bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–10–09
24 papers selected by
Connor Rogerson, University of Cambridge
  1. p300/CBP sustains Polycomb silencing by non-enzymatic functions.
  2. High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.
  3. Capicua suppresses YAP1 to limit tumorigenesis and maintain drug sensitivity in human cancer.
  4. TFSyntax: a database of transcription factors binding syntax in mammalian genomes.
  5. Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells.
  6. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.
  7. Functional inference of gene regulation using single-cell multi-omics.
  8. DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.
  9. Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
  10. Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.
  11. The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A.
  12. AgeAnno: a knowledgebase of single-cell annotation of aging in human.
  13. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.
  14. The chromatin remodeler RSC prevents ectopic CENP-A propagation into pericentromeric heterochromatin at the chromatin boundary.
  15. CARM1-mediated methylation of ASXL2 impairs tumor-suppressive function of MLL3/COMPASS.
  16. Inferring and perturbing cell fate regulomes in human brain organoids.
  17. MYC oncogene elicits tumorigenesis associated with embryonic, ribosomal biogenesis, and tissue-lineage dedifferentiation gene expression changes.
  18. Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation.
  19. CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.
  20. H3K18 lactylation marks tissue-specific active enhancers.
  21. Nuclear position modulates long-range chromatin interactions.
  22. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
  23. POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity.
  24. AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells.
  1. Mol Cell. 2022 Oct 06. pii: S1097-2765(22)00894-2. [Epub ahead of print]82(19): 3580-3597.e9
    p300/CBP sustains Polycomb silencing by non-enzymatic functions.
    George Hunt, Ann Boija, Mattias Mannervik.
      Maintenance of appropriate cell states involves epigenetic mechanisms, including Polycomb-group (PcG)-mediated transcriptional repression. While PcG proteins are known to induce chromatin compaction, how PcG proteins gain access to DNA in compact chromatin to achieve long-term silencing is poorly understood. Here, we show that the p300/CREB-binding protein (CBP) co-activator is associated with two-thirds of PcG regions and required for PcG occupancy at many of these in Drosophila and mouse cells. CBP stabilizes RNA polymerase II (Pol II) at PcG-bound repressive sites and promotes Pol II pausing independently of its histone acetyltransferase activity. CBP and Pol II pausing are necessary for RNA-DNA hybrid (R-loop) formation and nucleosome depletion at Polycomb Response Elements (PREs), whereas transcription beyond the pause region is not. These results suggest that non-enzymatic activities of the CBP co-activator have been repurposed to support PcG-mediated silencing, revealing how chromatin regulator interplay maintains transcriptional states.
    Keywords:  CBP; Pol II pausing; Polycomb; R-loop; epigenetics; gene silencing; nucleosome depletion; p300; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2022.09.005
  2. Nat Commun. 2022 Oct 07. 13(1): 5827
    High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci.
    Claire Marchal, Nivedita Singh, Zachary Batz, Jayshree Advani, Catherine Jaeger, Ximena Corso-Díaz, Anand Swaroop.
      Chromatin organization and enhancer-promoter contacts establish unique spatiotemporal gene expression patterns in distinct cell types. Non-coding genetic variants can influence cellular phenotypes by modifying higher-order transcriptional hubs and consequently gene expression. To elucidate genomic regulation in human retina, we mapped chromatin contacts at high resolution and integrated with super-enhancers (SEs), histone marks, binding of CTCF and select transcription factors. We show that topologically associated domains (TADs) with central SEs exhibit stronger insulation and augmented contact with retinal genes relative to TADs with edge SEs. Merging genome-wide expression quantitative trait loci (eQTLs) with topology map reveals physical links between 100 eQTLs and corresponding eGenes associated with retinal neurodegeneration. Additionally, we uncover candidate genes for susceptibility variants linked to age-related macular degeneration and glaucoma. Our study of high-resolution genomic architecture of human retina provides insights into genetic control of tissue-specific functions, suggests paradigms for missing heritability, and enables the dissection of common blinding disease phenotypes.
    DOI:  https://doi.org/10.1038/s41467-022-33427-1
  3. Cell Rep. 2022 Oct 04. pii: S2211-1247(22)01284-0. [Epub ahead of print]41(1): 111443
    Capicua suppresses YAP1 to limit tumorigenesis and maintain drug sensitivity in human cancer.
