. REST, a predicted FOXJ2/3 target that acts as a transcriptional repressor of terminal neuronal genes, was identified with H3.3K27me3 at its promoter region. H3.3K27A mutant cells confirmed an upregulation of FOXJ2/3 targets upon the loss of methylation at H3.3K27. Thus, while canonical H3K27me3 has been characterized to regulate the expression of transcription factors that play a general role in differentiation, our work suggests H3.3K27me3 is essential for regulating distinct terminal differentiation genes. This work highlights the importance of understanding the effects of PTMs not only on canonical histones but also on specific histone variants, as they may exhibit distinct roles.

DOI: https://doi.org/10.1039/d1mo00352f
Genome Res. 2022 Jan 18. pii: gr.275394.121. [Epub ahead of print]

Domain adaptive neural networks improve cross-species prediction of transcription factor binding.

Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross C Hardison, Anshul Kundaje, Shaun Mahony.

The intrinsic DNA sequence preferences and cell-type specific cooperative partners of transcription factors (TFs) are typically highly conserved. Hence, despite the rapid evolutionary turnover of individual TF binding sites, predictive sequence models of cell-type specific genomic occupancy of a TF in one species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomic background and evaluate their performance within and across species. Cross-species predictive performance is consistently worse than within-species performance, which we show is caused in part by species-specific repeats. To account for this domain shift, we use an augmented network architecture to automatically discourage learning of training species-specific sequence features. This domain adaptation approach corrects for prediction errors on species-specific repeats and improves overall cross-species model performance. Our results demonstrate that cross-species TF binding prediction is feasible when models account for domain shifts driven by species-specific repeats.

DOI: https://doi.org/10.1101/gr.275394.121
Elife. 2022 Jan 20. pii: e70878. [Epub ahead of print]11

Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs.

Zeyang Shen, Rick Z Li, Thomas A Prohaska, Marten A Hoeksema, Nathan J Spann, Jenhan Tao, Gregory J Fonseca, Thomas Le, Lindsey K Stolze, Mashito Sakai, Casey E Romanoski, Christopher K Glass.

  Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 73 TFs in human K562 cells as determined by ChIP-seq. We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 45 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. These analyses suggested that spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. To experimentally validate this prediction, we introduced synthetic spacing alterations between PU.1 and C/EBPβ binding sites at six endogenous genomic loci in a macrophage cell line. Remarkably, collaborative binding of PU.1 and C/EBPβ at these locations tolerated changes in spacing ranging from 5-bp increase to >30-bp decrease. Collectively, these findings have implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.

Keywords:  chromosomes; gene expression; genetics; genomics; human; mouse

DOI:  https://doi.org/10.7554/eLife.70878
Sci Adv. 2022 Jan 21. 8(3): eabj5688

Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites.

Mariel Mendoza, Gabor Egervari, Simone Sidoli, Greg Donahue, Desi C Alexander, Payel Sen, Benjamin A Garcia, Shelley L Berger.

Histone acetylation is governed by nuclear acetyl-CoA pools generated, in part, from local acetate by metabolic enzyme acetyl-CoA synthetase 2 (ACSS2). We hypothesize that during gene activation, a local transfer of intact acetate occurs via sequential action of epigenetic and metabolic enzymes. Using stable isotope labeling, we detect transfer between histone acetylation sites both in vitro using purified mammalian enzymes and in vivo using quiescence exit in Saccharomyces cerevisiae as a change-of-state model. We show that Acs2, the yeast ortholog of ACSS2, is recruited to chromatin during quiescence exit and observe dynamic histone acetylation changes proximal to Acs2 peaks. We find that Acs2 is preferentially associated with the most up-regulated genes, suggesting that acetyl group transfer plays an important role in gene activation. Overall, our data reveal direct transfer of acetate between histone lysine residues to facilitate rapid transcriptional induction, an exchange that may be critical during changes in nutrient availability.

DOI: https://doi.org/10.1126/sciadv.abj5688
Dev Cell. 2022 Jan 11. pii: S1534-5807(21)01039-X. [Epub ahead of print]

Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration.

