bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2021‒06‒06
twenty papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. Epigenomic landscape and 3D genome structure in pediatric high-grade glioma.
  2. Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer.
  3. Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis.
  4. AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency.
  5. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
  6. Inhibiting an RBM39/MLL1 epigenomic regulatory complex with dominant-negative peptides disrupts cancer cell transcription and proliferation.
  7. Dynamic patterns of DNA methylation in the normal prostate epithelial differentiation program are targets of aberrant methylation in prostate cancer.
  8. Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation.
  9. Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.
  10. A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance.
  11. Histone tails cooperate to control the breathing of genomic nucleosomes.
  12. Targeting glutamine dependence through GLS1 inhibition suppresses ARID1A-inactivated clear cell ovarian carcinoma.
  13. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells.
  14. Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes.
  15. Acetylation of PAX7 controls muscle stem cell self-renewal and differentiation potential in mice.
  16. ATF3 coordinates serine and nucleotide metabolism to drive cell cycle progression in acute myeloid leukemia.
  17. Transcription factor Ascl2 promotes germinal center B cell responses by directly regulating AID transcription.
  18. A map of transcriptional heterogeneity and regulatory variation in human microglia.
  19. pyrpipe: a Python package for RNA-Seq workflows.
  20. Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment.
  1. Sci Adv. 2021 Jun;pii: eabg4126. [Epub ahead of print]7(23):
    Epigenomic landscape and 3D genome structure in pediatric high-grade glioma.
    Juan Wang, Tina Yi-Ting Huang, Ye Hou, Elizabeth Bartom, Xinyan Lu, Ali Shilatifard, Feng Yue, Amanda Saratsis.
      Pediatric high-grade gliomas (pHGGs), including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), are morbid brain tumors. Even with treatment survival is poor, making pHGG the number one cause of cancer death in children. Up to 80% of DIPGs harbor a somatic missense mutation in genes encoding histone H3. To investigate whether H3K27M is associated with distinct chromatin structure that alters transcription regulation, we generated the first high-resolution Hi-C maps of pHGG cell lines and tumor tissue. By integrating transcriptome (RNA-seq), enhancer landscape (ChIP-seq), genome structure (Hi-C), and chromatin accessibility (ATAC-seq) datasets from H3K27M and wild-type specimens, we identified tumor-specific enhancers and regulatory networks for known oncogenes. We identified genomic structural variations that lead to potential enhancer hijacking and gene coamplification, including A2M, JAG2, and FLRT1 Together, our results imply three-dimensional genome alterations may play a critical role in the pHGG epigenetic landscape and contribute to tumorigenesis.
    DOI:  https://doi.org/10.1126/sciadv.abg4126
  2. Gut. 2021 May 31. pii: gutjnl-2020-322835. [Epub ahead of print]
    Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer.
    Elias Orouji, Ayush T Raman, Anand K Singh, Alexey Sorokin, Emre Arslan, Archit K Ghosh, Jonathan Schulz, Christopher Terranova, Shan Jiang, Ming Tang, Mayinuer Maitituoheti, Scot C Callahan, Praveen Barrodia, Katarzyna Tomczak, Yingda Jiang, Zhiqin Jiang, Jennifer S Davis, Sukhen Ghosh, Hey Min Lee, Laura Reyes-Uribe, Kyle Chang, Yusha Liu, Huiqin Chen, Ali Azhdarinia, Jeffrey Morris, Eduardo Vilar, Kendra S Carmon, Scott E Kopetz, Kunal Rai.
      OBJECTIVE: Enhancer aberrations are beginning to emerge as a key epigenetic feature of colorectal cancers (CRC), however, a comprehensive knowledge of chromatin state patterns in tumour progression, heterogeneity of these patterns and imparted therapeutic opportunities remain poorly described.DESIGN: We performed comprehensive epigenomic characterisation by mapping 222 chromatin profiles from 69 samples (33 colorectal adenocarcinomas, 4 adenomas, 21 matched normal tissues and 11 colon cancer cell lines) for six histone modification marks: H3K4me3 for Pol II-bound and CpG-rich promoters, H3K4me1 for poised enhancers, H3K27ac for enhancers and transcriptionally active promoters, H3K79me2 for transcribed regions, H3K27me3 for polycomb repressed regions and H3K9me3 for heterochromatin.