    Ji Won Kim, Cuyler Luck, Wei Wu, Rovingaile Kriska Ponce, Yone Kawe Lin, Nehal Gupta, Ross A Okimoto.
      Inactivation of Capicua (CIC) or upregulation of yes-associated protein 1, YAP1, leads to broad RAS-RAF-MEK-ERK inhibitor resistance and tumor progression in multiple human cancers. Despite these shared malignant phenotypes, it remains unclear whether CIC and YAP1 are mechanistically linked. Here, we show that the ERK-regulated transcription factor CIC can directly repress YAP1 expression through non-consensus GGAAGGAA DNA-binding motifs in a proximal YAP1 regulatory element. Through binding at GGAA repeats, CIC regulates YAP1 transcriptional output in both normal and human cancer cells. Silencing YAP1 in CIC-deficient cells restores MAPK inhibitor sensitivity and suppresses tumor growth. Thus, we uncover a molecular link between the MAPK-ERK effector CIC and YAP1 in human cells and established YAP inhibition as a strategy to target CIC-deficient cancers.
    Keywords:  CIC; CP: Cancer; CP: Molecular biology; Capicua; MAPK inhibitor resistance; YAP1
    DOI:  https://doi.org/10.1016/j.celrep.2022.111443
  4. Nucleic Acids Res. 2022 Oct 06. pii: gkac849. [Epub ahead of print]
    TFSyntax: a database of transcription factors binding syntax in mammalian genomes.
    Yongbing Zhao.
      In mammals, transcriptional factors (TFs) drive gene expression by binding to regulatory elements in a cooperative manner. Deciphering the rules of such cooperation is crucial to obtain a full understanding of cellular homeostasis and development. Although this is a long-standing topic, there is no comprehensive database for biologists to access the syntax of TF binding sites. Here we present TFSyntax (https://tfsyntax.zhaopage.com), a database focusing on the arrangement of TF binding sites. TFSyntax maps the binding motif of 1299 human TFs and 890 mouse TFs across 382 cells and tissues, representing the most comprehensive TF binding map to date. In addition to location, TFSyntax defines motif positional preference, density and colocalization within accessible elements. Powered by a series of functional modules based on web interface, users can freely search, browse, analyze, and download data of interest. With comprehensive characterization of TF binding syntax across distinct tissues and cell types, TFSyntax represents a valuable resource and platform for studying the mechanism of transcriptional regulation and exploring how regulatory DNA variants cause disease.
    DOI:  https://doi.org/10.1093/nar/gkac849
  5. Dev Cell. 2022 Sep 28. pii: S1534-5807(22)00636-0. [Epub ahead of print]
    Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells.
    Austin S Hovland, Debadrita Bhattacharya, Ana Paula Azambuja, Dimitrius Pramio, Jacqueline Copeland, Megan Rothstein, Marcos Simoes-Costa.
      Yamanaka factors are essential for establishing pluripotency in embryonic stem cells, but their function in multipotent stem cell populations is poorly understood. Here, we show that OCT4 and SOX2 cooperate with tissue-specific transcription factors to promote neural crest formation. By assessing avian and human neural crest cells at distinct developmental stages, we characterized the epigenomic changes that occur during their specification, migration, and early differentiation. This analysis determined that the OCT4-SOX2 dimer is required to establish a neural crest epigenomic signature that is lost upon cell fate commitment. The OCT4-SOX2 genomic targets in the neural crest differ from those of embryonic stem cells, indicating the dimer displays context-specific functions. Binding of OCT4-SOX2 to neural crest enhancers requires pioneer factor TFAP2A, which physically interacts with the dimer to modify its genomic targets. Our results demonstrate how Yamanaka factors are repurposed in multipotent cells to control chromatin organization and define their developmental potential.
    Keywords:  OCT4; SOX2; TFAP2A; Yamanaka factors; epigenome; multipotency; neural crest; pioneer transcription factors; pluripotency; stem cells
    DOI:  https://doi.org/10.1016/j.devcel.2022.09.006
  6. Nat Genet. 2022 Oct;54(10): 1504-1513
    Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.
    Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J Najm, Yuanyuan Zhang, Molly M Moore, Vivian Hecht, Noam Shoresh, Bradley E Bernstein.
      Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in a locus or capture single-molecule dynamics. Here, we apply targeted nanopore sequencing to profile chromatin accessibility and DNA methylation on contiguous ~100-kb DNA molecules that span loci relevant to development, immunity and imprinting. We detect promoters, enhancers, insulators and transcription factor footprints on single molecules based on exogenous GpC methylation. We infer relationships among dynamic elements within immune loci, and order successive remodeling events during T cell stimulation. Finally, we phase primary sequence and regulatory elements across the H19/IGF2 locus, uncovering primate-specific features. These include a segmental duplication that stabilizes the imprinting control region and a noncanonical enhancer that drives biallelic IGF2 expression in specific contexts. Our study advances emerging strategies for phasing gene regulatory landscapes and reveals a mechanism that overrides IGF2 imprinting in human cells.
    DOI:  https://doi.org/10.1038/s41588-022-01188-8
  7. Cell Genom. 2022 Sep 14. pii: 100166. [Epub ahead of print]2(9):
    Functional inference of gene regulation using single-cell multi-omics.
    Vinay K Kartha, Fabiana M Duarte, Yan Hu, Sai Ma, Jennifer G Chew, Caleb A Lareau, Andrew Earl, Zach D Burkett, Andrew S Kohlway, Ronald Lebofsky, Jason D Buenrostro.
      Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
    DOI:  https://doi.org/10.1016/j.xgen.2022.100166
  8. PLoS Comput Biol. 2022 Oct 07. 18(10): e1010572
    DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.
    Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhenghao Guo, Kyungsook Han, De-Shuang Huang.
      In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions. Discriminating the loops from genome-wide contact interactions is crucial for dissecting three-dimensional(3D) genome structure and function. Here, we present a deep learning method to predict genome-wide chromatin loops, called DLoopCaller, by combining accessible chromatin landscapes and raw Hi-C contact maps. Some available orthogonal data ChIA-PET/HiChIP and Capture Hi-C were used to generate positive samples with a wider contact matrix which provides the possibility to find more potential genome-wide chromatin loops. The experimental results demonstrate that DLoopCaller effectively improves the accuracy of predicting genome-wide chromatin loops compared to the state-of-the-art method Peakachu. Moreover, compared to two of most popular loop callers, such as HiCCUPS and Fit-Hi-C, DLoopCaller identifies some unique interactions. We conclude that a combination of chromatin landscapes on the one-dimensional genome contributes to understanding the 3D genome organization, and the identified chromatin loops reveal cell-type specificity and transcription factor motif co-enrichment across different cell lines and species.
    DOI:  https://doi.org/10.1371/journal.pcbi.1010572
  9. Nature. 2022 Oct 05.
    Structure of the NuA4 acetyltransferase complex bound to the nucleosome.
    Keke Qu, Kangjing Chen, Hao Wang, Xueming Li, Zhucheng Chen.
      Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes1, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing2-4. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair5-10. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
    DOI:  https://doi.org/10.1038/s41586-022-05303-x
  10. Mol Cell. 2022 Sep 19. pii: S1097-2765(22)00854-1. [Epub ahead of print]
    Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.
    Ya Guo, Ediem Al-Jibury, Rosalba Garcia-Millan, Konstantinos Ntagiantas, James W D King, Alex J Nash, Niels Galjart, Boris Lenhard, Daniel Rueckert, Amanda G Fisher, Gunnar Pruessner, Matthias Merkenschlager.
      Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.
    Keywords:  3D genome folding; CTCF; cohesin; loop extrusion
    DOI:  https://doi.org/10.1016/j.molcel.2022.09.003
  11. Nat Cell Biol. 2022 Oct 06.
    The HASTER lncRNA promoter is a cis-acting transcriptional stabilizer of HNF1A.
    Anthony Beucher, Irene Miguel-Escalada, Diego Balboa, Matías G De Vas, Miguel Angel Maestro, Javier Garcia-Hurtado, Aina Bernal, Roser Gonzalez-Franco, Pierfrancesco Vargiu, Holger Heyn, Philippe Ravassard, Sagrario Ortega, Jorge Ferrer.