Lian-Yu Wu, Guan-Dong Shang, Fu-Xiang Wang, Jian Gao, Mu-Chun Wan, Zhou-Geng Xu, Jia-Wei Wang.

  Shoot regeneration is mediated by the sequential action of two phytohormones, auxin and cytokinin. However, the chromatin regulatory landscapes underlying this dynamic response have not yet been studied. In this study, we jointly profiled chromatin accessibility, histone modifications, and transcriptomes to demonstrate that a high auxin/cytokinin ratio environment primes Arabidopsis shoot regeneration by increasing the accessibility of the gene loci associated with pluripotency and shoot fate determination. Cytokinin signaling not only triggers the commitment of the shoot progenitor at later stages but also allows chromatin to maintain shoot identity genes at the priming stage. Our analysis of transcriptional regulatory dynamics further identifies a catalog of regeneration cis-elements dedicated to cell fate transitions and uncovers important roles of BES1, MYC, IDD, and PIF transcription factors in shoot regeneration. Our results, thus, provide a comprehensive resource for studying cell reprogramming in plants and provide potential targets for improving future shoot regeneration efficiency.

Keywords:  Arabidopsis; auxin; chromatin accessibility; cytokinin; pluripotency; shoot regeneration; transcription factor

DOI:  https://doi.org/10.1016/j.devcel.2021.12.019
Development. 2022 Jan 19. pii: dev.200074. [Epub ahead of print]

TAF4b transcription networks regulating early oocyte differentiation.

Megan A Gura, Soňa Relovská, Kimberly M Abt, Kimberly A Seymour, Tong Wu, Haskan Kaya, James M A Turner, Thomas G Fazzio, Richard N Freiman.

  Establishment of a healthy ovarian reserve is contingent upon numerous regulatory pathways during embryogenesis. Previously, mice lacking TBP-associated factor 4b (Taf4b) were shown to exhibit a diminished ovarian reserve. However, potential oocyte-intrinsic functions of TAF4b have not been examined. Here we use a combination of gene expression profiling and chromatin mapping to characterize TAF4b-dependent gene regulatory networks in mouse oocytes. We find that Taf4b-deficient oocytes display inappropriate expression of meiotic, chromatin, and X-linked genes. Furthermore, dysregulated genes in Taf4b-deficient oocytes exhibit an unexpected amount of overlap with dysregulated genes in Turner Syndrome oocytes. Using Cleavage Under Targets and Release Using Nuclease (CUT&RUN), we observed TAF4b enrichment at genes involved in chromatin remodeling and DNA repair, some of which are differentially expressed in Taf4b-deficient oocytes. Interestingly, TAF4b target genes were enriched for Sp/Klf family and NFY target motifs rather than TATA-box motifs, suggesting an alternate mode of promoter interaction. Together, our data connects several gene regulatory nodes that contribute to the precise development of the mammalian ovarian reserve.

Keywords:  Fetal oocyte attrition; Meiosis I; Oocytes; Oogenesis; POI; TAF4b; TFIID; Transcription

DOI:  https://doi.org/10.1242/dev.200074
Cells. 2022 Jan 11. pii: 241. [Epub ahead of print]11(2):

Expression of Lineage Transcription Factors Identifies Differences in Transition States of Induced Human Oligodendrocyte Differentiation.

Florian J Raabe, Marius Stephan, Jan Benedikt Waldeck, Verena Huber, Damianos Demetriou, Nirmal Kannaiyan, Sabrina Galinski, Laura V Glaser, Michael C Wehr, Michael J Ziller, Andrea Schmitt, Peter Falkai, Moritz J Rossner.

  Oligodendrocytes (OLs) are critical for myelination and are implicated in several brain disorders. Directed differentiation of human-induced OLs (iOLs) from pluripotent stem cells can be achieved by forced expression of different combinations of the transcription factors SOX10 (S), OLIG2 (O), and NKX6.2 (N). Here, we applied quantitative image analysis and single-cell transcriptomics to compare different transcription factor (TF) combinations for their efficacy towards robust OL lineage conversion. Compared with S alone, the combination of SON increases the number of iOLs and generates iOLs with a more complex morphology and higher expression levels of myelin-marker genes. RNA velocity analysis of individual cells reveals that S generates a population of oligodendrocyte-precursor cells (OPCs) that appear to be more immature than those generated by SON and to display distinct molecular properties. Our work highlights that TFs for generating iOPCs or iOLs should be chosen depending on the intended application or research question, and that SON might be beneficial to study more mature iOLs while S might be better suited to investigate iOPC biology.