    RESULTS: We demonstrate that H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumour-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was required for excessive proliferation. Consistently, combination of MEK plus bromodomain inhibition was found to have synergistic effects in CRC patient-derived xenograft models. Probing intertumour heterogeneity, we identified four distinct enhancer subtypes (EPIgenome-based Classification, EpiC), three of which correlate well with previously defined transcriptomic subtypes (consensus molecular subtypes, CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, TGFβi, mTORi and SRCi) for EpiC groups.
    CONCLUSION: Our data suggest that the dynamics of active enhancer underlies CRC progression and the patient-specific enhancer patterns can be leveraged for precision combination therapy.
    Keywords:  adenocarcinoma; cancer genetics; colon carcinogenesis; colorectal cancer
    DOI:  https://doi.org/10.1136/gutjnl-2020-322835
  3. Genome Res. 2021 Jun 03. pii: gr.273771.120. [Epub ahead of print]
    Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis.
    Ying Huang, Sanchari Sircar, Juan Sebastian Ramirez-Prado, Deborah Manza-Mianza, Javier Antunez-Sanchez, Rim Brik-Chaouche, Natalia Rodriguez-Granados, Jing An, Catherine Bergounioux, Magdy Mahfouz, Heribert Hirt, Martin Crespi, Lorenzo Concia, Fredy Barnech, Simon Amiard, Aline V Probst, Jose Gutierrez-Marcos, Federico Ariel, Cecile Raynaud, David Latrasse, Moussa Benhamed.
      In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 act directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics and alternative 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac - a histone modification associated with active transcription, thus indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.
    DOI:  https://doi.org/10.1101/gr.273771.120
  4. Proc Natl Acad Sci U S A. 2021 Jun 08. pii: e2104841118. [Epub ahead of print]118(23):
    AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency.
    Glenn J Markov, Thach Mai, Surag Nair, Anna Shcherbina, Yu Xin Wang, David M Burns, Anshul Kundaje, Helen M Blau.
      Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming; yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion with murine embryonic stem cells (ESCs). By assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing we identified enrichment for the activator protein 1 (AP-1) transcription factor c-Jun at regions of early transient accessibility at fibroblast-specific enhancers. Expression of a dominant negative AP-1 mutant (dnAP-1) reduced accessibility and expression of fibroblast genes, overcoming the barrier to reprogramming. Remarkably, efficient reprogramming of human fibroblasts to induced pluripotent stem cells was achieved by transduction with vectors expressing SOX2, KLF4, and inducible dnAP-1, demonstrating that dnAP-1 can substitute for exogenous human OCT4. Mechanistically, we show that the AP-1 component c-Jun has two unexpected temporally distinct functions in human reprogramming: 1) to potentiate fibroblast enhancer accessibility and fibroblast-specific gene expression, and 2) to bind to and repress OCT4 as a complex with MBD3. Our findings highlight AP-1 as a previously unrecognized potent dual gatekeeper of the somatic cell state.
    Keywords:  c-Jun; heterokaryon; reprogramming pluripotency; transcription factor
    DOI:  https://doi.org/10.1073/pnas.2104841118
  5. Nat Commun. 2021 06 02. 12(1): 3297
    Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
    Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C Frith, , Clément Chatelain, Piero Carninci, Michiel J L de Hoon, Wyeth W Wasserman, Laurent Bréhélin, Charles-Henri Lecellier.
      Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
    DOI:  https://doi.org/10.1038/s41467-021-23143-7
  6. Cell Rep. 2021 Jun 01. pii: S2211-1247(21)00498-8. [Epub ahead of print]35(9): 109156
    Inhibiting an RBM39/MLL1 epigenomic regulatory complex with dominant-negative peptides disrupts cancer cell transcription and proliferation.
    Pavan Kumar Puvvula, Yao Yu, Kaelan Renaldo Sullivan, Henok Eyob, Julian Rosenberg, Alana Welm, Chad Huff, Anne M Moon.
      RBM39 is a known splicing factor and coactivator. Here, we report that RBM39 functions as a master transcriptional regulator that interacts with the MLL1 complex to facilitate chromatin binding and H3K4 trimethylation in breast cancer cells. We identify RBM39 functional domains required for DNA and complex binding and show that the loss of RBM39 has widespread effects on H3K4me3 and gene expression, including key oncogenic pathways. RBM39's RNA recognition motif 3 (RRM3) functions as a dominant-negative domain; namely, it disrupts the complex and H3K4me trimethylation and expression of RBM/MLL1 target genes. RRM3-derived cell-penetrating peptides phenocopy the effects of the loss of RBM39 to decrease growth and survival of all major subtypes of breast cancer and yet are nontoxic to normal cells. These findings establish RBM39/MLL1 as a major contributor to the abnormal epigenetic landscape in breast cancer and lay the foundation for peptide-mediated cancer-specific therapy based on disruption of RBM39 epigenomic functions.
