bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–08–28
twenty papers selected by
Connor Rogerson, University of Cambridge
  1. Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells.
  2. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress.
  3. ATRX histone binding and helicase activities have distinct roles in neuronal differentiation.
  4. NetTIME: a Multitask and Base-pair Resolution Framework for Improved Transcription Factor Binding Site Prediction.
  5. Partitioned usage of chromatin remodelers by nucleosome-displacing factors.
  6. Paternally inherited H3K27me3 affects chromatin accessibility in mouse embryos produced by round spermatid injection.
  7. SOX transcription factors direct TCF-independent WNT/β-catenin responsive transcription to govern cell fate in human pluripotent stem cells.
  8. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer.
  9. Mediator kinase regulates intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF.
  10. Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains.
  11. DAXX-ATRX regulation of p53 chromatin binding and DNA damage response.
  12. RORγt expression in mature TH17 cells safeguards their lineage specification by inhibiting conversion to TH2 cells.
  13. FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples.
  14. Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors.
  15. Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency.
  16. KLF5 governs sphingolipid metabolism and barrier function of the skin.
  17. Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster.
  18. DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.
  19. Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression.
  20. RAD51 protects human cells from transcription-replication conflicts.
  1. Elife. 2022 Aug 23. pii: e79675. [Epub ahead of print]11
    Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells.
    Jakke Neiro, Divya Sridhar, Anish Dattani, Aziz Aboobaker.
      Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed. Here, by integrating epigenetic and expression data we use multiple sources of evidence to predict enhancer elements active in the adult stem cell populations that drive regeneration. We have used ChIP-seq data to identify regions with histone modifications consistent with enhancer identity and activity, and ATAC-seq data to identify accessible chromatin. Overlapping these signals allowed for the identification of a set of high confidence candidate enhancers predicted to be active in planarian adult stem cells. These enhancers are enriched for predicted transcription factor (TF) binding sites for TFs and TF families expressed in planarian adult stem cells. Foot-printing analyses provided further evidence that these potential TF binding sites are potentially occupied in adult stem cells. We integrated these analyses to build testable hypotheses for the regulatory function of transcription factors in stem cells, both with respect to how pluripotency might be regulated, and to how lineage differentiation programs are controlled. We found that our predicted GRNs were independently supported by existing TF RNAi/RNA-seq data sets, providing further evidence that our work predicts active enhancers regulating adult stem cells and regenerative mechanisms.
    Keywords:  developmental biology; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.79675
  2. Nat Commun. 2022 Aug 23. 13(1): 4941
    KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress.
    Jan-Renier Moonen, James Chappell, Minyi Shi, Tsutomu Shinohara, Dan Li, Maxwell R Mumbach, Fan Zhang, Ramesh V Nair, Joseph Nasser, Daniel H Mai, Shalina Taylor, Lingli Wang, Ross J Metzger, Howard Y Chang, Jesse M Engreitz, Michael P Snyder, Marlene Rabinovitch.
      Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote the expression of homeostatic endothelial genes. By combining molecular and computational approaches we discover enhancers that loop to promoters of KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2, SMAD5, and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.
    DOI:  https://doi.org/10.1038/s41467-022-32566-9
  3. Nucleic Acids Res. 2022 Aug 24. pii: gkac683. [Epub ahead of print]
    ATRX histone binding and helicase activities have distinct roles in neuronal differentiation.
    Anna Bieluszewska, Phillip Wulfridge, John Doherty, Wenqing Ren, Kavitha Sarma.
      ATRX is a chromatin remodeler, which is mutated in ATRX syndrome, a neurodevelopmental disorder. ATRX mutations that alter histone binding or chromatin remodeling activities cluster in the PHD finger or the helicase domain respectively. Using engineered mouse embryonic stem cells that exclusively express ATRX protein with mutations in the PHD finger (PHDmut) or helicase domains (K1584R), we examine how specific ATRX mutations affect neurodifferentiation. ATRX PHDmut and K1584R proteins interact with the DAXX histone chaperone but show reduced localization to pericentromeres. Neurodifferentiation is both delayed and compromised in PHDmut and K1584R, and manifest differently from complete ATRX loss. We observe reduced enrichment of PHDmut protein to ATRX targets, while K1584R accumulates at these sites. Interestingly, ATRX mutations have distinct effects on the genome-wide localization of the polycomb repressive complex 2 (PRC2), with PHDmut and ATRX knockout showing reduced PRC2 binding at polycomb targets and K1584R showing loss at some sites and gains at others. Notably, each mutation associated with unique gene signatures, suggesting distinct pathways leading to impaired neurodifferentiation. Our results indicate that the histone binding and chromatin remodeling functions of ATRX play non-redundant roles in neurodevelopment, and when mutated lead to ATRX syndrome through separate regulatory pathways.