      The biological purpose of long non-coding RNAs (lncRNAs) is poorly understood. Haploinsufficient mutations in HNF1A homeobox A (HNF1A), encoding a homeodomain transcription factor, cause diabetes mellitus. Here, we examine HASTER, the promoter of an lncRNA antisense to HNF1A. Using mouse and human models, we show that HASTER maintains cell-specific physiological HNF1A concentrations through positive and negative feedback loops. Pancreatic β cells from Haster mutant mice consequently showed variegated HNF1A silencing or overexpression, resulting in hyperglycaemia. HASTER-dependent negative feedback was essential to prevent HNF1A binding to inappropriate genomic regions. We demonstrate that the HASTER promoter DNA, rather than the lncRNA, modulates HNF1A promoter-enhancer interactions in cis and thereby regulates HNF1A transcription. Our studies expose a cis-regulatory element that is unlike classic enhancers or silencers, it stabilizes the transcription of its target gene and ensures the fidelity of a cell-specific transcription factor program. They also show that disruption of a mammalian lncRNA promoter can cause diabetes mellitus.
    DOI:  https://doi.org/10.1038/s41556-022-00996-8
  12. Nucleic Acids Res. 2022 Oct 06. pii: gkac847. [Epub ahead of print]
    AgeAnno: a knowledgebase of single-cell annotation of aging in human.
    Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim, Xiaobo Zhou.
      Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell level can help to understand the heterogeneous aging process and design targeted anti-aging therapeutics. Here, we built AgeAnno (https://relab.xidian.edu.cn/AgeAnno/#/), a knowledgebase of single cell annotation of aging in human, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy tissue samples with ages ranging from 0 to 110 years. We collected 5580 aging-related genes from previous resources and performed dynamic functional annotations of the cellular context. For the scRNA data, we performed analyses include differential gene expression, gene variation coefficient, cell communication network, transcription factor (TF) regulatory network, and immune cell proportionc. AgeAnno also provides differential chromatin accessibility analysis, motif/TF enrichment and footprint analysis, and co-accessibility peak analysis for scATAC data. AgeAnno will be a unique resource to systematically characterize aging-related genes across diverse tissue-cell types in human, and it could facilitate antiaging and aging-related disease research.
    DOI:  https://doi.org/10.1093/nar/gkac847
  13. Nat Methods. 2022 Oct 03.
    Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.
    Nadiya Khyzha, Steven Henikoff, Kami Ahmad.
      Whereas techniques to map chromatin-bound proteins are well developed, mapping chromatin-associated RNAs remains a challenge. Here, we describe Reverse Transcribe and Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates RNA/cDNA hybrids that are subsequently tagmented by Tn5 transposases for downstream sequencing. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling of chromatin-associated RNAs.
    DOI:  https://doi.org/10.1038/s41592-022-01618-9
  14. Nucleic Acids Res. 2022 Oct 06. pii: gkac827. [Epub ahead of print]
    The chromatin remodeler RSC prevents ectopic CENP-A propagation into pericentromeric heterochromatin at the chromatin boundary.
    Satoru Tsunemine, Hiromi Nakagawa, Yutaka Suzuki, Yota Murakami.
      Centromeres of most eukaryotes consist of two distinct chromatin domains: a kinetochore domain, identified by the histone H3 variant, CENP-A, and a heterochromatic domain. How these two domains are separated is unclear. Here, we show that, in Schizosaccharomyces pombe, mutation of the chromatin remodeler RSC induced CENP-ACnp1 misloading at pericentromeric heterochromatin, resulting in the mis-assembly of kinetochore proteins and a defect in chromosome segregation. We find that RSC functions at the kinetochore boundary to prevent CENP-ACnp1 from spreading into neighbouring heterochromatin, where deacetylated histones provide an ideal environment for the spread of CENP-ACnp1. In addition, we show that RSC decompacts the chromatin structure at this boundary, and propose that this RSC-directed chromatin decompaction prevents mis-propagation of CENP-ACnp1 into pericentromeric heterochromatin. Our study provides an insight into how the distribution of distinct chromatin domains is established and maintained.
    DOI:  https://doi.org/10.1093/nar/gkac827
  15. Sci Adv. 2022 Oct 07. 8(40): eadd3339
    CARM1-mediated methylation of ASXL2 impairs tumor-suppressive function of MLL3/COMPASS.
