bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2021‒03‒14
twenty-six papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. Cooperative binding between distant transcription factors is a hallmark of active enhancers.
  2. Interplay of BAF and MLL4 promotes cell type-specific enhancer activation.
  3. A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.
  4. Deep learning-based enhancement of epigenomics data with AtacWorks.
  5. Effects of DNA Methylation on TFs in Human Embryonic Stem Cells.
  6. Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.
  7. A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation.
  8. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease.
  9. Efficient RNA polymerase II pause release requires U2 snRNP function.
  10. Npac Is a Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells.
  11. A high-resolution protein architecture of the budding yeast genome.
  12. The epigenetic pioneer EGR2 initiates DNA demethylation in differentiating monocytes at both stable and transient binding sites.
  13. MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.
  14. Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 inhibition.
  15. Full methylation of H3K27 by PRC2 is dispensable for initial embryoid body formation but required to maintain differentiated cell identity.
  16. Functional cooperation between co-amplified genes promotes aggressive phenotypes of HER2-positive breast cancer.
  17. Structure of the human Mediator-bound transcription preinitiation complex.
  18. Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin.
  19. Cycling hypoxia selects for constitutive HIF stabilization.
  20. The LEAFY floral regulator displays pioneer transcription factor properties.
  21. RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression.
  22. BRD4 inhibition sensitizes cervical cancer to radiotherapy by attenuating DNA repair.
  23. Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes.
  24. The CBP/p300 histone acetyltransferases function as plant-specific MEDIATOR subunits in Arabidopsis.
  25. Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program.
  26. Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions.
  1. Mol Cell. 2021 Mar 05. pii: S1097-2765(21)00100-3. [Epub ahead of print]
    Cooperative binding between distant transcription factors is a hallmark of active enhancers.
    Satyanarayan Rao, Kami Ahmad, Srinivas Ramachandran.
      Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent of TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. Enrichment of short micrococcal nuclease (MNase)-protected DNA segments indicates that the majority of enhancers harbor two or more TF-binding sites, and we uncover protected fragments that correspond to co-bound sites in thousands of enhancers. From the analysis of co-binding, we find that cooperativity dominates TF binding in vivo at the majority of active enhancers. Cooperativity is highest between sites spaced 50 bp apart, indicating that cooperativity occurs without apparent protein-protein interactions. Our findings suggest nucleosomes promoting cooperativity because co-binding may effectively clear nucleosomes and promote enhancer function.
    Keywords:  chromatin dynamics; enhancer; enhancer cooperativity; nucleosome; transcription factor
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.014
  2. Nat Commun. 2021 Mar 12. 12(1): 1630
    Interplay of BAF and MLL4 promotes cell type-specific enhancer activation.
    Young-Kwon Park, Ji-Eun Lee, Zhijiang Yan, Kaitlin McKernan, Tommy O'Haren, Weidong Wang, Weiqun Peng, Kai Ge.
      Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF chromatin remodeling complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with MLL4 and LDTFs on active enhancers and is required for cell differentiation. In contrast, the promoter enriched SWI/SNF complex PBAF is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other's binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic pioneer transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence for an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings reveal a positive feedback between BAF and MLL4 in promoting LDTF-dependent activation of cell type-specific enhancers.
    DOI:  https://doi.org/10.1038/s41467-021-21893-y
  3. Genome Res. 2021 Mar 12.
    A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.
    Gurdeep Singh, Shanelle Mullany, Sakthi D Moorthy, Richard Zhang, Tahmid Mehdi, Ruxiao Tian, Andrew G Duncan, Alan M Moses, Jennifer A Mitchell.
      Transcriptional enhancers are critical for development and phenotype evolution and are often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. To examine the enhancer regulatory code for pluripotent stem cells, we identified genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs). Examination of these regions revealed that they contain on average 12.6 conserved transcription factor binding site (TFBS) sequences. Enriched TFBSs are a diverse repertoire of 70 different sequences representing the binding sequences of both known and novel ESC regulators. Using a diverse set of TFBSs from this repertoire was sufficient to construct short synthetic enhancers with activity comparable to native enhancers. Site-directed mutagenesis of conserved TFBSs in endogenous enhancers or TFBS deletion from synthetic sequences revealed a requirement for 10 or more different TFBSs. Furthermore, specific TFBSs, including the POU5F1:SOX2 comotif, are dispensable, despite cobinding the POU5F1 (also known as OCT4), SOX2, and NANOG master regulators of pluripotency. These findings reveal that a TFBS sequence diversity threshold overrides the need for optimized regulatory grammar and individual TFBSs that recruit specific master regulators.