    DOI:  https://doi.org/10.1093/nar/gkac683
  4. Bioinformatics. 2022 Aug 23. pii: btac569. [Epub ahead of print]
    NetTIME: a Multitask and Base-pair Resolution Framework for Improved Transcription Factor Binding Site Prediction.
    Ren Yi, Kyunghyun Cho, Richard Bonneau.
       MOTIVATION: Machine learning models for predicting cell-type-specific transcription factor (TF) binding sites have become increasingly more accurate thanks to the increased availability of next-generation sequencing data and more standardized model evaluation criteria. However, knowledge transfer from data-rich to data-limited TFs and cell types remains crucial for improving TF binding prediction models because available binding labels are highly skewed towards a small collection of TFs and cell types. Transfer prediction of TF binding sites can potentially benefit from a multitask learning approach; however, existing methods typically use shallow single-task models to generate low-resolution predictions. Here we propose NetTIME, a multitask learning framework for predicting cell-type-specific transcription factor binding sites with base-pair resolution.
    RESULTS: We show that the multitask learning strategy for TF binding prediction is more efficient than the single-task approach due to the increased data availability. NetTIME trains high-dimensional embedding vectors to distinguish TF and cell-type identities. We show that this approach is critical for the success of the multitask learning strategy and allows our model to make accurate transfer predictions within and beyond the training panels of TFs and cell types. We additionally train a linear-chain conditional random field (CRF) to classify binding predictions and show that this CRF eliminates the need for setting a probability threshold and reduces classification noise. We compare our method's predictive performance with two state-of-the-art methods, Catchitt and Leopard, and show that our method outperforms previous methods under both supervised and transfer learning settings.
    AVAILABILITY: NetTIME is freely available at https://github.com/ryi06/NetTIME.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btac569
  5. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01068-3. [Epub ahead of print]40(8): 111250
    Partitioned usage of chromatin remodelers by nucleosome-displacing factors.
    Hengye Chen, Hungyo Kharerin, Archana Dhasarathy, Michael Kladde, Lu Bai.
      Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we design a high-throughput method to systematically study the interplay between NDFs and CRs. By combining an integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measure the impact of CRs on NDRs generated by individual NDFs. We find that CRs are dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity toward certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and NDR length-dependent manner. Overall, our study provides a framework to investigate how NDFs and CRs cooperate to regulate chromatin opening.
    Keywords:  CP: Molecular biology; binding specificity; chromatin opening; chromatin remodeler; nucleosome invasion; nucleosome positioning; nucleosome remodeling; nucleosome-depleted regions; nucleosome-displacing factor; pioneer factor; synthetic oligonucleotide library; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2022.111250
  6. Development. 2022 Aug 19. pii: dev.200696. [Epub ahead of print]
    Paternally inherited H3K27me3 affects chromatin accessibility in mouse embryos produced by round spermatid injection.
    Mizuki Sakamoto, Daiyu Ito, Rei Inoue, Sayaka Wakayama, Yasuyuki Kikuchi, Li Yang, Erika Hayashi, Rina Emura, Hirosuke Shiura, Takashi Kohda, Satoshi H Namekawa, Takashi Ishiuchi, Teruhiko Wakayama, Masatoshi Ooga.
      Round spermatid injection (ROSI) results in a lower birth rate than intracytoplasmic sperm injection, which has hampered its clinical application. Inefficient development of ROSI-embryos has been attributed to epigenetic abnormalities. However, the chromatin-based mechanism that underpins the low birth rate in ROSI remains to be determined. Here, we show that a repressive histone mark H3K27me3 persists from mouse round spermatids into zygotes in ROSI and that round spermatid-derived H3K27me3 is associated with less accessible chromatin and impaired gene expression in ROSI-embryos. These loci are initially marked by H3K27me3 but undergo histone modification remodelling in spermiogenesis, resulting in reduced H3K27me3 in normal spermatozoa. Therefore, the absence of the epigenetic remodelling, presumably mediated by histone turnover during spermiogenesis, leads to dysregulation of chromatin accessibility and transcription in ROSI-embryos. Thus, our results unveil a molecular logic, in which chromatin states in round spermatids impinge on chromatin accessibility and transcription in ROSI-embryos, highlighting the importance of epigenetic remodelling during spermiogenesis in successful reproduction.