    Zibo Zhao, Emily Jane Rendleman, Aileen Patricia Szczepanski, Marc Alard Morgan, Lu Wang, Ali Shilatifard.
      An imbalance in the activities of the Polycomb and Trithorax complexes underlies numerous human pathologies, including cancer. The BRCA1 associated protein-1 (BAP1) deubiquitinase negatively regulates Polycomb activity and recruits the Trithorax histone H3K4 methyltransferase, mixed-lineage leukemia protein 3 (MLL3) within Complex Proteins Associated with Set1 (COMPASS), to the enhancers of tumor suppressor genes. We previously demonstrated that the BAP1-MLL3 pathway is mutated in several cancers, yet how BAP1 recruits MLL3 to its target loci remains an important unanswered question. We demonstrate that the ASXL2 subunit of the BAP1 complex mediates a direct interaction with MLL3/COMPASS. ASXL2 loss results in decreased MLL3 occupancy at enhancers and reduced BAP1-MLL3 target gene expression. Interaction between ASXL2 and MLL3 is negatively regulated by protein arginine methyltransferase 4 (PRMT4/CARM1), which methylates ASXL2 at R639/R641. ASXL2 methylation blocks binding to MLL3 and impairs the expression of MLL3/COMPASS-dependent genes. This previously unidentified transcriptional repressive function of CARM1 provides insight into the BAP1/MLL3-COMPASS axis and reveals a potential cancer therapeutic target.
    DOI:  https://doi.org/10.1126/sciadv.add3339
  16. Nature. 2022 Oct 05.
    Inferring and perturbing cell fate regulomes in human brain organoids.
    Jonas Simon Fleck, Sophie Martina Johanna Jansen, Damian Wollny, Fides Zenk, Makiko Seimiya, Akanksha Jain, Ryoko Okamoto, Malgorzata Santel, Zhisong He, J Gray Camp, Barbara Treutlein.
      Self-organizing neural organoids grown from pluripotent stem cells1-3 combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology.
    DOI:  https://doi.org/10.1038/s41586-022-05279-8
  17. Oncogene. 2022 Oct 07.
    MYC oncogene elicits tumorigenesis associated with embryonic, ribosomal biogenesis, and tissue-lineage dedifferentiation gene expression changes.
    Delaney K Sullivan, Anja Deutzmann, Josiah Yarbrough, Maya S Krishnan, Arvin M Gouw, David I Bellovin, Stacey J Adam, Daniel F Liefwalker, Renumathy Dhanasekaran, Dean W Felsher.
      MYC is a transcription factor frequently overexpressed in cancer. To determine how MYC drives the neoplastic phenotype, we performed transcriptomic analysis using a panel of MYC-driven autochthonous transgenic mouse models. We found that MYC elicited gene expression changes mostly in a tissue- and lineage-specific manner across B-cell lymphoma, T-cell acute lymphoblastic lymphoma, hepatocellular carcinoma, renal cell carcinoma, and lung adenocarcinoma. However, despite these gene expression changes being mostly tissue-specific, we uncovered a convergence on a common pattern of upregulation of embryonic stem cell gene programs and downregulation of tissue-of-origin gene programs across MYC-driven cancers. These changes are representative of lineage dedifferentiation, that may be facilitated by epigenetic alterations that occur during tumorigenesis. Moreover, while several cellular processes are represented among embryonic stem cell genes, ribosome biogenesis is most specifically associated with MYC expression in human primary cancers. Altogether, MYC's capability to drive tumorigenesis in diverse tissue types appears to be related to its ability to both drive a core signature of embryonic genes that includes ribosomal biogenesis genes as well as promote tissue and lineage specific dedifferentiation.
    DOI:  https://doi.org/10.1038/s41388-022-02458-9
  18. Elife. 2022 Oct 05. pii: e80147. [Epub ahead of print]11
    Depletion or cleavage of cohesin during anaphase differentially affects chromatin structure and segregation.
    Jonay Garcia-Luis, Hélène Bordelet, Agnès Thierry, Romain Koszul, Luis Aragon.
