bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–10–11
thirty-six papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency.
  2. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa.
  3. Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells.
  4. Genome-wide chromatin accessibility is restricted by ANP32E.
  5. Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells.
  6. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble.
  7. Active turnover of DNA methylation during cell fate decisions.
  8. Kctd15 regulates nephron segment development by repressing Tfap2a activity.
  9. Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes.
  10. An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.
  11. A small UTX stabilization domain of Trr is conserved within mammalian MLL3-4/COMPASS and is sufficient to rescue loss of viability in null animals.
  12. Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns.
  13. An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation.
  14. Transcription Factor RBPJ as a Molecular Switch in Regulating the Notch Response.
  15. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.
  16. The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells.
  17. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure.
  18. EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes.
  19. GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
  20. Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers.
  21. AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma.
  22. c-Myc inactivation of p53 through the pan-cancer lncRNA MILIP drives cancer pathogenesis.
  23. Zebrafish hif-3α modulates erythropoiesis via regulation of gata-1 to facilitate hypoxia tolerance.
  24. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.
  25. A STAT3 palmitoylation cycle promotes TH17 differentiation and colitis.
  26. Identification of a dynamic gene regulatory network required for pluripotency factor-induced reprogramming of mouse fibroblasts and hepatocytes.
  27. FACT and Ash1 promote long-range and bidirectional nucleosome eviction at the HO promoter.
  28. RUNX1 marks a luminal castration resistant lineage established at the onset of prostate development.
  29. SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation.
  30. Phenotypic landscape of intestinal organoid regeneration.
  31. The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure.
  32. METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA.
  33. Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors.
  34. The ETS-transcription factor Pointed is sufficient to regulate the posterior fate of the follicular epithelium.
  35. Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans.
  36. HIF-2α is indispensable for regulatory T cell function.
  1. Nat Commun. 2020 10 08. 11(1): 5061
    JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency.
    Yinghua Huang, Hui Zhang, Lulu Wang, Chuanqing Tang, Xiaogan Qin, Xinyu Wu, Meifang Pan, Yujia Tang, Zhongzhou Yang, Isaac A Babarinde, Runxia Lin, Guanyu Ji, Yiwei Lai, Xueting Xu, Jianbin Su, Xue Wen, Takashi Satoh, Tanveer Ahmed, Vikas Malik, Carl Ward, Giacomo Volpe, Lin Guo, Jinlong Chen, Li Sun, Yingying Li, Xiaofen Huang, Xichen Bao, Fei Gao, Baohua Liu, Hui Zheng, Ralf Jauch, Liangxue Lai, Guangjin Pan, Jiekai Chen, Giuseppe Testa, Shizuo Akira, Jifan Hu, Duanqing Pei, Andrew P Hutchins, Miguel A Esteban, Baoming Qin.
      The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles in mouse reprogramming. On one side, JMJD3 induces the pro-senescence factor Ink4a and degrades the pluripotency regulator PHF20 in a reprogramming factor-independent manner. On the other side, JMJD3 is specifically recruited by KLF4 to reduce H3K27me3 at both enhancers and promoters of epithelial and pluripotency genes. JMJD3 also promotes enhancer-promoter looping through the cohesin loading factor NIPBL and ultimately transcriptional elongation. This competition of forces can be shifted towards improved reprogramming by using early passage fibroblasts or boosting JMJD3's catalytic activity with vitamin C. Our work, thus, establishes a multifaceted role for JMJD3, placing it as a key partner of KLF4 and a scaffold that assists chromatin interactions and activates gene transcription.
    DOI:  https://doi.org/10.1038/s41467-020-18900-z
  2. Am J Hum Genet. 2020 Oct 05. pii: S0002-9297(20)30322-0. [Epub ahead of print]
    Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa.
    Suzanne E de Bruijn, Alessia Fiorentino, Daniele Ottaviani, Stephanie Fanucchi, Uirá S Melo, Julio C Corral-Serrano, Timo Mulders, Michalis Georgiou, Carlo Rivolta, Nikolas Pontikos, Gavin Arno, Lisa Roberts, Jacquie Greenberg, Silvia Albert, Christian Gilissen, Marco Aben, George Rebello, Simon Mead, F Lucy Raymond, Jordi Corominas, Claire E L Smith, Hannie Kremer, Susan Downes, Graeme C Black, Andrew R Webster, Chris F Inglehearn, L Ingeborgh van den Born, Robert K Koenekoop, Michel Michaelides, Raj S Ramesar, Carel B Hoyng, Stefan Mundlos, Musa M Mhlanga, Frans P M Cremers, Michael E Cheetham, Susanne Roosing, Alison J Hardcastle.
      The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.
    Keywords:  GDPD; Hi-C; RP17; dominant retinitis pigmentosa; ectopic expression; photoreceptor precursors cells; retinal organoids; stem cells; structural variants; topologically associated domains; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.ajhg.2020.09.002
  3. Nat Genet. 2020 Oct 05.
    Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells.
    Jesper G S Madsen, Maria S Madsen, Alexander Rauch, Sofie Traynor, Elvira L Van Hauwaert, Anders K Haakonsson, Biola M Javierre, Mette Hyldahl, Peter Fraser, Susanne Mandrup.
      Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the enhancer landscape and change the wiring of the promoter interactome. Here, we use high-throughput chromosome conformation enhancer capture to interrogate the role of enhancer-to-enhancer interactions during differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is dynamic during differentiation and coupled with changes in enhancer activity. Transcription factors (TFs) at baited enhancers amplify TF binding at target enhancers, a phenomenon we term cross-interaction stabilization of TFs. Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by the formation of three-dimensional enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that enhancer interactions play a key role in the regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome.
    DOI:  https://doi.org/10.1038/s41588-020-0709-z
  4. Nat Commun. 2020 10 08. 11(1): 5063
    Genome-wide chromatin accessibility is restricted by ANP32E.
    Kristin E Murphy, Fanju W Meng, Claire E Makowski, Patrick J Murphy.
      Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels.
    DOI:  https://doi.org/10.1038/s41467-020-18821-x
  5. Immunity. 2020 Sep 29. pii: S1074-7613(20)30402-7. [Epub ahead of print]
    Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells.