    Keywords:  CAPERalpha; MLL1; RBM39; breast cancer; pathologic coactivator; therapeutic cell-penetrating peptide
    DOI:  https://doi.org/10.1016/j.celrep.2021.109156
  7. Sci Rep. 2021 Jun 01. 11(1): 11405
    Dynamic patterns of DNA methylation in the normal prostate epithelial differentiation program are targets of aberrant methylation in prostate cancer.
    Mark D Long, Vineet K Dhiman, Hayley C Affronti, Qiang Hu, Song Liu, Dominic J Smiraglia.
      Understanding the epigenetic control of normal differentiation programs might yield principal information about critical regulatory states that are disturbed in cancer. We utilized the established non-malignant HPr1-AR prostate epithelial cell model that upon androgen exposure commits to a luminal cell differentiation trajectory from that of a basal-like state. We profile the dynamic transcriptome associated with this transition at multiple time points (0 h, 1 h, 24 h, 96 h), and confirm that expression patterns are strongly indicative of a progressive basal to luminal cell differentiation program based on human expression signatures. Furthermore, we establish dynamic patterns of DNA methylation associated with this program by use of whole genome bisulfite sequencing (WGBS). Expression patterns associated with androgen induced luminal cell differentiation were found to have significantly elevated DNA methylation dynamics. Shifts in methylation profiles were strongly associated with Polycomb repressed regions and to promoters associated with bivalency, and strongly enriched for binding motifs of AR and MYC. Importantly, we found that dynamic DNA methylation patterns observed in the normal luminal cell differentiation program were significant targets of aberrant methylation in prostate cancer. These findings suggest that the normal dynamics of DNA methylation in luminal differentiation contribute to the aberrant methylation patterns in prostate cancer.
    DOI:  https://doi.org/10.1038/s41598-021-91037-1
  8. Blood. 2021 Jun 01. pii: blood.2020009903. [Epub ahead of print]
    Regulation of RNA Polymerase II Activity is Essential for Terminal Erythroid Maturation.
    Zachary Murphy, Kristin Murphy, Jacquelyn A Myers, Michael Roger Getman, Tyler Couch, Vince Schulz, Kimberly Lezon-Geyda, Cal Palumbo, Hongxia Yan, Mohandas Narla, Patrick G Gallagher, Laurie Ann Steiner.
      The terminal maturation of human erythroblasts requires significant changes in gene expression in the context of dramatic nuclear condensation. Defects in this process are associated with inherited anemias and myelodysplastic syndromes. The progressively dense appearance of the condensing nucleus in maturing erythroblasts led to the assumption that heterochromatin accumulation underlies this process, but despite extensive study, the precise mechanisms underlying this essential biologic process remain elusive. To delineate the epigenetic changes associated with the terminal maturation of human erythroblasts, we performed mass spectrometry of histone post-translational modifications combined with ChIP-seq, ATAC-seq, and RNA-seq. Our studies revealed that the terminal maturation of human erythroblasts is associated with a dramatic decline in histone marks associated with active transcription elongation, without accumulation of heterochromatin. Chromatin structure and gene expression were instead correlated with dynamic changes in occupancy of elongation competent RNA polymerase II, suggesting that terminal erythroid maturation is controlled largely at the level of transcription. We further demonstrate that RNA Polymerase II "pausing" is highly correlated with transcriptional repression, with elongation competent RNA polymerase II becoming a scare resource in late stage erythroblasts, allocated to erythroid-specific genes. Functional studies confirmed an essential role for maturation stage-specific regulation of RNA polymerase II activity during erythroid maturation, and demonstrate a critical role for HEXIM1 in the regulation of gene expression and RNA polymerase II activity in maturing erythroblasts. Taken together, our findings reveal important insights into the mechanisms that regulate terminal erythroid maturation, and provide a novel paradigm for understanding normal and perturbed erythropoiesis.
