bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–10–02
nineteen papers selected by
Connor Rogerson, University of Cambridge
  1. ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers.
  2. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
  3. CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.
  4. Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.
  5. Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis.
  6. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors.
  7. Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses.
  8. PRC2-indepdendent actions of H3.3K27M in embryonic stem cell differentiation.
  9. Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis.
  10. A mechanism for oxidative damage repair at gene regulatory elements.
  11. Single-cell gene regulation network inference by large-scale data integration.
  12. Super-enhancers conserved within placental mammals maintain stem cell pluripotency.
  13. Systems-level identification of key transcription factors in immune cell specification.
  14. Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress.
  15. Human centromere repositioning activates transcription and opens chromatin fibre structure.
  16. The three-dimensional landscape of cortical chromatin accessibility in Alzheimer's disease.
  17. Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
  18. FOXA1 regulates alternative splicing in prostate cancer.
  19. Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements.
  1. BMC Biol. 2022 09 25. 20(1): 209
    ARID1A-dependent maintenance of H3.3 is required for repressive CHD4-ZMYND8 chromatin interactions at super-enhancers.
    Jake J Reske, Mike R Wilson, Brooke Armistead, Shannon Harkins, Cristina Perez, Joel Hrit, Marie Adams, Scott B Rothbart, Stacey A Missmer, Asgerally T Fazleabas, Ronald L Chandler.
       BACKGROUND: SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. Here, we investigate the function of ARID1A, a subunit of certain mammalian SWI/SNF chromatin remodeling complexes associated with malignancies and benign diseases originating from the uterine endometrium.
    RESULTS: Through genome-wide analysis of human endometriotic epithelial cells, we show that more than half of ARID1A binding sites are marked by the variant histone H3.3, including active regulatory elements such as super-enhancers. ARID1A knockdown leads to H3.3 depletion and gain of canonical H3.1/3.2 at ARID1A-bound active regulatory elements, and a concomitant redistribution of H3.3 toward genic elements. ARID1A interactions with the repressive chromatin remodeler CHD4 (NuRD) are associated with H3.3, and ARID1A is required for CHD4 recruitment to H3.3. ZMYND8 interacts with CHD4 to suppress a subset of ARID1A, CHD4, and ZMYND8 co-bound, H3.3+ H4K16ac+ super-enhancers near genes governing extracellular matrix, motility, adhesion, and epithelial-to-mesenchymal transition. Moreover, these gene expression alterations are observed in human endometriomas.
    CONCLUSIONS: These studies demonstrate that ARID1A-containing BAF complexes are required for maintenance of the histone variant H3.3 at active regulatory elements, such as super-enhancers, and this function is required for the physiologically relevant activities of alternative chromatin remodelers.
    Keywords:  ARID1A; Chromatin; Endometrioma; Endometrium; Gene expression; H3.3; NuRD; Remodeling; SWI/SNF; Variant histone
    DOI:  https://doi.org/10.1186/s12915-022-01407-y
  2. Cell. 2022 Sep 29. pii: S0092-8674(22)01128-X. [Epub ahead of print]185(20): 3689-3704.e21
    Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.
    Alessa R Ringel, Quentin Szabo, Andrea M Chiariello, Konrad Chudzik, Robert Schöpflin, Patricia Rothe, Alexandra L Mattei, Tobias Zehnder, Dermot Harnett, Verena Laupert, Simona Bianco, Sara Hetzel, Juliane Glaser, Mai H Q Phan, Magdalena Schindler, Daniel M Ibrahim, Christina Paliou, Andrea Esposito, Cesar A Prada-Medina, Stefan A Haas, Peter Giere, Martin Vingron, Lars Wittler, Alexander Meissner, Mario Nicodemi, Giacomo Cavalli, Frédéric Bantignies, Stefan Mundlos, Michael I Robson.
      Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
    Keywords:  3D genome organization; CTCF; DNA methylation; cohesin; developmental gene regulation; enhancer-promoter specificity; evolution; lamina-associated domain; loop extrusion; topologically associating domains
    DOI:  https://doi.org/10.1016/j.cell.2022.09.006
  3. Nucleic Acids Res. 2022 Sep 27. pii: gkac795. [Epub ahead of print]
    CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.
    Jiankang Wang, Ryuichiro Nakato.