    Giuseppe Sciumè, Yohei Mikami, Dragana Jankovic, Hiroyuki Nagashima, Alejandro V Villarino, Tasha Morrison, Chen Yao, Sadie Signorella, Hong-Wei Sun, Stephen R Brooks, Difeng Fang, Vittorio Sartorelli, Shingo Nakayamada, Kiyoshi Hirahara, Beatrice Zitti, Fred P Davis, Yuka Kanno, John J O'Shea, Han-Yu Shih.
      Innate immune responses rely on rapid and precise gene regulation mediated by accessibility of regulatory regions to transcription factors (TFs). In natural killer (NK) cells and other innate lymphoid cells, competent enhancers are primed during lineage acquisition, and formation of de novo enhancers characterizes the acquisition of innate memory in activated NK cells and macrophages. Here, we investigated how primed and de novo enhancers coordinate to facilitate high-magnitude gene induction during acute activation. Epigenomic and transcriptomic analyses of regions near highly induced genes (HIGs) in NK cells both in vitro and in a model of Toxoplasma gondii infection revealed de novo chromatin accessibility and enhancer remodeling controlled by signal-regulated TFs STATs. Acute NK cell activation redeployed the lineage-determining TF T-bet to de novo enhancers, independent of DNA-sequence-specific motif recognition. Thus, acute stimulation reshapes enhancer function through the combinatorial usage and repurposing of both lineage-determining and signal-regulated TFs to ensure an effective response.
    Keywords:  T-bet; Toxoplasma Gondii infection; de novo enhancers; innate lymphoid cells; lineage defining transcription factors; natural killer cells; poised enhancers; signal regulated transcription factors; signal transducer and activator of transcription (STAT) protein; super-enhancers
    DOI:  https://doi.org/10.1016/j.immuni.2020.09.008
  6. Nat Neurosci. 2020 Oct 05.
    Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble.
    Asaf Marco, Hiruy S Meharena, Vishnu Dileep, Ravikiran M Raju, Jose Davila-Velderrain, Amy Letao Zhang, Chinnakkaruppan Adaikkan, Jennie Z Young, Fan Gao, Manolis Kellis, Li-Huei Tsai.
      The epigenome and three-dimensional (3D) genomic architecture are emerging as key factors in the dynamic regulation of different transcriptional programs required for neuronal functions. In this study, we used an activity-dependent tagging system in mice to determine the epigenetic state, 3D genome architecture and transcriptional landscape of engram cells over the lifespan of memory formation and recall. Our findings reveal that memory encoding leads to an epigenetic priming event, marked by increased accessibility of enhancers without the corresponding transcriptional changes. Memory consolidation subsequently results in spatial reorganization of large chromatin segments and promoter-enhancer interactions. Finally, with reactivation, engram neurons use a subset of de novo long-range interactions, where primed enhancers are brought in contact with their respective promoters to upregulate genes involved in local protein translation in synaptic compartments. Collectively, our work elucidates the comprehensive transcriptional and epigenomic landscape across the lifespan of memory formation and recall in the hippocampal engram ensemble.
    DOI:  https://doi.org/10.1038/s41593-020-00717-0
  7. Nat Rev Genet. 2020 Oct 06.
    Active turnover of DNA methylation during cell fate decisions.
    Aled Parry, Steffen Rulands, Wolf Reik.
      DNA methylation is a key layer of epigenetic regulation. The deposition of methylation marks relies on the catalytic activity of DNA methyltransferases (DNMTs), and their active removal relies on the activity of ten-eleven translocation (TET) enzymes. Paradoxically, in important biological contexts these antagonistic factors are co-expressed and target overlapping genomic regions. The ensuing cyclic biochemistry of cytosine modifications gives rise to a continuous, out-of-thermal equilibrium transition through different methylation states. But what is the purpose of this intriguing turnover of DNA methylation? Recent evidence demonstrates that methylation turnover is enriched at gene distal regulatory elements, including enhancers, and can give rise to large-scale oscillatory dynamics. We discuss this phenomenon and propose that DNA methylation turnover might facilitate key lineage decisions.
    DOI:  https://doi.org/10.1038/s41576-020-00287-8
  8. Development. 2020 Oct 07. pii: dev.191973. [Epub ahead of print]
    Kctd15 regulates nephron segment development by repressing Tfap2a activity.
    Brooke E Chambers, Eleanor G Clark, Allison E Gatz, Rebecca A Wingert.
      A functional vertebrate kidney relies on structural units called nephrons, which are epithelial tubules with a sequence of segments each expressing a distinct repertoire of solute transporters. The transcriptional codes driving regional specification, solute transporter program activation, and terminal differentiation of segment populations remain poorly understood. Here, we demonstrate that the KCTD15 paralogs, kctd15a and kctd15b, function in concert to restrict distal early (DE)/thick ascending limb (TAL) segment lineage assignment in the developing zebrafish pronephros by repressing Tfap2a activity. During renal ontogeny, expression of these factors co-localized with tfap2a in distal tubule precursors. kctd15 loss primed nephron cells to adopt distal fates by driving slc12a1, kcnj1a.1, and stc1 expression. These phenotypes were resultant of Tfap2a hyperactivity, where kctd15a/b-deficient embryos exhibited increased abundance of this transcription factor. Interestingly, tfap2a reciprocally promoted kctd15 transcription, unveiling a circuit of autoregulation operating in nephron progenitors. Concomitant kctd15b knockdown with tfap2a overexpression further expanded the DE population. Our study reveals that a transcription factor-repressor feedback module employs tight regulation of Tfap2a and Kctd15 kinetics to control nephron segment fate choice and differentiation during kidney development.
    Keywords:  Kctd15; Kidney; Nephron; Segmentation; Tfap2; Zebrafish
    DOI:  https://doi.org/10.1242/dev.191973
  9. Epigenetics Chromatin. 2020 Oct 07. 13(1): 41
    Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes.
    Parna Saha, Divya Tej Sowpati, Mamilla Soujanya, Ishanee Srivastava, Rakesh Kumar Mishra.
       BACKGROUND: Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression.
    RESULTS: Here, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes.
    CONCLUSIONS: Distinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.
    Keywords:  5C; Drosophila melanogaster; H3K9me3; HP1a; Het TADs; Heterochromatic genes; Pericentromeres; Su(var)3-9; dADD1; dMES-4
    DOI:  https://doi.org/10.1186/s13072-020-00358-4
  10. Nat Commun. 2020 Oct 09. 11(1): 5095
    An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.