    DOI:  https://doi.org/10.1182/blood.2020009903
  9. Nucleic Acids Res. 2021 Jun 01. pii: gkab443. [Epub ahead of print]
    Altering transcription factor binding reveals comprehensive transcriptional kinetics of a basic gene.
    Achim P Popp, Johannes Hettich, J Christof M Gebhardt.
      Transcription is a vital process activated by transcription factor (TF) binding. The active gene releases a burst of transcripts before turning inactive again. While the basic course of transcription is well understood, it is unclear how binding of a TF affects the frequency, duration and size of a transcriptional burst. We systematically varied the residence time and concentration of a synthetic TF and characterized the transcription of a synthetic reporter gene by combining single molecule imaging, single molecule RNA-FISH, live transcript visualisation and analysis with a novel algorithm, Burst Inference from mRNA Distributions (BIRD). For this well-defined system, we found that TF binding solely affected burst frequency and variations in TF residence time had a stronger influence than variations in concentration. This enabled us to device a model of gene transcription, in which TF binding triggers multiple successive steps before the gene transits to the active state and actual mRNA synthesis is decoupled from TF presence. We quantified all transition times of the TF and the gene, including the TF search time and the delay between TF binding and the onset of transcription. Our quantitative measurements and analysis revealed detailed kinetic insight, which may serve as basis for a bottom-up understanding of gene regulation.
    DOI:  https://doi.org/10.1093/nar/gkab443
  10. Nat Cancer. 2020 Nov;1(11): 1082-1096
    A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance.
    Juan M Arriaga, Sukanya Panja, Mohammed Alshalalfa, Junfei Zhao, Min Zou, Arianna Giacobbe, Chioma J Madubata, Jaime Yeji Kim, Antonio Rodriguez, Ilsa Coleman, Renu K Virk, Hanina Hibshoosh, Onur Ertunc, Büşra Ozbek, Julia Fountain, R Jeffrey Karnes, Jun Luo, Emmanuel S Antonarakis, Peter S Nelson, Felix Y Feng, Mark A Rubin, Angelo M De Marzo, Raul Rabadan, Peter A Sims, Antonina Mitrofanova, Cory Abate-Shen.
      Understanding the intricacies of lethal prostate cancer poses specific challenges due to difficulties in accurate modeling of metastasis in vivo. Here we show that NPK EYFP mice (for Nkx3.1 CreERT2/+ ; Pten flox/flox ; Kras LSL-G12D/+ ; R26R-CAG-LSL-EYFP/+) develop prostate cancer with a high penetrance of metastasis to bone, thereby enabling detection and tracking of bone metastasis in vivo and ex vivo. Transcriptomic and whole-exome analyses of bone metastasis from these mice revealed distinct molecular profiles conserved between human and mouse and specific patterns of subclonal branching from the primary tumor. Integrating bulk and single-cell transcriptomic data from mouse and human datasets with functional studies in vivo unravels a unique MYC/RAS co-activation signature associated with prostate cancer metastasis. Finally, we identify a gene signature with prognostic value for time to metastasis and predictive of treatment response in human patients undergoing androgen receptor therapy across clinical cohorts, thus uncovering conserved mechanisms of metastasis with potential translational significance.
    DOI:  https://doi.org/10.1038/s43018-020-00125-0
  11. PLoS Comput Biol. 2021 Jun;17(6): e1009013
    Histone tails cooperate to control the breathing of genomic nucleosomes.
    Jan Huertas, Hans Robert Schöler, Vlad Cojocaru.
      Genomic DNA is packaged in chromatin, a dynamic fiber variable in size and compaction. In chromatin, repeating nucleosome units wrap 145-147 DNA basepairs around histone proteins. Genetic and epigenetic regulation of genes relies on structural transitions in chromatin which are driven by intra- and inter-nucleosome dynamics and modulated by chemical modifications of the unstructured terminal tails of histones. Here we demonstrate how the interplay between histone H3 and H2A tails control ample nucleosome breathing motions. We monitored large openings of two genomic nucleosomes, and only moderate breathing of an engineered nucleosome in atomistic molecular simulations amounting to 24 μs. Transitions between open and closed nucleosome conformations were mediated by the displacement and changes in compaction of the two histone tails. These motions involved changes in the DNA interaction profiles of clusters of epigenetic regulatory aminoacids in the tails. Removing the histone tails resulted in a large increase of the amplitude of nucleosome breathing but did not change the sequence dependent pattern of the motions. Histone tail modulated nucleosome breathing is a key mechanism of chromatin dynamics with important implications for epigenetic regulation.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009013
  12. Nat Cancer. 2021 Feb;2(2): 189-200
    Targeting glutamine dependence through GLS1 inhibition suppresses ARID1A-inactivated clear cell ovarian carcinoma.