Keywords:  RNA velocity; directed differentiation; hiPSC; human pluripotent stem cells; oligodendrocytes; scRNAseq

DOI:  https://doi.org/10.3390/cells11020241
Mol Cell. 2022 Jan 14. pii: S1097-2765(21)01085-6. [Epub ahead of print]

Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.

Nicole M Martinez, Amanda Su, Margaret C Burns, Julia K Nussbacher, Cassandra Schaening, Shashank Sathe, Gene W Yeo, Wendy V Gilbert.

  Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.

Keywords:  RNA modification; alternative cleavage and polyadenylation; alternative splicing; cotranscriptional; epitranscriptome; mRNA modification; pre-mRNA processing; pseudouridine; pseudouridine synthase

DOI:  https://doi.org/10.1016/j.molcel.2021.12.023
Nucleic Acids Res. 2022 Jan 17. pii: gkab1287. [Epub ahead of print]

Thyroid hormone dependent transcriptional programming by TRβ requires SWI/SNF chromatin remodelers.

Noelle E Gillis, Joseph R Boyd, Jennifer A Tomczak, Seth Frietze, Frances E Carr.

Transcriptional regulation in response to thyroid hormone (3,5,3'-triiodo-l-thyronine, T3) is a dynamic and cell-type specific process that maintains cellular homeostasis and identity in all tissues. However, our understanding of the mechanisms of thyroid hormone receptor (TR) actions at the molecular level are actively being refined. We used an integrated genomics approach to profile and characterize the cistrome of TRβ, map changes in chromatin accessibility, and capture the transcriptomic changes in response to T3 in normal human thyroid cells. There are significant shifts in TRβ genomic occupancy in response to T3, which are associated with differential chromatin accessibility, and differential recruitment of SWI/SNF chromatin remodelers. We further demonstrate selective recruitment of BAF and PBAF SWI/SNF complexes to TRβ binding sites, revealing novel differential functions in regulating chromatin accessibility and gene expression. Our findings highlight three distinct modes of TRβ interaction with chromatin and coordination of coregulator activity.

DOI: https://doi.org/10.1093/nar/gkab1287
iScience. 2022 Jan 21. 25(1): 103703

The isoquinoline PRL-295 increases the thermostability of Keap1 and disrupts its interaction with Nrf2.

Sharadha Dayalan Naidu, Takafumi Suzuki, Dina Dikovskaya, Elena V Knatko, Maureen Higgins, Miu Sato, Miroslav Novak, José A Villegas, Terry W Moore, Masayuki Yamamoto, Albena T Dinkova-Kostova.

  Transcription factor Nrf2 and its negative regulator Keap1 orchestrate a cytoprotective response against oxidative, metabolic, and inflammatory stress. Keap1 is a drug target, with several small molecules in drug development. Here, we show that the isoquinoline PRL-295 increased Keap1 thermostability in lysates from cells expressing fluorescently tagged Keap1. The thermostability of endogenous Keap1 also increased in intact cells and murine liver following PRL-295 treatment. Fluorescence Lifetime Imaging-Förster Resonance Energy Transfer (FLIM-FRET) experiments in cells co-expressing sfGFP-Nrf2 and Keap1-mCherry further showed that PRL-295 prolonged the donor fluorescence lifetime, indicating disruption of the Keap1-Nrf2 protein complex. Orally administered PRL-295 to mice activated the Nrf2transcriptional target NAD(P)H:quinone oxidoreductase 1 (NQO1) in liver and decreased the levels of plasma alanine aminotransferase and aspartate aminotransferase upon acetaminophen-induced hepatic injury. Thus, PRL-295 engages the Keap1 protein target in cells and in vivo, disrupting its interaction with Nrf2, leading to activation of Nrf2-dependent transcription and hepatocellular protection.