      Chromosome segregation requires both the separation of sister chromatids and the sustained condensation of chromatids during anaphase. In yeast cells, cohesin is not only required for sister chromatid cohesion but also plays a major role determining the structure of individual chromatids in metaphase. Separase cleavage is thought to remove all cohesin complexes from chromosomes to initiate anaphase. It is thus not clear how the length and organisation of segregating chromatids is maintained during anaphase in the absence of cohesin. Here we show that degradation of cohesin at the anaphase onset causes aberrant chromatid segregation. Hi-C analysis on segregating chromatids demonstrates that cohesin depletion causes loss of intrachromatid organisation. Surprisingly, TEV-mediated cleavage of cohesin does not dramatically disrupt chromatid organisation in anaphase, explaining why bulk segregation is achieved. In addition, we identified a small pool of cohesin complexes bound to telophase chromosomes in wildtype cells and show that they play a role in the organisation of centromeric regions. Our data demonstrates that in yeast cells cohesin function is not over in metaphase, but extends to the anaphase period when chromatids are segregating.
    Keywords:  S. cerevisiae; chromosomes; gene expression
    DOI:  https://doi.org/10.7554/eLife.80147
  19. Nat Cell Biol. 2022 Oct 06.
    CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.
    Yu Liu, Job Dekker.
      The ring-like cohesin complex mediates sister-chromatid cohesion by encircling pairs of sister chromatids. Cohesin also extrudes loops along chromatids. Whether the two activities involve similar mechanisms of DNA engagement is not known. We implemented an experimental approach based on isolated nuclei carrying engineered cleavable RAD21 proteins to precisely control cohesin ring integrity so that its role in chromatin looping could be studied under defined experimental conditions. This approach allowed us to identify cohesin complexes with distinct biochemical, and possibly structural, properties that mediate different sets of chromatin loops. When RAD21 is cleaved and the cohesin ring is opened, cohesin complexes at CTCF sites are released from DNA and loops at these elements are lost. In contrast, cohesin-dependent loops within chromatin domains that are not anchored at pairs of CTCF sites are more resistant to RAD21 cleavage. The results show that the cohesin complex mediates loops in different ways depending on the genomic context and suggests that it undergoes structural changes as it dynamically extrudes and encounters CTCF sites.
    DOI:  https://doi.org/10.1038/s41556-022-00992-y
  20. Genome Biol. 2022 Oct 03. 23(1): 207
    H3K18 lactylation marks tissue-specific active enhancers.
    Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R Ruiz, Ferdinand von Meyenn.
       BACKGROUND: Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation.
    RESULTS: Given the expected relevance of this modification and current limited knowledge of its function, we generate genome-wide datasets of H3K18la distribution in various in vitro and in vivo samples, including mouse embryonic stem cells, macrophages, adipocytes, and mouse and human skeletal muscle. We compare them to profiles of well-established histone modifications and gene expression patterns. Supervised and unsupervised bioinformatics analysis shows that global H3K18la distribution resembles H3K27ac, although we also find notable differences. H3K18la marks active CpG island-containing promoters of highly expressed genes across most tissues assessed, including many housekeeping genes, and positively correlates with H3K27ac and H3K4me3 as well as with gene expression. In addition, H3K18la is enriched at active enhancers that lie in proximity to genes that are functionally important for the respective tissue.
    CONCLUSIONS: Overall, our data suggests that H3K18la is not only a marker for active promoters, but also a mark of tissue specific active enhancers.
    Keywords:  Adipocyte; CUT&Tag; ChromHMM; Embryonic stem cell; Enhancer; Epigenetics; H3K18la; Histone post-translational modification; Lactate; Lactylation; Macrophage; Muscle; Promoter
    DOI:  https://doi.org/10.1186/s13059-022-02775-y
  21. PLoS Genet. 2022 Oct 07. 18(10): e1010451
    Nuclear position modulates long-range chromatin interactions.
    Elizabeth H Finn, Tom Misteli.
      The human genome is non-randomly organized within the cell nucleus. Spatial mapping of genome folding by biochemical methods and imaging has revealed extensive variation in locus interaction frequencies between cells in a population and between homologs within an individual cell. Commonly used mapping approaches typically examine either the relative position of genomic sites to each other or the position of individual loci relative to nuclear landmarks. Whether the frequency of specific chromatin-chromatin interactions is affected by where in the nuclear space a locus is located is unknown. Here, we have simultaneously mapped at the single cell level the interaction frequencies and radial position of more than a hundred locus pairs using high-throughput imaging to ask whether the location within the nucleus affects interaction frequency. We find strong enrichment of many interactions at specific radial positions. Position-dependency of interactions was cell-type specific, correlated with local chromatin type, and cell-type-specific enriched associations were marked by increased variability, sometimes without a significant decrease in mean spatial distance. These observations demonstrate that the folding of the chromatin fiber, which brings genomically distant loci into proximity, and the position of that chromatin fiber relative to nuclear landmarks, are closely linked.