    Shuai Wu, Takeshi Fukumoto, Jianhuang Lin, Timothy Nacarelli, Yemin Wang, Dionzie Ong, Heng Liu, Nail Fatkhutdinov, Joseph A Zundell, Sergey Karakashev, Wei Zhou, Lauren E Schwartz, Hsin-Yao Tang, Ronny Drapkin, Qin Liu, David G Huntsman, Andrew V Kossenkov, David W Speicher, Zachary T Schug, Chi Van Dang, Rugang Zhang.
      Alterations in components of the SWI/SNF chromatin-remodeling complex occur in ~20% of all human cancers. For example, ARID1A is mutated in up to 62% of clear cell ovarian carcinoma (OCCC), a disease currently lacking effective therapies. Here we show that ARID1A mutation creates a dependence on glutamine metabolism. SWI/SNF represses glutaminase (GLS1) and ARID1A inactivation upregulates GLS1. ARID1A inactivation increases glutamine utilization and metabolism through the tricarboxylic acid cycle to support aspartate synthesis. Indeed, glutaminase inhibitor CB-839 suppresses the growth of ARID1A mutant, but not wildtype, OCCCs in both orthotopic and patient-derived xenografts. In addition, glutaminase inhibitor CB-839 synergizes with immune checkpoint blockade anti-PDL1 antibody in a genetic OCCC mouse model driven by conditional Arid1a inactivation. Our data indicate that pharmacological inhibition of glutaminase alone or in combination with immune checkpoint blockade represents an effective therapeutic strategy for cancers involving alterations in the SWI/SNF complex such as ARID1A mutations.
    DOI:  https://doi.org/10.1038/s43018-020-00160-x
  13. Cell Rep. 2021 Jun 01. pii: S2211-1247(21)00544-1. [Epub ahead of print]35(9): 109198
    Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells.
    Shlomi Dvir, Amir Argoetti, Chen Lesnik, Mark Roytblat, Kohava Shriki, Michal Amit, Tamar Hashimshony, Yael Mandel-Gutfreund.
      Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
    Keywords:  DNA- and RNA-binding proteins; DRBPs; RBPs; RNA interactome capture; RNA-binding proteins; STAT3-RNA interaction; hESCs; human embryonic stem cells; pluripotency network; post-transcriptional regulation
    DOI:  https://doi.org/10.1016/j.celrep.2021.109198
  14. Commun Biol. 2021 Jun 03. 4(1): 675
    Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes.
    Hong Wang, Aiping Duan, Jing Zhang, Qi Wang, Yuexian Xing, Zhaohui Qin, Zhihong Liu, Jingping Yang.
      Elucidating transcription mediated by the glucocorticoid receptor (GR) is crucial for understanding the role of glucocorticoids (GCs) in the treatment of diseases. Podocyte is a useful model for studying GR regulation because GCs are the primary medication for podocytopathy. In this study, we integrated data from transcriptome, transcription factor binding, histone modification, and genome topology. Our data reveals that the GR binds and activates selective regulatory elements in podocyte. The 3D interactome captured by HiChIP facilitates the identification of remote targets of GR. We found that GR in podocyte is enriched at transcriptional interaction hubs and super-enhancers. We further demonstrate that the target gene of the top GR-associated super-enhancer is indispensable to the effective functioning of GC in podocyte. Our findings provided insights into the mechanisms underlying the protective effect of GCs on podocyte, and demonstrate the importance of considering transcriptional interactions in order to fine-map regulatory networks of GR.
    DOI:  https://doi.org/10.1038/s42003-021-02209-8
  15. Nat Commun. 2021 05 31. 12(1): 3253
    Acetylation of PAX7 controls muscle stem cell self-renewal and differentiation potential in mice.
    Marie-Claude Sincennes, Caroline E Brun, Alexander Y T Lin, Tabitha Rosembert, David Datzkiw, John Saber, Hong Ming, Yoh-Ichi Kawabe, Michael A Rudnicki.