    Keywords:  Chromatin accessibility; Epigenetic inheritance; H3K27me3; Round spermatid injection; Spermiogenesis; Zygotic genome activation
    DOI:  https://doi.org/10.1242/dev.200696
  7. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01065-8. [Epub ahead of print]40(8): 111247
    SOX transcription factors direct TCF-independent WNT/β-catenin responsive transcription to govern cell fate in human pluripotent stem cells.
    Shreyasi Mukherjee, David M Luedeke, Leslie McCoy, Makiko Iwafuchi, Aaron M Zorn.
      WNT/β-catenin signaling controls gene expression across biological contexts from development and stem cell homeostasis to diseases including cancer. How β-catenin is recruited to distinct enhancers to activate context-specific transcription is unclear, given that most WNT/ß-catenin-responsive transcription is thought to be mediated by TCF/LEF transcription factors (TFs). With time-resolved multi-omic analyses, we show that SOX TFs can direct lineage-specific WNT-responsive transcription during the differentiation of human pluripotent stem cells (hPSCs) into definitive endoderm and neuromesodermal progenitors. We demonstrate that SOX17 and SOX2 are required to recruit β-catenin to lineage-specific WNT-responsive enhancers, many of which are not occupied by TCFs. At TCF-independent enhancers, SOX TFs establish a permissive chromatin landscape and recruit a WNT-enhanceosome complex to activate SOX/ß-catenin-dependent transcription. Given that SOX TFs and the WNT pathway are critical for specification of most cell types, these results have broad mechanistic implications for the specificity of WNT responses across developmental and disease contexts.
    Keywords:  CP: stem cell research; NMP; SOX; TCF; WNT; WNT signaling; beta-catenin; endoderm; enhancer; mesoderm; transcription factors
    DOI:  https://doi.org/10.1016/j.celrep.2022.111247
  8. Sci Adv. 2022 Aug 26. 8(34): eabm4358
    Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer.
    Satyanarayan Rao, Amy L Han, Alexis Zukowski, Etana Kopin, Carol A Sartorius, Peter Kabos, Srinivas Ramachandran.
      Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish xenografts with distinct ER states. Furthermore, state-specific ER-binding signatures can partition human breast tumors into groups with significantly different ER expression and mortality. Last, TF footprints in human plasma samples can identify the presence of ER+ breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of breast cancer in humans and open vast possibilities for clinical applications across multiple tumor types.
    DOI:  https://doi.org/10.1126/sciadv.abm4358
  9. J Clin Invest. 2022 Aug 25. pii: e158593. [Epub ahead of print]
    Mediator kinase regulates intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF.
    Marius V Dannappel, Danxi Zhu, Xin Sun, Hui Kheng Chua, Marle Poppelaars, Monica Suehiro, Subash Khadka, Terry Cc Lim Kam Sian, Dhanya Sooraj, Melissa Loi, Hugh Gao, Daniel Croagh, Roger J Daly, Pouya Faridi, Thomas Boyer, Ron Firestein.
      Initiation and maintenance of transcriptional states are critical for controlling normal tissue homeostasis and differentiation. Cyclin Dependent Kinases CDK8/CDK19 (Mediator kinase) are regulatory components of Mediator, a highly conserved complex that orchestrates enhancer-mediated transcriptional output. While Mediator kinase has been implicated in the transcription of genes necessary for development and growth, its function in mammals has not been well defined. Using a suite of genetically defined models and pharmacological inhibitors, we show that Cdk8/19 function in a redundant manner to regulate intestinal lineage-specification in human and mouse. Mechanistically, we find that the Mediator kinase module binds and phosphorylates key components of the chromatin remodelling complex SWI/SNF in intestinal epithelial cells. Concomitantly, SWI/SNF and MED12-Mediator co-localise at distinct lineage-specifying enhancers in a CDK8/19 dependent manner. As such, these studies reveal a novel transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodelling complex SWI/SNF and Mediator kinase.