    Carmen Navarro, Jing Lyu, Anna-Maria Katsori, Rozina Caridha, Simon J Elsässer.
      Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.
    DOI:  https://doi.org/10.1038/s41467-020-18863-1
  11. Genes Dev. 2020 Oct 08.
    A small UTX stabilization domain of Trr is conserved within mammalian MLL3-4/COMPASS and is sufficient to rescue loss of viability in null animals.
    Ryan Rickels, Lu Wang, Marta Iwanaszko, Patrick A Ozark, Marc A Morgan, Andrea Piunti, Natalia Khalatyan, Shimaa H A Soliman, Emily J Rendleman, Jeffrey N Savas, Edwin R Smith, Ali Shilatifard.
      Catalytic-inactivating mutations within the Drosophila enhancer H3K4 mono-methyltransferase Trr and its mammalian homologs, MLL3/4, cause only minor changes in gene expression compared with whole-gene deletions for these COMPASS members. To identify essential histone methyltransferase-independent functions of Trr, we screened to identify a minimal Trr domain sufficient to rescue Trr-null lethality and demonstrate that this domain binds and stabilizes Utx in vivo. Using the homologous MLL3/MLL4 human sequences, we mapped a short ∼80-amino-acid UTX stabilization domain (USD) that promotes UTX stability in the absence of the rest of MLL3/4. Nuclear UTX stability is enhanced when the USD is fused with the MLL4 HMG-box. Thus, COMPASS-dependent UTX stabilization is an essential noncatalytic function of Trr/MLL3/MLL4, suggesting that stabilizing UTX could be a therapeutic strategy for cancers with MLL3/4 loss-of-function mutations.
    Keywords:  COMPASS; chromatin; epigenetics; transcription
    DOI:  https://doi.org/10.1101/gad.339762.120
  12. Development. 2020 Oct 07. pii: dev.194761. [Epub ahead of print]
    Differential abilities to engage inaccessible chromatin diversify vertebrate HOX binding patterns.
    Milica Bulajić, Divyanshi Srivastava, Jeremy S Dasen, Hynek Wichterle, Shaun Mahony, Esteban O Mazzoni.
      While Hox genes encode for conserved transcription factors (TFs), they are further divided into anterior, central, and posterior groups based on their DNA-binding domain similarity. The posterior Hox group expanded in the deuterostome clade and patterns caudal and distal structures. We aim to address how similar HOX TFs diverge to induce different positional identities. We studied HOX TF DNA-binding and regulatory activity during an in vitro motor neuron differentiation system that recapitulates embryonic development. We find diversity in the genomic binding profiles of different HOX TFs, even among the posterior group paralogs that share similar DNA binding domains. These differences in genomic binding are explained by differing abilities to bind to previously inaccessible sites. For example, the posterior group HOXC9 has a greater ability to bind occluded sites than the posterior HOXC10, producing different binding patterns and driving differential gene expression programs. From these results, we propose that the differential abilities of posterior HOX TFs to bind to previously inaccessible chromatin drive patterning diversification.
    Keywords:  Binding; Chromatin; HOX; Patterning; Spinal cord; Stem cell differentiation
    DOI:  https://doi.org/10.1242/dev.194761
  13. Genome Res. 2020 Oct 05.
    An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation.
    Andrew M Lerner, Austin J Hepperla, Gregory R Keele, Hashem A Meriesh, Hayretin Yumerefendi, David Restrepo, Seth Zimmerman, James E Bear, Brian Kuhlman, Ian J Davis, Brian D Strahl.
      Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light-activated nuclear shuttle (LANS) domain. Light activation resulted in efficient Set2-LANS nuclear localization followed by H3K36me3 deposition in vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes showed disparate levels of H3K36 methylation, relative rates of H3K36me3 accumulation were largely linear and consistent across genes, suggesting that H3K36me3 deposition occurs in a directed fashion on all transcribed genes regardless of their overall transcription frequency. Removal of H3K36me3 was highly dependent on the demethylase Rph1. However, the per-gene rate of H3K36me3 loss weakly correlated with RNA abundance and followed exponential decay, suggesting H3K36 demethylases act in a global, stochastic manner. Altogether, these data provide a detailed temporal view of H3K36 methylation and demethylation that suggests transcription-dependent and -independent mechanisms for H3K36me deposition and removal, respectively.
    DOI:  https://doi.org/10.1101/gr.264283.120
  14. Adv Exp Med Biol. 2021 ;1287 9-30
    Transcription Factor RBPJ as a Molecular Switch in Regulating the Notch Response.
    Benedetto Daniele Giaimo, Ellen K Gagliani, Rhett A Kovall, Tilman Borggrefe.
      The Notch signal transduction cascade requires cell-to-cell contact and results in the proteolytic processing of the Notch receptor and subsequent assembly of a transcriptional coactivator complex containing the Notch intracellular domain (NICD) and transcription factor RBPJ. In the absence of a Notch signal, RBPJ remains at Notch target genes and dampens transcriptional output. Like in other signaling pathways, RBPJ is able to switch from activation to repression by associating with corepressor complexes containing several chromatin-modifying enzymes. Here, we focus on the recent advances concerning RBPJ-corepressor functions, especially in regard to chromatin regulation. We put this into the context of one of the best-studied model systems for Notch, blood cell development. Alterations in the RBPJ-corepressor functions can contribute to the development of leukemia, especially in the case of acute myeloid leukemia (AML). The versatile role of transcription factor RBPJ in regulating pivotal target genes like c-MYC and HES1 may contribute to the better understanding of the development of leukemia.
    Keywords:  AML1/ETO; H2A.Z; KyoT2/FHL1C; L3MBTL3; Leukemia; Notch; SHARP; Tip60; p400
    DOI:  https://doi.org/10.1007/978-3-030-55031-8_2
  15. Cell Rep. 2020 Oct 06. pii: S2211-1247(20)31211-0. [Epub ahead of print]33(1): 108222
    Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.
    Ik Soo Kim, Jingyi Wu, Gilbert J Rahme, Sofia Battaglia, Atray Dixit, Elizabeth Gaskell, Huidong Chen, Luca Pinello, Bradley E Bernstein.