Keywords:  Biochemistry; Biological sciences; Molecular interaction

DOI:  https://doi.org/10.1016/j.isci.2021.103703
EMBO Rep. 2022 Jan 17. e53191

ZFP207 sustains pluripotency by coordinating OCT4 stability, alternative splicing and RNA export.

Sandhya Malla, Devi Prasad Bhattarai, Paula Groza, Dario Melguizo-Sanchis, Ionut Atanasoai, Carlos Martinez-Gamero, Ángel-Carlos Román, Dandan Zhu, Dung-Fang Lee, Claudia Kutter, Francesca Aguilo.

  The pluripotent state is not solely governed by the action of the core transcription factors OCT4, SOX2, and NANOG, but also by a series of co-transcriptional and post-transcriptional events, including alternative splicing (AS) and the interaction of RNA-binding proteins (RBPs) with defined subpopulations of RNAs. Zinc Finger Protein 207 (ZFP207) is an essential transcription factor for mammalian embryonic development. Here, we employ multiple functional analyses to characterize its role in mouse embryonic stem cells (ESCs). We find that ZFP207 plays a pivotal role in ESC maintenance, and silencing of Zfp207 leads to severe neuroectodermal differentiation defects. In striking contrast to human ESCs, mouse ZFP207 does not transcriptionally regulate neuronal and stem cell-related genes but exerts its effects by controlling AS networks and by acting as an RBP. Our study expands the role of ZFP207 in maintaining ESC identity, and underscores the functional versatility of ZFP207 in regulating neural fate commitment.

Keywords:  RNA-binding protein; ZFP207; Zinc finger protein; alternative splicing; pluripotency

DOI:  https://doi.org/10.15252/embr.202153191
Cell Death Differ. 2022 Jan 20.

E2F and STAT3 provide transcriptional synergy for histone variant H2AZ activation to sustain glioblastoma chromatin accessibility and tumorigenicity.

Jeehyun Yoon, Oleg V Grinchuk, Roberto Tirado-Magallanes, Zhen Kai Ngian, Emmy Xue Yun Tay, You Heng Chuah, Bernice Woon Li Lee, Jia Feng, Karen Carmelina Crasta, Chin Tong Ong, Touati Benoukraf, Derrick Sek Tong Ong.

The histone variant H2AZ is overexpressed in diverse cancer types where it facilitates the accessibility of transcriptional regulators to the promoters of cell cycle genes. However, the molecular basis for its dysregulation in cancer remains unknown. Here, we report that glioblastomas (GBM) and glioma stem cells (GSCs) preferentially overexpress H2AZ for their proliferation, stemness and tumorigenicity. Chromatin accessibility analysis of H2AZ2 depleted GSC revealed that E2F1 occupies the enhancer region within H2AZ2 gene promoter, thereby activating H2AZ2 transcription. Exploration of other H2AZ2 transcriptional activators using a customized "anti-H2AZ2" query signature for connectivity map analysis identified STAT3. Co-targeting E2F and STAT3 synergistically reduced the levels of H2AZ, histone 3 lysine 27 acetylation (H3K27ac) and cell cycle gene transcription, indicating that E2F1 and STAT3 synergize to activate H2AZ gene transcription in GSCs. Remarkably, an E2F/STAT3 inhibitor combination durably suppresses GSC tumorigenicity in an orthotopic GBM xenograft model. In glioma patients, high STAT3 signaling is associated with high E2F1 and H2AZ2 expression. Thus, GBM has uniquely opted the use of E2F1- and STAT3-containing "enhanceosomes" that integrate multiple signaling pathways to achieve H2AZ gene activation, supporting a translational path for the E2F/STAT3 inhibitor combination to be applied in GBM treatment.

DOI: https://doi.org/10.1038/s41418-021-00926-5
PLoS Genet. 2022 Jan 18. 18(1): e1010010

Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve.

Arnaud Chignon, Déborah Argaud, Marie-Chloé Boulanger, Ghada Mkannez, Valentin Bon-Baret, Zhonglin Li, Sébastien Thériault, Yohan Bossé, Patrick Mathieu.