    DOI:  https://doi.org/10.1101/gr.272468.120
  4. Nat Commun. 2021 03 08. 12(1): 1507
    Deep learning-based enhancement of epigenomics data with AtacWorks.
    Avantika Lal, Zachary D Chiang, Nikolai Yakovenko, Fabiana M Duarte, Johnny Israeli, Jason D Buenrostro.
      ATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks, a deep learning toolkit to denoise sequencing coverage and identify regulatory peaks at base-pair resolution from low cell count, low-coverage, or low-quality ATAC-seq data. Models trained by AtacWorks can detect peaks from cell types not seen in the training data, and are generalizable across diverse sample preparations and experimental platforms. We demonstrate that AtacWorks enhances the sensitivity of single-cell experiments by producing results on par with those of conventional methods using ~10 times as many cells, and further show that this framework can be adapted to enable cross-modality inference of protein-DNA interactions. Finally, we establish that AtacWorks can enable new biological discoveries by identifying active regulatory regions associated with lineage priming in rare subpopulations of hematopoietic stem cells.
    DOI:  https://doi.org/10.1038/s41467-021-21765-5
  5. Front Genet. 2021 ;12 639461
    Effects of DNA Methylation on TFs in Human Embryonic Stem Cells.
    Ximei Luo, Tianjiao Zhang, Yixiao Zhai, Fang Wang, Shumei Zhang, Guohua Wang.
      DNA methylation is an important epigenetic mechanism for gene regulation. The conventional view of DNA methylation is that DNA methylation could disrupt protein-DNA interactions and repress gene expression. Several recent studies reported that DNA methylation could alter transcription factors (TFs) binding sequence specificity in vitro. Here, we took advantage of the large sets of ChIP-seq data for TFs and whole-genome bisulfite sequencing data in many cell types to perform a systematic analysis of the protein-DNA methylation in vivo. We observed that many TFs could bind methylated DNA regions, especially in H1-hESC cells. By locating binding sites, we confirmed that some TFs could bind to methylated CpGs directly. The different proportion of CpGs at TF binding specificity motifs in different methylation statuses shows that some TFs are sensitive to methylation and some could bind to the methylated DNA with different motifs, such as CEBPB and CTCF. At the same time, TF binding could interactively alter local DNA methylation. The TF hypermethylation binding sites extensively overlap with enhancers. And we also found that some DNase I hypersensitive sites were specifically hypermethylated in H1-hESC cells. At last, compared with TFs' binding regions in multiple cell types, we observed that CTCF binding to high methylated regions in H1-hESC were not conservative. These pieces of evidence indicate that TFs that bind to hypermethylation DNA in H1-hESC cells may associate with enhancers to regulate special biological functions.
    Keywords:  CEBPB; CTCF; DNA methylation; H1-hESC; transcription factors
    DOI:  https://doi.org/10.3389/fgene.2021.639461
  6. Nucleic Acids Res. 2021 Mar 08. pii: gkab102. [Epub ahead of print]
    Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.
    Weiwu Gao, Wai Lim Ku, Lixia Pan, Jonathan Perrie, Tingting Zhao, Gangqing Hu, Yuzhang Wu, Jun Zhu, Bing Ni, Keji Zhao.
      Single cell chromatin accessibility assays reveal epigenomic variability at cis-regulatory elements among individual cells. We previously developed a single-cell DNase-seq assay (scDNase-seq) to profile accessible chromatin in a limited number of single cells. Here, we report a novel indexing strategy to resolve single-cell DNase hypersensitivity profiles based on bulk cell analysis. This new technique, termed indexing single-cell DNase sequencing (iscDNase-seq), employs the activities of terminal DNA transferase (TdT) and T4 DNA ligase to add unique cell barcodes to DNase-digested chromatin ends. By a three-layer indexing strategy, it allows profiling genome-wide DHSs for >15 000 single-cells in a single experiment. Application of iscDNase-seq to human white blood cells accurately revealed specific cell types and inferred regulatory transcription factors (TF) specific to each cell type. We found that iscDNase-seq detected DHSs with specific properties related to gene expression and conservation missed by scATAC-seq for the same cell type. Also, we found that the cell-to-cell variation in accessibility computed using iscDNase-seq data is significantly correlated with the cell-to-cell variation in gene expression. Importantly, this correlation is significantly higher than that between scATAC-seq and scRNA-seq, suggesting that iscDNase-seq data can better predict the cellular heterogeneity in gene expression compared to scATAC-seq. Thus, iscDNase-seq is an attractive alternative method for single-cell epigenomics studies.