      Early developmental specification can be modeled by differentiating embryonic stem cells (ESCs) to embryoid bodies (EBs), a heterogeneous mixture of three germ layers. Here, we combine single-cell transcriptomics and genetic recording to characterize EB differentiation. We map transcriptional states along a time course and model cell fate trajectories and branchpoints as cells progress to distinct germ layers. To validate this inferential model, we propose an innovative inducible genetic recording technique that leverages recombination to generate cell-specific, timestamp barcodes in a narrow temporal window. We validate trajectory architecture and key branchpoints, including early specification of a primordial germ cell (PGC)-like lineage from preimplantation epiblast-like cells. We further identify a temporally defined role of DNA methylation in this PGC-epiblast decision. Our study provides a high-resolution lineage map for an organoid model of embryogenesis, insights into epigenetic determinants of fate specification, and a strategy for lineage mapping of rapid differentiation processes.
    Keywords:  differentiation; embryogenesis; lineage tracing; single-cell RNA sequencing; stem cells
    DOI:  https://doi.org/10.1016/j.celrep.2020.108222
  16. Cancer Discov. 2020 Oct 06. pii: CD-20-0331. [Epub ahead of print]
    The RNA m6A reader YTHDF2 maintains oncogene expression and is a targetable dependency in glioblastoma stem cells.
    Deobrat Dixit, Briana C Prager, Ryan C Gimple, Hui Xian Poh, Yang Wang, Qiulian Wu, Zhixin Qiu, Reilly L Kidwell, Leo J Y Kim, Qi Xie, Kristoffer Vitting-Seerup, Shruti Bhargava, Zhen Dong, Li Jiang, Zhe Zhu, Petra Hamerlik, Samie R Jaffrey, Jing Crystal Zhao, Xiuxing Wang, Jeremy N Rich.
      Glioblastoma is a universally lethal cancer driven by glioblastoma stem cells (GSCs). Here, we interrogated N6-methyladenosine (m6A) mRNA modifications in GSCs by methyl RNA-immunoprecipitation followed by sequencing (meRIP-seq) and transcriptome analysis, finding transcripts marked by m6A often upregulated compared to normal neural stem cells (NSCs). Interrogating m6A regulators, GSCs displayed preferential expression, as well as in vitro and in vivo dependency, of the m6A reader, YTHDF2, in contrast to NSCs. While YTHDF2 has been reported to destabilize mRNAs, YTHDF2 stabilized MYC and VEGFA transcripts in GSCs in an m6A-dependent manner. We identified IGFBP3 as a downstream effector of the YTHDF2-MYC axis in GSCs. The IGF1/IGF1R inhibitor, linsitinib, preferentially targeted YTHDF2-expressing cells, inhibiting GSC viability without affecting NSCs and impairing in vivo glioblastoma growth. Thus, YTHDF2 links RNA epitranscriptomic modifications and GSC growth, laying the foundation for the YTHDF2-MYC-IGFBP3 axis as a specific and novel therapeutic target in glioblastoma.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0331
  17. Nat Genet. 2020 Oct 05.
    Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure.
    Kadir C Akdemir, Victoria T Le, Justin M Kim, Sarah Killcoyne, Devin A King, Ya-Ping Lin, Yanyan Tian, Akira Inoue, Samirkumar B Amin, Frederick S Robinson, Manjunath Nimmakayalu, Rafael E Herrera, Erica J Lynn, Kin Chan, Sahil Seth, Leszek J Klimczak, Moritz Gerstung, Dmitry A Gordenin, John O'Brien, Lei Li, Yonathan Lissanu Deribe, Roel G Verhaak, Peter J Campbell, Rebecca Fitzgerald, Ashby J Morrison, Jesse R Dixon, P Andrew Futreal.
      Somatic mutations in driver genes may ultimately lead to the development of cancer. Understanding how somatic mutations accumulate in cancer genomes and the underlying factors that generate somatic mutations is therefore crucial for developing novel therapeutic strategies. To understand the interplay between spatial genome organization and specific mutational processes, we studied 3,000 tumor-normal-pair whole-genome datasets from 42 different human cancer types. Our analyses reveal that the change in somatic mutational load in cancer genomes is co-localized with topologically-associating-domain boundaries. Domain boundaries constitute a better proxy to track mutational load change than replication timing measurements. We show that different mutational processes lead to distinct somatic mutation distributions where certain processes generate mutations in active domains, and others generate mutations in inactive domains. Overall, the interplay between three-dimensional genome organization and active mutational processes has a substantial influence on the large-scale mutation-rate variations observed in human cancers.
    DOI:  https://doi.org/10.1038/s41588-020-0708-0
  18. Front Genet. 2020 ;11 566569
    EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes.
    Sangrea Shim, Pil Joon Seo.
      EAT-UpTF (Enrichment Analysis Tool for Upstream Transcription Factors of a group of plant genes) is an open-source Python script that analyzes the enrichment of upstream transcription factors (TFs) in a group of genes-of-interest (GOIs). EAT-UpTF utilizes genome-wide lists of TF-target genes generated by DNA affinity purification followed by sequencing (DAP-seq) or chromatin immunoprecipitation followed by sequencing (ChIP-seq). Unlike previous methods based on the two-step prediction of cis-motifs and DNA-element-binding TFs, our EAT-UpTF analysis enabled a one-step identification of enriched upstream TFs in a set of GOIs using lists of empirically determined TF-target genes. The tool is designed particularly for plant researches, due to the lack of analytic tools for upstream TF enrichment, and available at https://github.com/sangreashim/EAT-UpTF and http://chromatindynamics.snu.ac.kr:8080/EatupTF.
    Keywords:  Arabidopsis; DAP-seq; cis-elements; plant; transcription factor
    DOI:  https://doi.org/10.3389/fgene.2020.566569
  19. BMC Bioinformatics. 2020 Oct 07. 21(1): 443
    GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
    Ewoud Ewing, Nuria Planell-Picola, Maja Jagodic, David Gomez-Cabrero.