      Muscle stem cell function has been suggested to be regulated by Acetyl-CoA and NAD+ availability, but the mechanisms remain unclear. Here we report the identification of two acetylation sites on PAX7 that positively regulate its transcriptional activity. Lack of PAX7 acetylation reduces DNA binding, specifically to the homeobox motif. The acetyltransferase MYST1 stimulated by Acetyl-CoA, and the deacetylase SIRT2 stimulated by NAD +, are identified as direct regulators of PAX7 acetylation and asymmetric division in muscle stem cells. Abolishing PAX7 acetylation in mice using CRISPR/Cas9 mutagenesis leads to an expansion of the satellite stem cell pool, reduced numbers of asymmetric stem cell divisions, and increased numbers of oxidative IIA myofibers. Gene expression analysis confirms that lack of PAX7 acetylation preferentially affects the expression of target genes regulated by homeodomain binding motifs. Therefore, PAX7 acetylation status regulates muscle stem cell function and differentiation potential to facilitate metabolic adaptation of muscle tissue.
    DOI:  https://doi.org/10.1038/s41467-021-23577-z
  16. Mol Cell. 2021 May 25. pii: S1097-2765(21)00365-8. [Epub ahead of print]
    ATF3 coordinates serine and nucleotide metabolism to drive cell cycle progression in acute myeloid leukemia.
    Daniela Di Marcantonio, Esteban Martinez, Joice S Kanefsky, Jacklyn M Huhn, Rashid Gabbasov, Anushk Gupta, John J Krais, Suraj Peri, YinFei Tan, Tomasz Skorski, Adrienne Dorrance, Ramiro Garzon, Aaron R Goldman, Hsin-Yao Tang, Neil Johnson, Stephen M Sykes.
      Metabolic reprogramming is a common feature of many human cancers, including acute myeloid leukemia (AML). However, the upstream regulators that promote AML metabolic reprogramming and the benefits conferred to leukemia cells by these metabolic changes remain largely unknown. We report that the transcription factor ATF3 coordinates serine and nucleotide metabolism to maintain cell cycling, survival, and the differentiation blockade in AML. Analysis of mouse and human AML models demonstrate that ATF3 directly activates the transcription of genes encoding key enzymatic regulators of serine synthesis, one-carbon metabolism, and de novo purine and pyrimidine synthesis. Total steady-state polar metabolite and heavy isotope tracing analyses show that ATF3 inhibition reduces de novo serine synthesis, impedes the incorporation of serine-derived carbons into newly synthesized purines, and disrupts pyrimidine metabolism. Importantly, exogenous nucleotide supplementation mitigates the anti-leukemia effects of ATF3 inhibition. Together, these findings reveal the dependence of AML on ATF3-regulated serine and nucleotide metabolism.
    Keywords:  AML; ATF3; ATF4; cell cycle; differentiation; leukemia; metabolism; purines; pyrimidines; serine
    DOI:  https://doi.org/10.1016/j.molcel.2021.05.008
  17. Cell Rep. 2021 Jun 01. pii: S2211-1247(21)00534-9. [Epub ahead of print]35(9): 109188
    Transcription factor Ascl2 promotes germinal center B cell responses by directly regulating AID transcription.
    Lin Sun, Xiaohong Zhao, Xindong Liu, Bo Zhong, Hong Tang, Wei Jin, Hans Clevers, Hui Wang, Xiaohu Wang, Chen Dong.
      During germinal center (GC) reactions, activated B cells undergo clonal expansion and functional maturation to produce high-affinity antibodies and differentiate into plasma and memory cells, accompanied with class-switching recombination (CSR) and somatic hypermutation (SHM). Activation-induced cytidine deaminase (AID) is responsible for both CSR and SHM in GC B cells. Transcriptional mechanisms underlying AID regulation and GC B cell reactions are still not well understood. Here, we show that expression of Ascl2 transcription factor is upregulated in GC B cells. Ectopic expression of Ascl2 promotes GC B cell development and enhances antibody production and affinity maturation. Conversely, deletion of Ascl2 in B cells impairs the GC response. Genome-wide analysis reveals that Ascl2 directly regulates GC B cell-related genes, including AID; ectopic expression of AID in Ascl2-deficient B cells rescues their antibody defects. Thus, Ascl2 regulates AID transcription and promotes GC B cell responses.
    DOI:  https://doi.org/10.1016/j.celrep.2021.109188
  18. Nat Genet. 2021 Jun 03.
    A map of transcriptional heterogeneity and regulatory variation in human microglia.