    DOI:  https://doi.org/10.1093/nar/gkab102
  7. Genome Res. 2021 Mar 11. pii: gr.260745.120. [Epub ahead of print]
    A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation.
    René A M Dirks, Peter C Thomas, Haoyu Wu, Robert C Jones, Hendrik G Stunnenberg, Hendrik Marks.
      Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious, time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelisation. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 minutes hands-on time and 4.5 hours machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the Plug and Play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We demonstrate high-quality ChIP-seq on hundreds to few thousands of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naïve and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the 2-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert labs worldwide to conveniently run robust, standardized ChIP-seq, while its high-throughput, consistency and sensitivity paves the way towards large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.
    DOI:  https://doi.org/10.1101/gr.260745.120
  8. Cell Syst. 2021 Mar 03. pii: S2405-4712(21)00041-7. [Epub ahead of print]
    Tissue-specific enhancer functional networks for associating distal regulatory regions to disease.
    Xi Chen, Jian Zhou, Ran Zhang, Aaron K Wong, Christopher Y Park, Chandra L Theesfeld, Olga G Troyanskaya.
      Systematic study of tissue-specific function of enhancers and their disease associations is a major challenge. We present an integrative machine-learning framework, FENRIR, that integrates thousands of disparate epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers for 140 diverse human tissues and cell types, providing a regulatory-region-centric approach to systematically identify disease-associated enhancers. We demonstrated its power to accurately prioritize enhancers associated with 25 complex diseases. In a case study on autism, FENRIR-prioritized enhancers showed a significant proband-specific de novo mutation enrichment in a large, sibling-controlled cohort, indicating pathogenic signal. We experimentally validated transcriptional regulatory activities of eight enhancers, including enhancers not previously reported with autism, and demonstrated their differential regulatory potential between proband and sibling alleles. Thus, FENRIR is an accurate and effective framework for the study of tissue-specific enhancers and their role in disease. FENRIR can be accessed at fenrir.flatironinstitute.org/.
    Keywords:  GWAS; autism; brain; de novo mutation; enhancer; functional network
    DOI:  https://doi.org/10.1016/j.cels.2021.02.002
  9. Mol Cell. 2021 Feb 26. pii: S1097-2765(21)00126-X. [Epub ahead of print]
    Efficient RNA polymerase II pause release requires U2 snRNP function.
    Livia Caizzi, Sara Monteiro-Martins, Björn Schwalb, Kseniia Lysakovskaia, Jana Schmitzova, Anna Sawicka, Ying Chen, Michael Lidschreiber, Patrick Cramer.
      Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
    Keywords:  RNA polymerase II; SF3B; U2 AMO; U2 snRNP; co-transcriptional pre-mRNA splicing; pladienolide B; spliceostatin A; splicing; transcription; transcription elongation
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.016
  10. Genomics Proteomics Bioinformatics. 2021 Mar 03. pii: S1672-0229(21)00053-X. [Epub ahead of print]
    Npac Is a Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells.
    Sue Yu, Jia Li, Guanxu Ji, Zhen Long Ng, Jiamin Siew, Wan Ning Lo, Ying Ye, Yuan Yuan Chew, Yun Chau Long, Wensheng Zhang, Ernesto Guccione, Yuin Han Loh, Zhi-Hong Jiang, Henry Yang, Qiang Wu.
      Chromatin modification contributes to pluripotency maintenance in embryonic stem cells (ESCs). However, the related mechanisms remain obscure. Here, we show that Npac, a "reader" of histone H3 lysine 36 trimethylation (H3K36me3), is required to maintain mouse ESC (mESC) pluripotency since knockdown of Npac causes mESC differentiation. Depletion of Npac in mouse embryonic fibroblasts (MEFs) inhibits reprogramming efficiency. Furthermore, our Npac ChIP-seq results reveal that Npac co-localizes with histone H3K36me3 in gene bodies of actively transcribed genes in mESCs. Interestingly, we find that Npac interacts with p-TEFb, RNA Pol II Ser2, and Ser5. Depletion of Npac disrupts transcriptional elongation of pluripotency genes Nanog and Rif1. Taken together, we propose that Npac is essential for transcriptional elongation of pluripotency genes by recruiting of p-TEFb and interacting with RNA Pol II Ser2 and Ser5.