       BACKGROUND: Gene-set analysis tools, which make use of curated sets of molecules grouped based on their shared functions, aim to identify which gene-sets are over-represented in the set of features that have been associated with a given trait of interest. Such tools are frequently used in gene-centric approaches derived from RNA-sequencing or microarrays such as Ingenuity or GSEA, but they have also been adapted for interval-based analysis derived from DNA methylation or ChIP/ATAC-sequencing. Gene-set analysis tools return, as a result, a list of significant gene-sets. However, while these results are useful for the researcher in the identification of major biological insights, they may be complex to interpret because many gene-sets have largely overlapping gene contents. Additionally, in many cases the result of gene-set analysis consists of a large number of gene-sets making it complicated to identify the major biological insights.
    RESULTS: We present GeneSetCluster, a novel approach which allows clustering of identified gene-sets, from one or multiple experiments and/or tools, based on shared genes. GeneSetCluster calculates a distance score based on overlapping gene content, which is then used to cluster them together and as a result, GeneSetCluster identifies groups of gene-sets with similar gene-set definitions (i.e. gene content). These groups of gene-sets can aid the researcher to focus on such groups for biological interpretations.
    CONCLUSIONS: GeneSetCluster is a novel approach for grouping together post gene-set analysis results based on overlapping gene content. GeneSetCluster is implemented as a package in R. The package and the vignette can be downloaded at https://github.com/TranslationalBioinformaticsUnit.
    Keywords:  Clustering gene-sets; Clustering pathways; Data-mining; Gene-set enrichment; Overlapping pathways
    DOI:  https://doi.org/10.1186/s12859-020-03784-z
  20. Nat Commun. 2020 Oct 09. 11(1): 5102
    Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers.
    Matthieu Dos Santos, Stéphanie Backer, Benjamin Saintpierre, Brigitte Izac, Muriel Andrieu, Franck Letourneur, Frederic Relaix, Athanassia Sotiropoulos, Pascal Maire.
      Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. Here we show by snRNA-seq and snATAC-seq that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we show that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential panel of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a previously undefined mechanism of coordination of gene expression in a syncytium.
    DOI:  https://doi.org/10.1038/s41467-020-18789-8
  21. Nat Commun. 2020 10 08. 11(1): 5079
    AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma.
    Catherine D Yao, Daniel Haensel, Sadhana Gaddam, Tiffany Patel, Scott X Atwood, Kavita Y Sarin, Ramon J Whitson, Siegen McKellar, Gautam Shankar, Sumaira Aasi, Kerri Rieger, Anthony E Oro.
      Tumor heterogeneity and lack of knowledge about resistant cell states remain a barrier to targeted cancer therapies. Basal cell carcinomas (BCCs) depend on Hedgehog (Hh)/Gli signaling, but can develop mechanisms of Smoothened (SMO) inhibitor resistance. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies noncanonical Gli1 activity, but characteristics and drivers of the nMRTF cell state remain unknown. Here, we use single cell RNA-sequencing of patient tumors to identify three prognostic surface markers (LYPD3, TACSTD2, and LY6D) which correlate with nMRTF and resistance to SMO inhibitors. The nMRTF cell state resembles transit-amplifying cells of the hair follicle matrix, with AP-1 and TGFß cooperativity driving nMRTF activation. JNK/AP-1 signaling commissions chromatin accessibility and Smad3 DNA binding leading to a transcriptional program of RhoGEFs that facilitate nMRTF activity. Importantly, small molecule AP-1 inhibitors selectively target LYPD3+/TACSTD2+/LY6D+ nMRTF human BCCs ex vivo, opening an avenue for improving combinatorial therapies.
    DOI:  https://doi.org/10.1038/s41467-020-18762-5
  22. Nat Commun. 2020 10 05. 11(1): 4980
    c-Myc inactivation of p53 through the pan-cancer lncRNA MILIP drives cancer pathogenesis.
    Yu Chen Feng, Xiao Ying Liu, Liu Teng, Qiang Ji, Yongyan Wu, Jin Ming Li, Wei Gao, Yuan Yuan Zhang, Ting La, Hessam Tabatabaee, Xu Guang Yan, M Fairuz B Jamaluddin, Didi Zhang, Su Tang Guo, Rodney J Scott, Tao Liu, Rick F Thorne, Xu Dong Zhang, Lei Jin.
      The functions of the proto-oncoprotein c-Myc and the tumor suppressor p53 in controlling cell survival and proliferation are inextricably linked as "Yin and Yang" partners in normal cells to maintain tissue homeostasis: c-Myc induces the expression of ARF tumor suppressor (p14ARF in human and p19ARF in mouse) that binds to and inhibits mouse double minute 2 homolog (MDM2) leading to p53 activation, whereas p53 suppresses c-Myc through a combination of mechanisms involving transcriptional inactivation and microRNA-mediated repression. Nonetheless, the regulatory interactions between c-Myc and p53 are not retained by cancer cells as is evident from the often-imbalanced expression of c-Myc over wildtype p53. Although p53 repression in cancer cells is frequently associated with the loss of ARF, we disclose here an alternate mechanism whereby c-Myc inactivates p53 through the actions of the c-Myc-Inducible Long noncoding RNA Inactivating P53 (MILIP). MILIP functions to promote p53 polyubiquitination and turnover by reducing p53 SUMOylation through suppressing tripartite-motif family-like 2 (TRIML2). MILIP upregulation is observed amongst diverse cancer types and is shown to support cell survival, division and tumourigenicity. Thus our results uncover an inhibitory axis targeting p53 through a pan-cancer expressed RNA accomplice that links c-Myc to suppression of p53.
    DOI:  https://doi.org/10.1038/s41467-020-18735-8
  23. Development. 2020 Oct 09. pii: dev.185116. [Epub ahead of print]
    Zebrafish hif-3α modulates erythropoiesis via regulation of gata-1 to facilitate hypoxia tolerance.
    Xiaolian Cai, Ziwen Zhou, Junji Zhu, Qian Liao, Dawei Zhang, Xing Liu, Jing Wang, Gang Ouyang, Wuhan Xiao.