      Cohesin is a multifunctional protein responsible for transcriptional regulation and chromatin organization. Cohesin binds to chromatin at tens of thousands of distinct sites in a conserved or tissue-specific manner, whereas the function of cohesin varies greatly depending on the epigenetic properties of specific chromatin loci. Cohesin also extensively mediates cis-regulatory modules (CRMs) and chromatin loops. Even though next-generation sequencing technologies have provided a wealth of information on different aspects of cohesin, the integration and exploration of the resultant massive cohesin datasets are not straightforward. Here, we present CohesinDB (https://cohesindb.iqb.u-tokyo.ac.jp), a comprehensive multiomics cohesin database in human cells. CohesinDB includes 2043 epigenomics, transcriptomics and 3D genomics datasets from 530 studies involving 176 cell types. By integrating these large-scale data, CohesinDB summarizes three types of 'cohesin objects': 751 590 cohesin binding sites, 957 868 cohesin-related chromatin loops and 2 229 500 cohesin-related CRMs. Each cohesin object is annotated with locus, cell type, classification, function, 3D genomics and cis-regulatory information. CohesinDB features a user-friendly interface for browsing, searching, analyzing, visualizing and downloading the desired information. CohesinDB contributes a valuable resource for all researchers studying cohesin, epigenomics, transcriptional regulation and chromatin organization.
    DOI:  https://doi.org/10.1093/nar/gkac795
  4. Proc Natl Acad Sci U S A. 2022 Oct 04. 119(40): e2206450119
    Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC.
    Honggui Wu, Xiang Li, Fanchong Jian, Ayijiang Yisimayi, Yinghui Zheng, Longzhi Tan, Dong Xing, X Sunney Xie.
      Recent advances in single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) and its coassays have transformed the field of single-cell epigenomics and transcriptomics. However, the low detection efficiency of current methods has limited our understanding of the true complexity of chromatin accessibility and its relationship with gene expression in single cells. Here, we report a high-sensitivity scATAC-seq method, termed multiplexed end-tagging amplification of transposase accessible chromatin (METATAC), which detects a large number of accessible sites per cell and is compatible with automation. Our high detectability and statistical framework allowed precise linking of enhancers to promoters without merging single cells. We systematically investigated allele-specific accessibility in the mouse cerebral cortex, revealing allele-specific accessibility of promotors of certain imprinted genes but biallelic accessibility of their enhancers. Finally, we combined METATAC with our high-sensitivity single-cell RNA sequencing (scRNA-seq) method, multiple annealing and looping based amplification cycles for digital transcriptomics (MALBAC-DT), to develop a joint ATAC-RNA assay, termed METATAC and MALBAC-DT coassay by sequencing (M2C-seq). M2C-seq achieved significant improvements for both ATAC and RNA compared with previous methods, with consistent performance across cell lines and early mouse embryos.
    Keywords:  coaccessibility; imprinted gene; joint ATAC–RNA; scATAC-seq
    DOI:  https://doi.org/10.1073/pnas.2206450119
  5. Genome Biol. 2022 Sep 26. 23(1): 202
    Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis.
    Stephen J Clark, Ricard Argelaguet, Tim Lohoff, Felix Krueger, Deborah Drage, Berthold Göttgens, John C Marioni, Jennifer Nichols, Wolf Reik.
       BACKGROUND: Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood.
    RESULTS: Here we report a single-cell transcriptomic atlas from Dnmt and Tet mutant mouse embryos during early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos.
    CONCLUSIONS: This study provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at a whole organism scale and affords new insights into the regulatory mechanisms of cell fate decisions.
    DOI:  https://doi.org/10.1186/s13059-022-02762-3
  6. Nat Commun. 2022 Sep 28. 13(1): 5703
    The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors.
    Hui Wang, Boyuan Li, Linyu Zuo, Bo Wang, Yan Yan, Kai Tian, Rong Zhou, Chenlu Wang, Xizi Chen, Yongpeng Jiang, Haonan Zheng, Fangfei Qin, Bin Zhang, Yang Yu, Chao-Pei Liu, Yanhui Xu, Juntao Gao, Zhi Qi, Wulan Deng, Xiong Ji.
      RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional clusters. Whether protein factors control these clusters remains unknown. In this study, we find that the ATPase-associated with diverse cellular activities (AAA + ) ATPase RUVBL2 co-occupies promoters with Pol II and various transcription factors. RUVBL2 interacts with unphosphorylated Pol II in chromatin to promote RPB1 carboxy-terminal domain (CTD) clustering and transcription initiation. Rapid depletion of RUVBL2 leads to a decrease in the number of Pol II clusters and inhibits nascent RNA synthesis, and tethering RUVBL2 to an active promoter enhances Pol II clustering at the promoter. We also identify target genes that are directly linked to the RUVBL2-Pol II axis. Many of these genes are hallmarks of cancers and encode proteins with diverse cellular functions. Our results demonstrate an emerging activity for RUVBL2 in regulating Pol II cluster formation in the nucleus.
    DOI:  https://doi.org/10.1038/s41467-022-33433-3
  7. Proc Natl Acad Sci U S A. 2022 Oct 04. 119(40): e2208935119
    Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses.
    Christopher M Uyehara, Mary Leatham-Jensen, Daniel J McKay.
      Steroid hormones perform diverse biological functions in developing and adult animals. However, the mechanistic basis for their tissue specificity remains unclear. In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its nuclear receptor, a heterodimer of the EcR and ultraspiracle proteins. Ligand binding to EcR triggers a transcriptional cascade, including activation of a set of primary response transcription factors. The hierarchical organization of this pathway has left the direct role of EcR in mediating ecdysone responses obscured. Here, we investigate the role of EcR in controlling tissue-specific ecdysone responses, focusing on two tissues that diverge in their response to rising ecdysone titers: the larval salivary gland, which undergoes programmed destruction, and the wing imaginal disc, which initiates morphogenesis. We find that EcR functions bimodally, with both gene repressive and activating functions, even at the same developmental stage. EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. Finally, despite a strong correlation between tissue-specific EcR binding and tissue-specific open chromatin, we find that EcR does not control chromatin accessibility at genomic targets. We conclude that EcR contributes extensively to tissue-specific ecdysone responses. However, control over access to its binding sites is subordinated to other transcription factors.
    Keywords:  chromatin accessibility; hormone; nuclear receptor
    DOI:  https://doi.org/10.1073/pnas.2208935119
  8. Nucleic Acids Res. 2022 Sep 26. pii: gkac800. [Epub ahead of print]
    PRC2-indepdendent actions of H3.3K27M in embryonic stem cell differentiation.
    Lea R Z Cohen, Binyamin Kaffe, Eden Deri, Chen Leibson, Malka Nissim-Rafinia, Moria Maman, Nofar Harpaz, Guy Ron, Efrat Shema, Eran Meshorer.
      The histone H3 variant, H3.3, is localized at specific regions in the genome, especially promoters and active enhancers, and has been shown to play important roles in development. A lysine to methionine substitution in position 27 (H3.3K27M) is a main cause of Diffuse Intrinsic Pontine Glioma (specifically Diffuse Midline Glioma, K27M-mutant), a lethal type of pediatric cancer. H3.3K27M has a dominant-negative effect by inhibiting the Polycomb Repressor Complex 2 (PRC2) activity. Here, we studied the immediate, genome-wide, consequences of the H3.3K27M mutation independent of PRC2 activity. We developed Doxycycline (Dox)-inducible mouse embryonic stem cells (ESCs) carrying a single extra copy of WT-H3.3, H3.3K27M and H3.3K27L, all fused to HA. We performed RNA-Seq and ChIP-Seq at different times following Dox induction in undifferentiated and differentiated ESCs. We find increased binding of H3.3 around transcription start sites in cells expressing both H3.3K27M and H3.3K27L compared with WT, but not in cells treated with PRC2 inhibitors. Differentiated cells carrying either H3.3K27M or H3.3K27L retain expression of ESC-active genes, in expense of expression of genes related to neuronal differentiation. Taken together, our data suggest that a modifiable H3.3K27 is required for proper histone incorporation and cellular maturation, independent of PRC2 activity.
    DOI:  https://doi.org/10.1093/nar/gkac800
  9. Commun Biol. 2022 Sep 29. 5(1): 1036
    Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis.
    Xuyang Wen, Tianyi Ding, Fang Li, Jiayan Fan, Xianqun Fan, Renbing Jia, He Zhang.