    Keywords:  Histone H3K36me3; Npac; Pluripotency; Reprogramming; Transcriptional elongation
    DOI:  https://doi.org/10.1016/j.gpb.2020.08.004
  11. Nature. 2021 Mar 10.
    A high-resolution protein architecture of the budding yeast genome.
    Matthew J Rossi, Prashant K Kuntala, William K M Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P Farrell, Thomas R Blanda, Joshua D Mairose, Ann V Basting, Katelyn S Mistretta, David J Rocco, Emily S Perkinson, Gretta D Kellogg, Shaun Mahony, B Franklin Pugh.
      The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.
    DOI:  https://doi.org/10.1038/s41586-021-03314-8
  12. Nat Commun. 2021 03 10. 12(1): 1556
    The epigenetic pioneer EGR2 initiates DNA demethylation in differentiating monocytes at both stable and transient binding sites.
    Karina Mendes, Sandra Schmidhofer, Julia Minderjahn, Dagmar Glatz, Claudia Kiesewetter, Johanna Raithel, Julia Wimmer, Claudia Gebhard, Michael Rehli.
      The differentiation of human blood monocytes (MO), the post-mitotic precursors of macrophages (MAC) and dendritic cells (moDC), is accompanied by the active turnover of DNA methylation, but the extent, consequences and mechanisms of DNA methylation changes remain unclear. Here, we profile and compare epigenetic landscapes during IL-4/GM-CSF-driven MO differentiation across the genome and detect several thousand regions that are actively demethylated during culture, both with or without accompanying changes in chromatin accessibility or transcription factor (TF) binding. We further identify TF that are globally associated with DNA demethylation processes. While interferon regulatory factor 4 (IRF4) is found to control hallmark dendritic cell functions with less impact on DNA methylation, early growth response 2 (EGR2) proves essential for MO differentiation as well as DNA methylation turnover at its binding sites. We also show that ERG2 interacts with the 5mC hydroxylase TET2, and its consensus binding sequences show a characteristic DNA methylation footprint at demethylated sites with or without detectable protein binding. Our findings reveal an essential role for EGR2 as epigenetic pioneer in human MO and suggest that active DNA demethylation can be initiated by the TET2-recruiting TF both at stable and transient binding sites.
    DOI:  https://doi.org/10.1038/s41467-021-21661-y
  13. Genomics Proteomics Bioinformatics. 2021 Mar 04. pii: S1672-0229(21)00057-7. [Epub ahead of print]
    MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.
    Guangyu Wang, Bo Xia, Man Zhou, Jie Lv, Dongyu Zhao, Yanqiang Li, Yiwen Bu, Xin Wang, John P Cooke, Qi Cao, Min Gyu Lee, Lili Zhang, Kaifu Chen.
      Numerous studies of relationship between epigenomic features have focused on their strong correlation across the genome, likely because such relationship can be easily identified by many established methods for correlation analysis. However, two features with little correlation may still colocalize at many genomic sites to implement important functions. There is no bioinformatic tool for researchers to specifically identify such feature pairs. Here, we develop a method to identify feature pairs in which two features have maximal colocalization but minimal correlation (MACMIC) across the genome. By MACMIC analysis of 3385 feature pairs in 15 cell types, we reveal a dual role of CCCTC-binding factor (CTCF) in epigenetic regulation of cell identity genes. Although super-enhancers are associated with activation of target genes, only a subset of super-enhancers colocalized with CTCF regulate cell identity genes. At super-enhancers colocalized with CTCF, CTCF is required for the active marker H3K27ac in cell types requiring the activation, and also required for the repressive marker H3K27me3 in other cell types requiring repression. Our work demonstrates the biological utility of the MACMIC analysis and reveals a key role for CTCF in epigenetic regulation of cell identity. The code for MACMIC is available at the website GitHub, https://github.com/bxia888/MACMIC.
    Keywords:  CCCTC-binding factor; H3K27ac; H3K27me3; Mutual information; correlation
    DOI:  https://doi.org/10.1016/j.gpb.2020.10.008
  14. Elife. 2021 Mar 11. pii: e63512. [Epub ahead of print]10
    Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 inhibition.
    Emily Hsu, Nathan R Zemke, Arnold J Berk.