      The hypoxia-inducible factors 1α and 2α (HIF-1α and HIF-2α) are master regulators of the cellular response to O2. In addition to HIF-1α and HIF-2α, HIF-3α is another identified member of the HIF-α gene family. Even though whether some HIF-3α isoforms have transcriptional activity or repressive activity is still under debate, it is evident that the full length of HIF-3α acts as a transcription factor. However, its function in hypoxia signaling is largely unknown. Here, we showed that loss of hif-3α in zebrafish reduced hypoxia tolerance. Further assays indicated that erythrocyte number was decreased because red blood cell maturation was impeded by hif-3α disruption. We found that gata-1 expression was downregulated in hif-3α-null zebrafish, as were several hematopoietic marker genes, including alas2, band3, hbae1, hbae3 and hbbe1 hif-3α recognized the hypoxia response element (HRE) located in the promoter of gata-1 and directly bound to the promoter to transactivate gata-1 expression. Our results suggested that hif-3α facilities hypoxia tolerance by modulating erythropoiesis via gata-1 regulation.
    Keywords:  Erythropoiesis; Gata-1; Hif-3α; Hypoxia; Zebrafish
    DOI:  https://doi.org/10.1242/dev.185116
  24. Science. 2020 Oct 09. 370(6513): 208-214
    The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.
    Francisca M Real, Stefan A Haas, Paolo Franchini, Peiwen Xiong, Oleg Simakov, Heiner Kuhl, Robert Schöpflin, David Heller, M-Hossein Moeinzadeh, Verena Heinrich, Thomas Krannich, Annkatrin Bressin, Michaela F Hartmann, Stefan A Wudy, Dina K N Dechmann, Alicia Hurtado, Francisco J Barrionuevo, Magdalena Schindler, Izabela Harabula, Marco Osterwalder, Michael Hiller, Lars Wittler, Axel Visel, Bernd Timmermann, Axel Meyer, Martin Vingron, Rafael Jiménez, Stefan Mundlos, Darío G Lupiáñez.
      Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.
    DOI:  https://doi.org/10.1126/science.aaz2582
  25. Nature. 2020 Oct 07.
    A STAT3 palmitoylation cycle promotes TH17 differentiation and colitis.
    Mingming Zhang, Lixing Zhou, Yuejie Xu, Min Yang, Yilai Xu, Garrison Paul Komaniecki, Tatsiana Kosciuk, Xiao Chen, Xuan Lu, Xiaoping Zou, Maurine E Linder, Hening Lin.
      Cysteine palmitoylation (S-palmitoylation) is a reversible post-translational modification that is installed by the DHHC family of palmitoyltransferases and is reversed by several acyl protein thioesterases1,2. Although thousands of human proteins are known to undergo S-palmitoylation, how this modification is regulated to modulate specific biological functions is poorly understood. Here we report that the key T helper 17 (TH17) cell differentiation stimulator, STAT33,4, is subject to reversible S-palmitoylation on cysteine 108. DHHC7 palmitoylates STAT3 and promotes its membrane recruitment and phosphorylation. Acyl protein thioesterase 2 (APT2, also known as LYPLA2) depalmitoylates phosphorylated STAT3 (p-STAT3) and enables it to translocate to the nucleus. This palmitoylation-depalmitoylation cycle enhances STAT3 activation and promotes TH17 cell differentiation; perturbation of either palmitoylation or depalmitoylation negatively affects TH17 cell differentiation. Overactivation of TH17 cells is associated with several inflammatory diseases, including inflammatory bowel disease (IBD). In a mouse model, pharmacological inhibition of APT2 or knockout of Zdhhc7-which encodes DHHC7-relieves the symptoms of IBD. Our study reveals not only a potential therapeutic strategy for the treatment of IBD but also a model through which S-palmitoylation regulates cell signalling, which might be broadly applicable for understanding the signalling functions of numerous S-palmitoylation events.
    DOI:  https://doi.org/10.1038/s41586-020-2799-2
  26. EMBO J. 2020 Oct 09. e102236
    Identification of a dynamic gene regulatory network required for pluripotency factor-induced reprogramming of mouse fibroblasts and hepatocytes.
    Maria Papathanasiou, Stefanos A Tsiftsoglou, Alexander P Polyzos, Deppie Papadopoulou, Dimitrios Valakos, Eleftheria Klagkou, Panagiota Karagianni, Maria Pliatska, Iannis Talianidis, Marios Agelopoulos, Dimitris Thanos.
      The generation of induced pluripotent stem cells (iPSCs) from somatic cells provides an excellent model to study mechanisms of transcription factor-induced global alterations of the epigenome and genome function. Here, we have investigated the early transcriptional events of cellular reprogramming triggered by the co-expression of Oct4, Sox2, Klf4, and c-Myc (OSKM) in mouse embryonic fibroblasts (MEFs) and mouse hepatocytes (mHeps). In this analysis, we identified a gene regulatory network composed of nine transcriptional regulators (9TR; Cbfa2t3, Gli2, Irf6, Nanog, Ovol1, Rcan1, Taf1c, Tead4, and Tfap4), which are directly targeted by OSKM, in vivo. Functional studies using single and double shRNA knockdowns of any of these factors caused disruption of the network and dramatic reductions in reprogramming efficiency, indicating that this network is essential for the induction and establishment of pluripotency. We demonstrate that the stochastic co-expression of 9TR network components occurs in a remarkably small number of cells, approximating the percentage of terminally reprogrammed cells as a result of dynamic molecular events. Thus, the early DNA-binding patterns of OSKM and the subsequent probabilistic co-expression of essential 9TR components in subpopulations of cells undergoing reprogramming steer the reconstruction of a gene regulatory network marking the transition to pluripotency.
    Keywords:  cellular reprogramming; gene regulatory networks; transcriptional regulators
    DOI:  https://doi.org/10.15252/embj.2019102236
  27. Nucleic Acids Res. 2020 Oct 03. pii: gkaa819. [Epub ahead of print]
    FACT and Ash1 promote long-range and bidirectional nucleosome eviction at the HO promoter.
    Yaxin Yu, Robert M Yarrington, David J Stillman.