      RB transcriptional corepressor 1 (RB1) is a critical regulatory gene in physiological and pathological processes. Genetic mutation is considered to be the main cause of RB1 inactivation. However, accumulating evidence has shown that not all RB1 dysfunction is triggered by gene mutations, and the additional mechanism underlying RB1 dysfunction remains unclear. Here, we firstly reveal that a CCCTC binding factor (CTCF) mediated intrachromosomal looping served as a regulatory inducer to inactivate RB1. Once the core genomic fragment was deleted by Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9), this intrachromosomal looping was disrupted. After the open of chromatin, Enhancer of Zeste Homolog 2 (EZH2) was released and decreased the level of Tri-Methyl-Histone H3 Lys27 (H3K27me3) at the RB1 promoter, which substantially restored the expression of RB protein (pRB) and inhibited tumorigenesis. In addition, targeted correction of abnormal RB1 looping using the small-molecule compound GSK503 efficiently restored RB1 transcription and suppressed tumorigenesis. Our study reveals an alternative transcriptional mechanism underlying RB1 dysfunction independent of gene mutation, and advancing the discovery of potential therapeutic chemicals based on aberrant chromatin looping.
    DOI:  https://doi.org/10.1038/s42003-022-04007-2
  10. Nature. 2022 Sep;609(7929): 1038-1047
    A mechanism for oxidative damage repair at gene regulatory elements.
    Swagat Ray, Arwa A Abugable, Jacob Parker, Kirsty Liversidge, Nelma M Palminha, Chunyan Liao, Adelina E Acosta-Martin, Cleide D S Souza, Mateusz Jurga, Ian Sudbery, Sherif F El-Khamisy.
      Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
    DOI:  https://doi.org/10.1038/s41586-022-05217-8
  11. Nucleic Acids Res. 2022 Sep 26. pii: gkac819. [Epub ahead of print]
    Single-cell gene regulation network inference by large-scale data integration.
    Xin Dong, Ke Tang, Yunfan Xu, Hailin Wei, Tong Han, Chenfei Wang.
      Single-cell ATAC-seq (scATAC-seq) has proven to be a state-of-art approach to investigating gene regulation at the single-cell level. However, existing methods cannot precisely uncover cell-type-specific binding of transcription regulators (TRs) and construct gene regulation networks (GRNs) in single-cell. ChIP-seq has been widely used to profile TR binding sites in the past decades. Here, we developed SCRIP, an integrative method to infer single-cell TR activity and targets based on the integration of scATAC-seq and a large-scale TR ChIP-seq reference. Our method showed improved performance in evaluating TR binding activity compared to the existing motif-based methods and reached a higher consistency with matched TR expressions. Besides, our method enables identifying TR target genes as well as building GRNs at the single-cell resolution based on a regulatory potential model. We demonstrate SCRIP's utility in accurate cell-type clustering, lineage tracing, and inferring cell-type-specific GRNs in multiple biological systems. SCRIP is freely available at https://github.com/wanglabtongji/SCRIP.
    DOI:  https://doi.org/10.1093/nar/gkac819
  12. Proc Natl Acad Sci U S A. 2022 Oct 04. 119(40): e2204716119
    Super-enhancers conserved within placental mammals maintain stem cell pluripotency.
    Juqing Zhang, Yaqi Zhou, Wei Yue, Zhenshuo Zhu, Xiaolong Wu, Shuai Yu, Qiaoyan Shen, Qin Pan, Wenjing Xu, Rui Zhang, Xiaojie Wu, Xinmei Li, Yayu Li, Yunxiang Li, Yu Wang, Sha Peng, Shiqiang Zhang, Anmin Lei, Xinbao Ding, Fan Yang, Xingqi Chen, Na Li, Mingzhi Liao, Wei Wang, Jinlian Hua.
      Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.
    Keywords:  BRD4; evolution; pigs; pluripotency; super-enhancer
    DOI:  https://doi.org/10.1073/pnas.2204716119
  13. PLoS Comput Biol. 2022 Sep 26. 18(9): e1010116
    Systems-level identification of key transcription factors in immune cell specification.
    Cong Liu, Kyla Omilusik, Clara Toma, Nadia S Kurd, John T Chang, Ananda W Goldrath, Wei Wang.
      Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
    DOI:  https://doi.org/10.1371/journal.pcbi.1010116
  14. Nucleic Acids Res. 2022 Sep 26. pii: gkac796. [Epub ahead of print]
    Direct hOGG1-Myc interactions inhibit hOGG1 catalytic activity and recruit Myc to its promoters under oxidative stress.
    Disha M Bangalore, Ingrid Tessmer.
      The base excision repair (BER) glycosylase hOGG1 (human oxoguanine glycosylase 1) is responsible for repairing oxidative lesions in the genome, in particular oxidised guanine bases (oxoG). In addition, a role of hOGG1 in transcription regulation by recruitment of various transcription factors has been reported. Here, we demonstrate direct interactions between hOGG1 and the medically important oncogene transcription factor Myc that is involved in transcription initiation of a large number of genes including inflammatory genes. Using single molecule atomic force microscopy (AFM), we reveal recruitment of Myc to its E-box promoter recognition sequence by hOGG1 specifically under oxidative stress conditions, and conformational changes in hOGG1-Myc complexes at oxoG lesions that suggest loading of Myc at oxoG lesions by hOGG1. Importantly, our data show suppression of hOGG1 catalytic activity in oxoG repair by Myc. Furthermore, mutational analyses implicate the C28 residue in hOGG1 in oxidation induced protein dimerisation and suggest a role of hOGG1 dimerisation under oxidising conditions in hOGG1-Myc interactions. From our data we develop a mechanistic model for Myc recruitment by hOGG1 under oxidising, inflammatory conditions, which may be responsible for the observed enhanced gene expression of Myc target genes.
    DOI:  https://doi.org/10.1093/nar/gkac796
  15. Nat Commun. 2022 Sep 24. 13(1): 5609
    Human centromere repositioning activates transcription and opens chromatin fibre structure.
    Catherine Naughton, Covadonga Huidobro, Claudia R Catacchio, Adam Buckle, Graeme R Grimes, Ryu-Suke Nozawa, Stefania Purgato, Mariano Rocchi, Nick Gilbert.
      Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. Centromere repositioning is accompanied by RNA polymerase II recruitment and active transcription to form a decompacted, negatively supercoiled domain enriched in 'open' chromatin fibres. In contrast, centromerisation causes a spreading of repressive epigenetic marks to surrounding regions, delimited by H3K27me3 polycomb boundaries and divergent genes. This flanking domain is transcriptionally silent and partially remodelled to form 'compact' chromatin, similar to satellite-containing DNA sequences, and exhibits genomic instability. We suggest transcription disrupts chromatin to provide a foundation for kinetochore formation whilst compact pericentromeric heterochromatin generates mechanical rigidity.
    DOI:  https://doi.org/10.1038/s41467-022-33426-2
  16. Nat Neurosci. 2022 Sep 28.
    The three-dimensional landscape of cortical chromatin accessibility in Alzheimer's disease.
    Jaroslav Bendl, Mads E Hauberg, Kiran Girdhar, Eunju Im, James M Vicari, Samir Rahman, Michael B Fernando, Kayla G Townsley, Pengfei Dong, Ruth Misir, Steven P Kleopoulos, Sarah M Reach, Pasha Apontes, Biao Zeng, Wen Zhang, Georgios Voloudakis, Kristen J Brennand, Ralph A Nixon, Vahram Haroutunian, Gabriel E Hoffman, John F Fullard, Panos Roussos.
      To characterize the dysregulation of chromatin accessibility in Alzheimer's disease (AD), we generated 636 ATAC-seq libraries from neuronal and nonneuronal nuclei isolated from the superior temporal gyrus and entorhinal cortex of 153 AD cases and 56 controls. By analyzing a total of ~20 billion read pairs, we expanded the repertoire of known open chromatin regions (OCRs) in the human brain and identified cell-type-specific enhancer-promoter interactions. We show that interindividual variability in OCRs can be leveraged to identify cis-regulatory domains (CRDs) that capture the three-dimensional structure of the genome (3D genome). We identified AD-associated effects on chromatin accessibility, the 3D genome and transcription factor (TF) regulatory networks. For one of the most AD-perturbed TFs, USF2, we validated its regulatory effect on lysosomal genes. Overall, we applied a systematic approach to understanding the role of the 3D genome in AD. We provide all data as an online resource for widespread community-based analysis.