      Regulation of RNA Polymerase II (Pol2) elongation in the promoter proximal region is an important and ubiquitous control point for gene expression in metazoans. We report that transcription of the adenovirus 5 E4 region is regulated during the release of paused Pol2 into productive elongation by recruitment of the super elongation complex (SEC), dependent on promoter H3K18/27 acetylation by CBP/p300. We also establish that this is a general transcriptional regulatory mechanism that applies to ~6% of expressed protein-coding genes in primary human airway epithelial cells. We observed that a homeostatic mechanism maintains promoter, but not enhancer H3K18/27ac in response to extensive inhibition of CBP/p300 acetyl transferase activity by the highly specific small molecule inhibitor A-485. Further, our results suggest a function for BRD4 association at enhancers in regulating paused Pol2 release at nearby promoters. Taken together, our results uncover processes regulating transcriptional elongation by promoter region histone H3 acetylation and homeostatic maintenance of promoter, but not enhancer, H3K18/27ac in response to inhibition of CBP/p300 acetyl transferase activity.
    Keywords:  chromosomes; gene expression; human
    DOI:  https://doi.org/10.7554/eLife.63512
  15. Development. 2021 Mar 09. pii: dev.196329. [Epub ahead of print]
    Full methylation of H3K27 by PRC2 is dispensable for initial embryoid body formation but required to maintain differentiated cell identity.
    Sara A Miller, Manashree Damle, Jongmin Kim, Robert E Kingston.
      Polycomb repressive complex 2 (PRC2) catalyzes methylation of histone H3 on lysine 27 and is required for normal development of complex eukaryotes. The nature of that requirement is not clear. H3K27me3 is associated with repressed genes, however the modification is not sufficient to induce repression, and in some instances is not required. We blocked full methylation of H3K27 with both a small molecule inhibitor, GSK343 and by introducing a point mutation into EZH2, the catalytic subunit of PRC2. Cells with substantively decreased H3K27 methylation differentiate into embryoid bodies, which contrasts with EZH2 null cells. PRC2 targets had varied requirements for H3K27me3, with a subset that maintained normal levels of repression in the absence of methylation. The primary cellular phenotype of blocked H3K27 methylation was an inability of altered cells to maintain a differentiated state when challenged. This phenotype was determined by H3K27 methylation in embryonic stem cells through the first four days of differentiation. Full H3K27 methylation therefore was not necessary for formation of differentiated cell states during embryoid body formation but was required to maintain a stable differentiated state.
    Keywords:  Differentiation; EZH2; Embryoid body; H3K27 methylation; Maintenance; PRC2
    DOI:  https://doi.org/10.1242/dev.196329
  16. Cell Rep. 2021 Mar 09. pii: S2211-1247(21)00136-4. [Epub ahead of print]34(10): 108822
    Functional cooperation between co-amplified genes promotes aggressive phenotypes of HER2-positive breast cancer.
    Yongguang Yang, Marissa Leonard, Zhenhua Luo, Syn Yeo, Gregory Bick, Mingang Hao, Chunmiao Cai, Mahmoud Charif, Jiang Wang, Jun-Lin Guan, Elyse E Lower, Xiaoting Zhang.
      MED1 (mediator subunit 1) co-amplifies with HER2, but its role in HER2-driven mammary tumorigenesis is still unknown. Here, we generate MED1 mammary-specific overexpression mice and cross them with mouse mammary tumor virus (MMTV)-HER2 mice. We observe significantly promoted onset, growth, metastasis, and multiplicity of HER2 tumors by MED1 overexpression. Further studies reveal critical roles for MED1 in epithelial-mesenchymal transition, cancer stem cell formation, and response to anti-HER2 therapy. Mechanistically, RNA sequencing (RNA-seq) transcriptome analyses and clinical sample correlation studies identify Jab1, a component of the COP9 signalosome complex, as the key direct target gene of MED1 contributing to these processes. Further studies reveal that Jab1 can also reciprocally regulate the stability and transcriptional activity of MED1. Together, our findings support a functional cooperation between these co-amplified genes in HER2+ mammary tumorigenesis and their potential usage as therapeutic targets for the treatment of HER2+ breast cancers.
    Keywords:  HER2; Jab1; MED1; cancer stem cell; therapeutic resistance; tumor metastasis
    DOI:  https://doi.org/10.1016/j.celrep.2021.108822
  17. Science. 2021 Mar 11. pii: eabg3074. [Epub ahead of print]
    Structure of the human Mediator-bound transcription preinitiation complex.