    DOI:  https://doi.org/10.1371/journal.pgen.1010451
  22. Science. 2022 Oct 07. 378(6615): 68-78
    A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation.
    Connor Yanchus, Kristen L Drucker, Thomas M Kollmeyer, Ricky Tsai, Warren Winick-Ng, Minggao Liang, Ahmad Malik, Judy Pawling, Silvana B De Lorenzo, Asma Ali, Paul A Decker, Matt L Kosel, Arijit Panda, Khalid N Al-Zahrani, Lingyan Jiang, Jared W L Browning, Chris Lowden, Michael Geuenich, J Javier Hernandez, Jessica T Gosio, Musaddeque Ahmed, Sampath Kumar Loganathan, Jacob Berman, Daniel Trcka, Kulandaimanuvel Antony Michealraj, Jerome Fortin, Brittany Carson, Ethan W Hollingsworth, Sandra Jacinto, Parisa Mazrooei, Lily Zhou, Andrew Elia, Mathieu Lupien, Housheng Hansen He, Daniel J Murphy, Liguo Wang, Alexej Abyzov, James W Dennis, Philipp G Maass, Kieran Campbell, Michael D Wilson, Daniel H Lachance, Margaret Wrensch, John Wiencke, Tak Mak, Len A Pennacchio, Diane E Dickel, Axel Visel, Jeffrey Wrana, Michael D Taylor, Gelareh Zadeh, Peter Dirks, Jeanette E Eckel-Passow, Liliana Attisano, Ana Pombo, Cristiane M Ida, Evgeny Z Kvon, Robert B Jenkins, Daniel Schramek.
      Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase (IDH)-mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1R132H-driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.
    DOI:  https://doi.org/10.1126/science.abj2890
  23. Sci Adv. 2022 Oct 07. 8(40): eabq2403
    POU2AF2/C11orf53 functions as a coactivator of POU2F3 by maintaining chromatin accessibility and enhancer activity.
    Aileen Patricia Szczepanski, Natsumi Tsuboyama, Jun Watanabe, Rintaro Hashizume, Zibo Zhao, Lu Wang.
      Small cell lung cancer (SCLC), accounting for around 13% of all lung cancers, often results in rapid tumor growth, early metastasis, and acquired therapeutic resistance. The POU class 2 homeobox 3 (POU2F3) is a master regulator of tuft cell identity and defines the SCLC-P subtype that lacks the neuroendocrine markers. Here, we have identified a previously uncharacterized protein, C11orf53, which is coexpressed with POU2F3 in both SCLC cell lines and patient samples. Mechanistically, C11orf53 directly interacts with POU2F3 and is recruited to chromatin by POU2F3. Depletion of C11orf53 reduced enhancer H3K27ac levels and chromatin accessibility, resulting in a reduction of POU2F3-dependent gene expression. On the basis of the molecular function of C11orf53, we renamed it as "POU Class 2 Homeobox Associating Factor 2" (POU2AF2). In summary, our study has identified a new coactivator of POU2F3 and sheds light on the therapeutic potential of targeting POU2AF2/POU2F3 heterodimer in human SCLC.
    DOI:  https://doi.org/10.1126/sciadv.abq2403
  24. PLoS One. 2022 ;17(10): e0269077
    AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells.
    Takao Kitagawa, Daiki Kobayashi, Byron Baron, Hajime Okita, Tatsuo Miyamoto, Rie Takai, Durga Paudel, Tohru Ohta, Yoichi Asaoka, Masayuki Tokunaga, Koji Nakagawa, Makoto Furutani-Seiki, Norie Araki, Yasuhiro Kuramitsu, Masanobu Kobayashi.
      Ewing's sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing's sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.
    DOI:  https://doi.org/10.1371/journal.pone.0269077
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