Calcific aortic valve disease (CAVD) is characterized by a fibrocalcific process. The regulatory mechanisms that drive the fibrotic response in the aortic valve (AV) are poorly understood. Long noncoding RNAs derived from super-enhancers (lncRNA-SE) control gene expression and cell fate. Herein, multidimensional profiling including chromatin immunoprecipitation and sequencing, transposase-accessible chromatin sequencing, genome-wide 3D chromatin contacts of enhancer-promoter identified LINC01013 as an overexpressed lncRNA-SE during CAVD. LINC01013 is within a loop anchor, which has contact with the promoter of CCN2 (CTGF) located at ~180 kb upstream. Investigation showed that LINC01013 acts as a decoy factor for the negative transcription elongation factor E (NELF-E), whereby it controls the expression of CCN2. LINC01013-CCN2 is part of a transforming growth factor beta 1 (TGFB1) network and exerts a control over fibrogenesis. These findings illustrate a novel mechanism whereby a dysregulated lncRNA-SE controls, through a looping process, the expression of CCN2 and fibrogenesis of the AV.

DOI: https://doi.org/10.1371/journal.pgen.1010010
Sci Rep. 2022 Jan 17. 12(1): 855

Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro.

Hae In Choi, Ga Yeong An, Eunyoung Yoo, Mina Baek, Jin Choul Chai, Bert Binas, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai.

The proto-oncogene MYC is important for development and cell growth, however, its abnormal regulation causes cancer. Recent studies identified distinct enhancers of MYC in various cancers, but any MYC enhancer(s) in hepatocellular carcinoma (HCC) remain(s) elusive. By analyzing H3K27ac enrichment and enhancer RNA (eRNA) expression in cultured HCC cells, we identified six putative MYC enhancer regions. Amongst these, two highly active enhancers, located ~ 800 kb downstream of the MYC gene, were identified by qRT-PCR and reporter assays. We functionally confirmed these enhancers by demonstrating a significantly reduced MYC expression and cell proliferation upon CRISPR/Cas9-based deletion and/or antisense oligonucleotide (ASO)-mediated inhibition. In conclusion, we identified potential MYC enhancers of HCC and propose that the associated eRNAs may be suitable targets for HCC treatment.

DOI: https://doi.org/10.1038/s41598-022-04869-w
Nat Biotechnol. 2022 Jan 20.

scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.

Yingxin Lin, Tung-Yu Wu, Sheng Wan, Jean Y H Yang, Wing H Wong, Y X Rachel Wang.

Single-cell multiomics data continues to grow at an unprecedented pace. Although several methods have demonstrated promising results in integrating several data modalities from the same tissue, the complexity and scale of data compositions present in cell atlases still pose a challenge. Here, we present scJoint, a transfer learning method to integrate atlas-scale, heterogeneous collections of scRNA-seq and scATAC-seq data. scJoint leverages information from annotated scRNA-seq data in a semisupervised framework and uses a neural network to simultaneously train labeled and unlabeled data, allowing label transfer and joint visualization in an integrative framework. Using atlas data as well as multimodal datasets generated with ASAP-seq and CITE-seq, we demonstrate that scJoint is computationally efficient and consistently achieves substantially higher cell-type label accuracy than existing methods while providing meaningful joint visualizations. Thus, scJoint overcomes the heterogeneity of different data modalities to enable a more comprehensive understanding of cellular phenotypes.

DOI: https://doi.org/10.1038/s41587-021-01161-6
Nat Commun. 2022 Jan 18. 13(1): 360

53BP1 regulates heterochromatin through liquid phase separation.

Lei Zhang, Xinran Geng, Fangfang Wang, Jinshan Tang, Yu Ichida, Arishya Sharma, Sora Jin, Mingyue Chen, Mingliang Tang, Franklin Mayca Pozo, Wenxiu Wang, Janet Wang, Michal Wozniak, Xiaoxia Guo, Masaru Miyagi, Fulai Jin, Yongjie Xu, Xinsheng Yao, Youwei Zhang.