      The Saccharomyces cerevisiae HO gene is a model regulatory system with complex transcriptional regulation. Budding yeast divide asymmetrically and HO is expressed only in mother cells where a nucleosome eviction cascade along the promoter during the cell cycle enables activation. HO expression in daughter cells is inhibited by high concentration of Ash1 in daughters. To understand how Ash1 represses transcription, we used a myo4 mutation which boosts Ash1 accumulation in both mothers and daughters and show that Ash1 inhibits promoter recruitment of SWI/SNF and Gcn5. We show Ash1 is also required for the efficient nucleosome repopulation that occurs after eviction, and the strongest effects of Ash1 are seen when Ash1 has been degraded and at promoter locations distant from where Ash1 bound. Additionally, we defined a specific nucleosome/nucleosome-depleted region structure that restricts HO activation to one of two paralogous DNA-binding factors. We also show that nucleosome eviction occurs bidirectionally over a large distance. Significantly, eviction of the more distant nucleosomes is dependent upon the FACT histone chaperone, and FACT is recruited to these regions when eviction is beginning. These last observations, along with ChIP experiments involving the SBF factor, suggest a long-distance loop transiently forms at the HO promoter.
    DOI:  https://doi.org/10.1093/nar/gkaa819
  28. Elife. 2020 Oct 07. pii: e60225. [Epub ahead of print]9
    RUNX1 marks a luminal castration resistant lineage established at the onset of prostate development.
    Renaud Mevel, Ivana Steiner, Susan Mason, Laura Ca Galbraith, Rahima Patel, Muhammad Zh Fadlullah, Imran Ahmad, Hing Y Leung, Pedro Oliveira, Karen Blyth, Esther Baena, Georges Lacaud.
      The characterization of prostate epithelial hierarchy and lineage heterogeneity is critical to understand its regenerative properties and malignancies. Here, we report that the transcription factor RUNX1 marks a specific subpopulation of proximal luminal cells (PLCs), enriched in the periurethral region of the developing and adult mouse prostate, and distinct from the previously identified NKX3.1+ luminal castration resistant cells. Using scRNA-seq profiling and genetic lineage tracing, we show that RUNX1+ PLCs are unaffected by androgen deprivation, and do not contribute to the regeneration of the distal luminal compartments. Furthermore, we demonstrate that a transcriptionally similar RUNX1+ population emerges at the onset of embryonic prostate specification to populate the proximal region of the ducts. Collectively, our results reveal that RUNX1+ PLCs is an intrinsic castration-resistant and self-sustained lineage that emerges early during prostate development and provide new insights into the lineage relationships of the prostate epithelium.
    Keywords:  developmental biology; mouse; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.60225
  29. NAR Genom Bioinform. 2020 Dec;2(4): lqaa077
    SIMPLEs: a single-cell RNA sequencing imputation strategy preserving gene modules and cell clusters variation.
    Zhirui Hu, Songpeng Zu, Jun S Liu.
      A main challenge in analyzing single-cell RNA sequencing (scRNA-seq) data is to reduce technical variations yet retain cell heterogeneity. Due to low mRNAs content per cell and molecule losses during the experiment (called 'dropout'), the gene expression matrix has a substantial amount of zero read counts. Existing imputation methods treat either each cell or each gene as independently and identically distributed, which oversimplifies the gene correlation and cell type structure. We propose a statistical model-based approach, called SIMPLEs (SIngle-cell RNA-seq iMPutation and celL clustErings), which iteratively identifies correlated gene modules and cell clusters and imputes dropouts customized for individual gene module and cell type. Simultaneously, it quantifies the uncertainty of imputation and cell clustering via multiple imputations. In simulations, SIMPLEs performed significantly better than prevailing scRNA-seq imputation methods according to various metrics. By applying SIMPLEs to several real datasets, we discovered gene modules that can further classify subtypes of cells. Our imputations successfully recovered the expression trends of marker genes in stem cell differentiation and can discover putative pathways regulating biological processes.
    DOI:  https://doi.org/10.1093/nargab/lqaa077
  30. Nature. 2020 Oct;586(7828): 275-280
    Phenotypic landscape of intestinal organoid regeneration.
    Ilya Lukonin, Denise Serra, Ludivine Challet Meylan, Katrin Volkmann, Janine Baaten, Rui Zhao, Shelly Meeusen, Karyn Colman, Francisca Maurer, Michael B Stadler, Jeremy Jenkins, Prisca Liberali.
      The development of intestinal organoids from single adult intestinal stem cells in vitro recapitulates the regenerative capacity of the intestinal epithelium1,2. Here we unravel the mechanisms that orchestrate both organoid formation and the regeneration of intestinal tissue, using an image-based screen to assay an annotated library of compounds. We generate multivariate feature profiles for hundreds of thousands of organoids to quantitatively describe their phenotypic landscape. We then use these phenotypic fingerprints to infer regulatory genetic interactions, establishing a new approach to the mapping of genetic interactions in an emergent system. This allows us to identify genes that regulate cell-fate transitions and maintain the balance between regeneration and homeostasis, unravelling previously unknown roles for several pathways, among them retinoic acid signalling. We then characterize a crucial role for retinoic acid nuclear receptors in controlling exit from the regenerative state and driving enterocyte differentiation. By combining quantitative imaging with RNA sequencing, we show the role of endogenous retinoic acid metabolism in initiating transcriptional programs that guide the cell-fate transitions of intestinal epithelium, and we identify an inhibitor of the retinoid X receptor that improves intestinal regeneration in vivo.
    DOI:  https://doi.org/10.1038/s41586-020-2776-9
  31. Gene. 2020 Oct 05. pii: S0378-1119(20)30874-X. [Epub ahead of print] 145205
    The ubiquitous transcriptional protein ZNF143 activates a diversity of genes while assisting to organize chromatin structure.
    Laura Huning, Gary R Kunkel.
      Zinc Finger Protein 143 (ZNF143) is a pervasive C2H2 zinc-finger transcriptional activator protein regulating the efficiency of eukaryotic promoter regions. ZNF143 is able to activate transcription at both protein coding genes and small RNA genes transcribed by either RNA polymerase II or RNA polymerase III. Target genes regulated by ZNF143 are involved in an array of different cellular processes including both cancer and development. Although a key player in regulating eukaryotic genes, the molecular mechanism by with ZNF143 binds and activates genes transcribed by two different polymerases is still relatively unknown. In addition to its role as a transcriptional regulator, recent genomics experiments have implicated ZNF143 as a potential co-factor involved in chromatin looping and establishing higher order structure within the genome. This review focuses primarily on possible activation mechanisms of promoters by ZNF143, with less emphasis on the role of ZNF143 in cancer and development, and its function in establishing higher order chromatin contacts within the genome.