    Adam M H Young, Natsuhiko Kumasaka, Fiona Calvert, Timothy R Hammond, Andrew Knights, Nikolaos Panousis, Jun Sung Park, Jeremy Schwartzentruber, Jimmy Liu, Kousik Kundu, Michael Segel, Natalia A Murphy, Christopher E McMurran, Harry Bulstrode, Jason Correia, Karol P Budohoski, Alexis Joannides, Mathew R Guilfoyle, Rikin Trivedi, Ramez Kirollos, Robert Morris, Matthew R Garnett, Ivan Timofeev, Ibrahim Jalloh, Katherine Holland, Richard Mannion, Richard Mair, Colin Watts, Stephen J Price, Peter J Kirkpatrick, Thomas Santarius, Edward Mountjoy, Maya Ghoussaini, Nicole Soranzo, Omer A Bayraktar, Beth Stevens, Peter J Hutchinson, Robin J M Franklin, Daniel J Gaffney.
      Microglia, the tissue-resident macrophages of the central nervous system (CNS), play critical roles in immune defense, development and homeostasis. However, isolating microglia from humans in large numbers is challenging. Here, we profiled gene expression variation in primary human microglia isolated from 141 patients undergoing neurosurgery. Using single-cell and bulk RNA sequencing, we identify how age, sex and clinical pathology influence microglia gene expression and which genetic variants have microglia-specific functions using expression quantitative trait loci (eQTL) mapping. We follow up one of our findings using a human induced pluripotent stem cell-based macrophage model to fine-map a candidate causal variant for Alzheimer's disease at the BIN1 locus. Our study provides a population-scale transcriptional map of a critically important cell for human CNS development and disease.
    DOI:  https://doi.org/10.1038/s41588-021-00875-2
  19. NAR Genom Bioinform. 2021 Jun;3(2): lqab049
    pyrpipe: a Python package for RNA-Seq workflows.
    Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele.
      The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. There is a pressing requirement for a framework that allows for fast, efficient, manageable, and reproducible RNA-Seq analysis. We have developed a Python package, (pyrpipe), that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in Python, in an object-oriented manner. pyrpipe provides access to popular RNA-Seq tools, within Python, via high-level APIs. Pipelines can be customized by integrating new Python code, third-party programs, or Python libraries. Users can create checkpoints in the pipeline or integrate pyrpipe into a workflow management system, thus allowing execution on multiple computing environments, and enabling efficient resource management. pyrpipe produces detailed analysis, and benchmark reports which can be shared or included in publications. pyrpipe is implemented in Python and is compatible with Python versions 3.6 and higher. To illustrate the rich functionality of pyrpipe, we provide case studies using RNA-Seq data from GTEx, SARS-CoV-2-infected human cells, and Zea mays. All source code is freely available at https://github.com/urmi-21/pyrpipe; the package can be installed from the source, from PyPI (https://pypi.org/project/pyrpipe), or from bioconda (https://anaconda.org/bioconda/pyrpipe). Documentation is available at (http://pyrpipe.rtfd.io).
    DOI:  https://doi.org/10.1093/nargab/lqab049
  20. Commun Biol. 2021 Jun 02. 4(1): 661
    Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment.
    Jonathan D Rubin, Jacob T Stanley, Rutendo F Sigauke, Cecilia B Levandowski, Zachary L Maas, Jessica Westfall, Dylan J Taatjes, Robin D Dowell.
      Detecting changes in the activity of a transcription factor (TF) in response to a perturbation provides insights into the underlying cellular process. Transcription Factor Enrichment Analysis (TFEA) is a robust and reliable computational method that detects positional motif enrichment associated with changes in transcription observed in response to a perturbation. TFEA detects positional motif enrichment within a list of ranked regions of interest (ROIs), typically sites of RNA polymerase initiation inferred from regulatory data such as nascent transcription. Therefore, we also introduce muMerge, a statistically principled method of generating a consensus list of ROIs from multiple replicates and conditions. TFEA is broadly applicable to data that informs on transcriptional regulation including nascent transcription (eg. PRO-Seq), CAGE, histone ChIP-Seq, and accessibility data (e.g., ATAC-Seq). TFEA not only identifies the key regulators responding to a perturbation, but also temporally unravels regulatory networks with time series data. Consequently, TFEA serves as a hypothesis-generating tool that provides an easy, rigorous, and cost-effective means to broadly assess TF activity yielding new biological insights.
    DOI:  https://doi.org/10.1038/s42003-021-02153-7
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