Human 53BP1 is primarily known as a key player in regulating DNA double strand break (DSB) repair choice; however, its involvement in other biological process is less well understood. Here, we report a previously uncharacterized function of 53BP1 at heterochromatin, where it undergoes liquid-liquid phase separation (LLPS) with the heterochromatin protein HP1α in a mutually dependent manner. Deletion of 53BP1 results in a reduction in heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNA. We identify domains and residues of 53BP1 required for its LLPS, which overlap with, but are distinct from, those involved in DSB repair. Further, 53BP1 mutants deficient in DSB repair, but proficient in LLPS, rescue heterochromatin de-repression and protect cells from stress-induced DNA damage and senescence. Our study suggests that in addition to DSB repair modulation, 53BP1 contributes to the maintenance of heterochromatin integrity and genome stability through LLPS.

DOI: https://doi.org/10.1038/s41467-022-28019-y
Stem Cell Reports. 2022 Jan 03. pii: S2213-6711(21)00651-2. [Epub ahead of print]

YAP1 regulates the self-organized fate patterning of hESC-derived gastruloids.

Eleonora Stronati, Servando Giraldez, Ling Huang, Elizabeth Abraham, Gillian R McGuire, Hui-Ting Hsu, Kathy A Jones, Conchi Estarás.

  The gastrulation process relies on complex interactions between developmental signaling pathways that are not completely understood. Here, we interrogated the contribution of the Hippo signaling effector YAP1 to the formation of the three germ layers by analyzing human embryonic stem cell (hESC)-derived 2D-micropatterned gastruloids. YAP1 knockout gastruloids display a reduced ectoderm layer and enlarged mesoderm and endoderm layers compared with wild type. Furthermore, our epigenome and transcriptome analysis revealed that YAP1 attenuates Nodal signaling by directly repressing the chromatin accessibility and transcription of key genes in the Nodal pathway, including the NODAL and FOXH1 genes. Hence, in the absence of YAP1, hyperactive Nodal signaling retains SMAD2/3 in the nuclei, impeding ectoderm differentiation of hESCs. Thus, our work revealed that YAP1 is a master regulator of Nodal signaling, essential for instructing germ layer fate patterning in human gastruloids.

Keywords:  Hippo; Nodal; Smad2/3; YAP1; ectoderm; gastrulation; gastruloids; hESCs; iPSCs; micropatterns

DOI:  https://doi.org/10.1016/j.stemcr.2021.12.012
iScience. 2022 Jan 21. 25(1): 103679

Recruitment of MLL1 complex is essential for SETBP1 to induce myeloid transformation.

Nhu Nguyen, Kristbjorn O Gudmundsson, Anthony R Soltis, Kevin Oakley, Kartik R Roy, Yufen Han, Carmelo Gurnari, Jaroslaw P Maciejewski, Gary Crouch, Patricia Ernst, Clifton L Dalgard, Yang Du.

  Abnormal activation of SETBP1 due to overexpression or missense mutations occurs frequently in various myeloid neoplasms and associates with poor prognosis. Direct activation of Hoxa9/Hoxa10/Myb transcription by SETBP1 and its missense mutants is essential for their transforming capability; however, the underlying epigenetic mechanisms remain elusive. We found that both SETBP1 and its missense mutant SETBP1(D/N) directly interact with histone methyltransferase MLL1. Using a combination of ChIP-seq and RNA-seq analysis in primary hematopoietic stem and progenitor cells, we uncovered extensive overlap in their genomic occupancy and their cooperation in activating many oncogenic transcription factor genes including Hoxa9/Hoxa10/Myb and a large group of ribosomal protein genes. Genetic ablation of Mll1 as well as treatment with an inhibitor of the MLL1 complex OICR-9429 abrogated Setbp1/Setbp1(D/N)-induced transcriptional activation and transformation. Thus, the MLL1 complex plays a critical role in Setbp1-induced transcriptional activation and transformation and represents a promising target for treating myeloid neoplasms with SETBP1 activation.

Keywords:  Biological sciences; Cancer; Cell biology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2021.103679
PLoS Genet. 2022 Jan 21. 18(1): e1009666

Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation.

Reem Elorbany, Joshua M Popp, Katherine Rhodes, Benjamin J Strober, Kenneth Barr, Guanghao Qi, Yoav Gilad, Alexis Battle.

Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.

DOI: https://doi.org/10.1371/journal.pgen.1009666