    R Abdella, A Talyzina, S Chen, C J Inouye, R Tjian, Y He.
      Eukaryotic transcription requires the assembly of a multi-subunit preinitiation complex (PIC) comprised of RNA polymerase II (Pol II) and the general transcription factors. The co-activator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at sub-4 Å. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.
    DOI:  https://doi.org/10.1126/science.abg3074
  18. Sci Adv. 2021 Mar;pii: eabd6030. [Epub ahead of print]7(11):
    Inhibition of CRISPR-Cas12a DNA targeting by nucleosomes and chromatin.
    Isabel Strohkendl, Fatema A Saifuddin, Bryan A Gibson, Michael K Rosen, Rick Russell, Ilya J Finkelstein.
      Genome engineering nucleases must access chromatinized DNA. Here, we investigate how AsCas12a cleaves DNA within human nucleosomes and phase-condensed nucleosome arrays. Using quantitative kinetics approaches, we show that dynamic nucleosome unwrapping regulates target accessibility to Cas12a and determines the extent to which both steps of binding-PAM recognition and R-loop formation-are inhibited by the nucleosome. Relaxing DNA wrapping within the nucleosome by reducing DNA bendability, adding histone modifications, or introducing target-proximal dCas9 enhances DNA cleavage rates over 10-fold. Unexpectedly, Cas12a readily cleaves internucleosomal linker DNA within chromatin-like, phase-separated nucleosome arrays. DNA targeting is reduced only ~5-fold due to neighboring nucleosomes and chromatin compaction. This work explains the observation that on-target cleavage within nucleosomes occurs less often than off-target cleavage within nucleosome-depleted genomic regions in cells. We conclude that nucleosome unwrapping regulates accessibility to CRISPR-Cas nucleases and propose that increasing nucleosome breathing dynamics will improve DNA targeting in eukaryotic cells.
    DOI:  https://doi.org/10.1126/sciadv.abd6030
  19. Sci Rep. 2021 Mar 11. 11(1): 5777
    Cycling hypoxia selects for constitutive HIF stabilization.
    Mariyah Pressley, Jill A Gallaher, Joel S Brown, Michal R Tomaszewski, Punit Borad, Mehdi Damaghi, Robert J Gillies, Christopher J Whelan.
      Tumors experience temporal and spatial fluctuations in oxygenation. Hypoxia inducible transcription factors (HIF-α) respond to low levels of oxygen and induce re-supply oxygen. HIF-α stabilization is typically facultative, induced by hypoxia and reduced by normoxia. In some cancers, HIF-α stabilization becomes constitutive under normoxia. We develop a mathematical model that predicts how fluctuating oxygenation affects HIF-α stabilization and impacts net cell proliferation by balancing the base growth rate, the proliferative cost of HIF-α expression, and the mortality from not expressing HIF-α during hypoxia. We compare optimal net cell proliferation rate between facultative and constitutive HIF-α regulation in environments with different oxygen profiles. We find that that facultative HIF-α regulation promotes greater net cell proliferation than constitutive regulation with stochastic or slow periodicity in oxygenation. However, cell fitness is nearly identical for both HIF-α regulation strategies under rapid periodic oxygenation fluctuations. The model thus indicates that cells constitutively expressing HIF-α may be at a selective advantage when the cost of expression is low. In cancer, this condition is known as pseudohypoxia or the "Warburg Effect". We conclude that rapid and regular cycling of oxygenation levels selects for pseudohypoxia, and that this is consistent with the ecological theory of optimal defense.
    DOI:  https://doi.org/10.1038/s41598-021-85184-8
  20. Mol Plant. 2021 Mar 05. pii: S1674-2052(21)00079-4. [Epub ahead of print]
    The LEAFY floral regulator displays pioneer transcription factor properties.
    Xuelei Lai, Romain Blanc-Mathieu, Loïc GrandVuillemin, Ying Huang, Arnaud Stigliani, Jérémy Lucas, Emmanuel Thévenon, Jeanne Loue-Manifel, Laura Turchi, Hussein Daher, Eugenia Brun-Hernandez, Gilles Vachon, David Latrasse, Moussa Benhamed, Renaud Dumas, Chloe Zubieta, François Parcy.
      Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly methylated. Subsequently, pioneer TFs are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes, APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launch the floral gene expression program.
    DOI:  https://doi.org/10.1016/j.molp.2021.03.004
  21. Mol Metab. 2021 Mar 08. pii: S2212-8778(21)00049-1. [Epub ahead of print] 101209
    RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression.