    Keywords:  chromatin looping; eukaryotic transcriptional activation; gene regulation; transcription factors
    DOI:  https://doi.org/10.1016/j.gene.2020.145205
  32. Nucleic Acids Res. 2020 Oct 09. pii: gkaa816. [Epub ahead of print]
    METTL3 counteracts premature aging via m6A-dependent stabilization of MIS12 mRNA.
    Zeming Wu, Yue Shi, Mingming Lu, Moshi Song, Zihui Yu, Jilu Wang, Si Wang, Jie Ren, Yun-Gui Yang, Guang-Hui Liu, Weiqi Zhang, Weimin Ci, Jing Qu.
      N6-Methyladenosine (m6A) messenger RNA methylation is a well-known epitranscriptional regulatory mechanism affecting central biological processes, but its function in human cellular senescence remains uninvestigated. Here, we found that levels of both m6A RNA methylation and the methyltransferase METTL3 were reduced in prematurely senescent human mesenchymal stem cell (hMSC) models of progeroid syndromes. Transcriptional profiling of m6A modifications further identified MIS12, for which m6A modifications were reduced in both prematurely senescent hMSCs and METTL3-deficient hMSCs. Knockout of METTL3 accelerated hMSC senescence whereas overexpression of METTL3 rescued the senescent phenotypes. Mechanistically, loss of m6A modifications accelerated the turnover and decreased the expression of MIS12 mRNA while knockout of MIS12 accelerated cellular senescence. Furthermore, m6A reader IGF2BP2 was identified as a key player in recognizing and stabilizing m6A-modified MIS12 mRNA. Taken together, we discovered that METTL3 alleviates hMSC senescence through m6A modification-dependent stabilization of the MIS12 transcript, representing a novel epitranscriptional mechanism in premature stem cell senescence.
    DOI:  https://doi.org/10.1093/nar/gkaa816
  33. Nat Commun. 2020 Oct 09. 11(1): 5089
    Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors.
    Xiaoyu Tu, María Katherine Mejía-Guerra, Jose A Valdes Franco, David Tzeng, Po-Yu Chu, Wei Shen, Yingying Wei, Xiuru Dai, Pinghua Li, Edward S Buckler, Silin Zhong.
      The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.
    DOI:  https://doi.org/10.1038/s41467-020-18832-8
  34. Development. 2020 Oct 07. pii: dev.189787. [Epub ahead of print]
    The ETS-transcription factor Pointed is sufficient to regulate the posterior fate of the follicular epithelium.
    Cody A Stevens, Nicole T Revaitis, Rumkan Caur, Nir Yakoby.
      The Janus-kinase/Signal Transducers and Activators of Transcription (JAK/STAT) pathway regulates the anterior posterior axis of the Drosophila follicle cells. In the anterior, it activates the bone morphogenetic protein (BMP) signaling pathway through expression of the BMP ligand, decapentaplegic (dpp). In the posterior, JAK/STAT works with the epidermal growth factor receptor (EGFR) pathway to express the T-box transcription factor midline (mid). While MID is necessary in establishing the posterior fate of the egg chamber, we show that it is not sufficient to determine a posterior fate. The ETS-transcription factor pointed (pnt) is expressed in an overlapping domain to mid in the follicle cells. This study shows that pnt is upstream of mid, and it is sufficient to induce a posterior fate in the anterior end, which is characterized by the induction of mid, the prevention of the stretched cells formation, and the abrogation of border cells migration. We demonstrate that the anterior BMP signaling is abolished by PNT through dpp repression. However, ectopic DPP cannot rescue this repression, suggesting additional targets of PNT participate in the posterior fate determination.
    Keywords:  Anterior-posterior axis coordination; Cell morphogenesis; EGFR signaling; ETS-transcription factor
    DOI:  https://doi.org/10.1242/dev.189787
  35. Genetics. 2020 Oct 09. pii: genetics.303774.2020. [Epub ahead of print]
    Tissue-Specific Transcription Footprinting Using RNA PoI DamID (RAPID) in Caenorhabditis elegans.
    Georgina Gómez-Saldivar, Jaime Osuna-Luque, Jennifer I Semple, Dominique A Glauser, Sophie Jarriault, Peter Meister.
      Differential gene expression across cell types underlies the development and cell physiology in multicellular organisms. C. elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates, however, to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA Pol DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit in order to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, sorted embryonic blastomeres and in different tissues from intact young adults by driving Dam fusion expression tissue-specifically. We obtained meaningful transcriptional footprints in line with RNA-seq studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 2362 candidate genes with putatively active transcription in XXX cells, among which the few known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging.
    Keywords:  C. elegans; DNA methyltransferase identification; RNA polymerase footprinting; tissue-specific gene expression
    DOI:  https://doi.org/10.1534/genetics.120.303774
  36. Nat Commun. 2020 10 06. 11(1): 5005
    HIF-2α is indispensable for regulatory T cell function.
    Tzu-Sheng Hsu, Yen-Lin Lin, Yu-An Wang, Shu-Ting Mo, Po-Yu Chi, Alan Chuan-Ying Lai, Hsuan-Yin Pan, Ya-Jen Chang, Ming-Zong Lai.
      Hypoxia-inducible factor 1α (HIF-1α) and HIF-2α are master transcription factors that regulate cellular responses to hypoxia, but the exact function in regulatory T (Treg) cells is controversial. Here, we show that Treg cell development is normal in mice with Foxp3-specific knockout (KO) of HIF-1α or HIF-2α. However, HIF-2α-KO (but not HIF-1α-KO) Treg cells are functionally defective in suppressing effector T cell-induced colitis and inhibiting airway hypersensitivity. HIF-2α-KO Treg cells have enhanced reprogramming into IL-17-secreting cells. We show crosstalk between HIF-2α and HIF-1α, and that HIF-2α represses HIF-1α expression. HIF-1α is upregulated in HIF-2α-KO Treg cells and further deletion of HIF-1α restores the inhibitory function of HIF-2α-KO Treg cells. Mice with Foxp3-conditional KO of HIF-2α are resistant to growth of MC38 colon adenocarcinoma and metastases of B16F10 melanoma. Together, these results indicate that targeting HIF-2α to destabilize Treg cells might be an approach for regulating the functional activity of Treg cells.
    DOI:  https://doi.org/10.1038/s41467-020-18731-y
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