    DOI:  https://doi.org/10.1038/s41593-022-01166-7
  17. Nat Commun. 2022 Sep 29. 13(1): 5566
    Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
    Mary L Stackpole, Weihua Zeng, Shuo Li, Chun-Chi Liu, Yonggang Zhou, Shanshan He, Angela Yeh, Ziye Wang, Fengzhu Sun, Qingjiao Li, Zuyang Yuan, Asli Yildirim, Pin-Jung Chen, Paul Winograd, Benjamin Tran, Yi-Te Lee, Paul Shize Li, Zorawar Noor, Megumi Yokomizo, Preeti Ahuja, Yazhen Zhu, Hsian-Rong Tseng, James S Tomlinson, Edward Garon, Samuel French, Clara E Magyar, Sarah Dry, Clara Lajonchere, Daniel Geschwind, Gina Choi, Sammy Saab, Frank Alber, Wing Hung Wong, Steven M Dubinett, Denise R Aberle, Vatche Agopian, Steven-Huy B Han, Xiaohui Ni, Wenyuan Li, Xianghong Jasmine Zhou.
      Early cancer detection by cell-free DNA faces multiple challenges: low fraction of tumor cell-free DNA, molecular heterogeneity of cancer, and sample sizes that are not sufficient to reflect diverse patient populations. Here, we develop a cancer detection approach to address these challenges. It consists of an assay, cfMethyl-Seq, for cost-effective sequencing of the cell-free DNA methylome (with > 12-fold enrichment over whole genome bisulfite sequencing in CpG islands), and a computational method to extract methylation information and diagnose patients. Applying our approach to 408 colon, liver, lung, and stomach cancer patients and controls, at 97.9% specificity we achieve 80.7% and 74.5% sensitivity in detecting all-stage and early-stage cancer, and 89.1% and 85.0% accuracy for locating tissue-of-origin of all-stage and early-stage cancer, respectively. Our approach cost-effectively retains methylome profiles of cancer abnormalities, allowing us to learn new features and expand to other cancer types as training cohorts grow.
    DOI:  https://doi.org/10.1038/s41467-022-32995-6
  18. Cell Rep. 2022 Sep 27. pii: S2211-1247(22)01241-4. [Epub ahead of print]40(13): 111404
    FOXA1 regulates alternative splicing in prostate cancer.
    Marco Del Giudice, John G Foster, Serena Peirone, Alberto Rissone, Livia Caizzi, Federica Gaudino, Caterina Parlato, Francesca Anselmi, Rebecca Arkell, Simonetta Guarrera, Salvatore Oliviero, Giuseppe Basso, Prabhakar Rajan, Matteo Cereda.
      Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1. By controlling trans-acting factor expression, FOXA1 exploits an "exon definition" mechanism calibrating alternative splicing toward dominant isoform production. This regulation especially impacts splicing factors themselves and leads to a reduction of nonsense-mediated decay (NMD)-targeted isoforms. Inclusion of the NMD-determinant FLNA exon 30 by FOXA1-controlled oncogene SRSF1 promotes cell growth in vitro and predicts disease recurrence. Overall, we report a role for FOXA1 in rewiring the alternative splicing landscape in prostate cancer through a cascade of events from chromatin access, to splicing factor regulation, and, finally, to alternative splicing of exons influencing patient survival.
    Keywords:  CP: Cancer; CP: Molecular biology; FLNA; FOXA1; HNRNPK; SRSF1; alternative splicing; biomarkers; nonsense-mediated decay; poison exons; prostate cancer; splicing factors
    DOI:  https://doi.org/10.1016/j.celrep.2022.111404
  19. Nat Genet. 2022 Sep 26.
    Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements.
    Lovelace J Luquette, Michael B Miller, Zinan Zhou, Craig L Bohrson, Yifan Zhao, Hu Jin, Doga Gulhan, Javier Ganz, Sara Bizzotto, Samantha Kirkham, Tino Hochepied, Claude Libert, Alon Galor, Junho Kim, Michael A Lodato, Juan I Garaycoechea, Charles Gawad, Jay West, Christopher A Walsh, Peter J Park.
      Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.
    DOI:  https://doi.org/10.1038/s41588-022-01180-2
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