    Laura Regué, Liping Zhao, Fei Ji, Hua Wang, Joe Avruch, Ning Dai.
      Type 2 diabetes (T2D) is a common metabolic disease. Variants in IMP2 (IGF2BP2) associated with increased risk of T2D impair insulin secretion. However, the underlying mechanism is not known. IMP2 is an RNA binding protein that preferentially recognize N6-methyladenosine (m6A) modified mRNAs. Here we report that the deletion of IMP2 in pancreatic β-cells leads to reduced compensatory β-cell proliferation and function in mice. Mechanically, IMP2 directly binds to Pdx1 mRNA and stimulates its translation in a m6A dependent manner. In addition, IMP2 also orchestrates IGF2-AKT-GSK3-PDX1 signaling to promotes insulin secretion. In human EndoC-βH1 cells, the expression of IMP2 is capable to enhance cell proliferation, PDX1 expression, IGF2 signaling as well as insulin secretion. Our work therefore reveals IMP2 as a critical regulator of β-cell function and highlights the importance of posttranscriptional gene expression in T2D pathology.
    Keywords:  IMP2/IGF2BP2; T2D; insulin secretion; m6A; post-transcriptional gene expression regulation
    DOI:  https://doi.org/10.1016/j.molmet.2021.101209
  22. Oncogene. 2021 Mar 12.
    BRD4 inhibition sensitizes cervical cancer to radiotherapy by attenuating DNA repair.
    Mengdong Ni, Jiajia Li, Haiyun Zhao, Fei Xu, Jingyi Cheng, Min Yu, Guihao Ke, Xiaohua Wu.
      Cisplatin-based chemoradiotherapy is the recommended treatment for local advanced cervical cancer, but radioresistance remains one of the most important and unresolved clinical problems. Investigations have revealed aberrant epigenetic modifications as one of the chief culprits for the development of radioresistance. Here, we attempt to identify a radiosensitizer from an epigenetic drug synergy screen and explore the underlying mechanism. We integrated epigenetic inhibitors and radiotherapy in cervical cancer cell lines to identify potential radiosensitizers. We further verified the sensitization effect of the drug and the function of its target gene both in vitro and in vivo. Finally, we validated the clinical significance of its target gene in clinical cervical cancer specimens. We identified JQ1, a BRD4 inhibitor, as a potent radiosensitizer. Functional assays demonstrated that repressing BRD4 activity led to significant radiosensitization and potentiation of DNA damage in cervical cancer cell lines. By using RNA-seq to determine JQ1-mediated changes in transcription, we identified RAD51AP1 as a major BRD4 target gene involved in radiosensitivity. A dual-luciferase reporter assay and ChIP-qPCR showed that BRD4 binds to the promoter region of RAD51AP1 and promotes its transcription, whereas this activity was attenuated by BRD4 inhibition. The in vivo experiments also suggested a synergy between BRD4 inhibition and radiotherapy. High BRD4 expression was found to be related to a worse prognosis and radiation resistance. BRD4 inhibition sensitizes cervical cancer to radiotherapy by inhibiting RAD51AP1 transcription. The combination of JQ1 with radiotherapy merits further evaluation as a therapeutic strategy for improving local control in cervical cancer.
    DOI:  https://doi.org/10.1038/s41388-021-01735-3
  23. Nat Commun. 2021 Mar 12. 12(1): 1610
    Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes.
    Gloriia Novikova, Manav Kapoor, Julia Tcw, Edsel M Abud, Anastasia G Efthymiou, Steven X Chen, Haoxiang Cheng, John F Fullard, Jaroslav Bendl, Yiyuan Liu, Panos Roussos, Johan Lm Björkegren, Yunlong Liu, Wayne W Poon, Ke Hao, Edoardo Marcora, Alison M Goate.
      Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer's disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1, and ZYX) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.
    DOI:  https://doi.org/10.1038/s41467-021-21823-y
  24. J Integr Plant Biol. 2020 Dec 15.
    The CBP/p300 histone acetyltransferases function as plant-specific MEDIATOR subunits in Arabidopsis.
    Jing Guo, Long Wei, Shan-Shan Chen, Xue-Wei Cai, Yin-Na Su, Lin Li, She Chen, Xin-Jian He.
      In eukaryotes, MEDIATOR is a conserved multi-subunit complex that links transcription factors and RNA polymerase II and that thereby facilitates transcriptional initiation. Although the composition of MEDIATOR has been well studied in yeast and mammals, relatively little is known about the composition of MEDIATOR in plants. By affinity purification followed by mass spectrometry, we identified 28 conserved MEDIATOR subunits in Arabidopsis thaliana, including putative MEDIATOR subunits that were not previously validated. Our results indicated that MED34, MED35, MED36, and MED37 are not Arabidopsis MEDIATOR subunits, as previously proposed. Our results also revealed that two homologous CBP/p300 histone acetyltransferases, HAC1 and HAC5 (HAC1/5) are in fact plant-specific MEDIATOR subunits. The MEDIATOR subunits MED8 and MED25 (MED8/25) are partially responsible for the association of MEDIATOR with HAC1/5, MED8/25 and HAC1/5 co-regulate gene expression and thereby affect flowering time and floral development. Our in vitro observations indicated that MED8 and HAC1 form liquid-like droplets by phase separation, and our in vivo observations indicated that these droplets co-localize in the nuclear bodies at a subset of nuclei. The formation of liquid-like droplets is required for MED8 to interact with RNA polymerase II. In summary, we have identified all of the components of Arabidopsis MEDIATOR and revealed the mechanism underlying the link of histone acetylation and transcriptional regulation.
    Keywords:  MEDIATOR; complex; development; flowering time; histone acetylation; phase separation; transcription
    DOI:  https://doi.org/10.1111/jipb.13052
  25. Nat Immunol. 2021 Mar 08.
    Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program.
    Mariya London, Angelina M Bilate, Tiago B R Castro, Tomohisa Sujino, Daniel Mucida.
      Mesenteric lymph node (mLN) T cells undergo tissue adaptation upon migrating to intestinal lamina propria and epithelium, ensuring appropriate balance between tolerance and resistance. By combining mouse genetics with single-cell and chromatin analyses, we uncovered the molecular imprinting of gut epithelium on T cells. Transcriptionally, conventional and regulatory (Treg) CD4+ T cells from mLN, lamina propria and intestinal epithelium segregate based on the gut layer they occupy; trajectory analysis suggests a stepwise loss of CD4 programming and acquisition of an intraepithelial profile. Treg cell fate mapping coupled with RNA sequencing and assay for transposase-accessible chromatin followed by sequencing revealed that the Treg cell program shuts down before an intraepithelial program becomes fully accessible at the epithelium. Ablation of CD4-lineage-defining transcription factor ThPOK results in premature acquisition of an intraepithelial lymphocyte profile by mLN Treg cells, partially recapitulating epithelium imprinting. Thus, coordinated replacement of the circulating lymphocyte program with site-specific transcriptional and chromatin changes is necessary for tissue imprinting.
    DOI:  https://doi.org/10.1038/s41590-021-00883-8
  26. Cell Rep. 2021 Mar 09. pii: S2211-1247(21)00132-7. [Epub ahead of print]34(10): 108818
    Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions.
    Luca Orlando, Borko Tanasijevic, Mio Nakanishi, Jennifer C Reid, Juan L García-Rodríguez, Kapil Dev Chauhan, Deanna P Porras, Lili Aslostovar, Justin D Lu, Zoya Shapovalova, Ryan R Mitchell, Allison L Boyd, Mickie Bhatia.
      Histone variants (HVs) are a subfamily of epigenetic regulators implicated in embryonic development, but their role in human stem cell fate remains unclear. Here, we reveal that the phosphorylation state of the HV H2A.X (γH2A.X) regulates self-renewal and differentiation of human pluripotent stem cells (hPSCs) and leukemic progenitors. As demonstrated by CRISPR-Cas deletion, H2A.X is essential in maintaining normal hPSC behavior. However, reduced levels of γH2A.X enhances hPSC differentiation toward the hematopoietic lineage with concomitant inhibition of neural development. In contrast, activation and sustained levels of phosphorylated H2A.X enhance hPSC neural fate while suppressing hematopoiesis. This controlled lineage bias correlates to occupancy of γH2A.X at genomic loci associated with ectoderm versus mesoderm specification. Finally, drug modulation of H2A.X phosphorylation overcomes differentiation block of patient-derived leukemic progenitors. Our study demonstrates HVs may serve to regulate pluripotent cell fate and that this biology could be extended to somatic cancer stem cell control.
    Keywords:  differentiation; epigenetics; histone variants; pluripotent stem cells; self-renewal
    DOI:  https://doi.org/10.1016/j.celrep.2021.108818
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