    Keywords:  Gastroenterology; Genetics; Molecular genetics; Mouse models; Oncogenes
    DOI:  https://doi.org/10.1172/JCI158593
  10. Int J Mol Sci. 2022 Aug 18. pii: 9290. [Epub ahead of print]23(16):
    Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains.
    Matthew D Gibbons, Yu Fang, Austin P Spicola, Niko Linzer, Stephen M Jones, Breanna R Johnson, Lu Li, Mingyi Xie, Jörg Bungert.
      Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast have been shown to recruit components of the RNA polymerase II (Pol II) transcription machinery. At least a fraction of Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA). In contrast, UASs in yeast do not recruit transcription factor TFIIH, which is required for transcription initiation. For both yeast and mammalian systems, it was shown that Pol II is transferred from enhancers/UASs to promoters. We propose that there are two modes of Pol II recruitment to enhancers in higher eukaryotes. Pol II complexes that generate eRNAs are recruited via TFIID, similar to mechanisms operating at promoters. This may involve the binding of TFIID to acetylated nucleosomes flanking the enhancer. The resulting eRNA, together with enhancer-bound transcription factors and co-regulators, contributes to the second mode of Pol II recruitment through the formation of a transcription initiation domain. Transient contacts with target genes, governed by proteins and RNA, lead to the transfer of Pol II from enhancers to TFIID-bound promoters.
    Keywords:  RNA polymerase II; eRNA; enhancer; super-enhancer; transcription; transcription initiation domain
    DOI:  https://doi.org/10.3390/ijms23169290
  11. Nat Commun. 2022 Aug 26. 13(1): 5033
    DAXX-ATRX regulation of p53 chromatin binding and DNA damage response.
    Nitish Gulve, Chenhe Su, Zhong Deng, Samantha S Soldan, Olga Vladimirova, Jayamanna Wickramasinghe, Hongwu Zheng, Andrew V Kossenkov, Paul M Lieberman.
      DAXX and ATRX are tumor suppressor proteins that form a histone H3.3 chaperone complex and are frequently mutated in cancers with the alternative lengthening of telomeres (ALT). Here, we show that DAXX and ATRX knock-out (KO) U87-T cells that have acquired ALT-like features have defects in p53 chromatin binding and DNA damage response. RNA-seq analysis revealed that p53 pathway is among the most perturbed. ChIP-seq and ATAC-seq revealed a genome-wide reduction in p53 DNA-binding and corresponding loss of chromatin accessibility at many p53 response elements across the genome. Both DAXX and ATRX null cells showed a depletion of histone H3.3 and accumulation of γH2AX at many p53 sites, including subtelomeres. These findings indicate that loss of DAXX or ATRX can compromise p53 chromatin binding and p53 DNA damage response in ALT-like cells, providing a link between histone composition, chromatin accessibility and tumor suppressor function of p53.
    DOI:  https://doi.org/10.1038/s41467-022-32680-8
  12. Sci Adv. 2022 Aug 26. 8(34): eabn7774
    RORγt expression in mature TH17 cells safeguards their lineage specification by inhibiting conversion to TH2 cells.
    Xinxin Chi, Wei Jin, Xiaohong Zhao, Tian Xie, Jing Shao, Xue Bai, Yu Jiang, Xiaohu Wang, Chen Dong.
      RORγt is the lineage-specific transcription factor for T helper 17 (TH17) cells and an attractive drug target for treating TH17-associated diseases. Although the critical role of RORγt in early TH17 cell differentiation has been well recognized, its function in mature TH17 cell maintenance remains largely unknown. Here, we show that genetic deletion of Rorc in mature TH17 cells inhibited their pathogenic functions. Mechanistically, loss of RORγt led to a closed chromatin configuration at key TH17-specific gene loci, particularly at the "super-enhancer" regions. Unexpectedly, RORγt directly bound and inhibited Il4 transcription, whereas pharmaceutically or genetically targeting RORγt caused spontaneous conversion of TH17 cells to TH2-like cells in vitro and in vivo. Our results thus reveal dual crucial functions of RORγt in effector TH17 cells in maintaining TH17 cell program and constraining TH2 cell conversion, offering previously unidenified considerations in therapeutic targeting of RORγt.
    DOI:  https://doi.org/10.1126/sciadv.abn7774
  13. Curr Protoc. 2022 Aug;2(8): e535
    FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples.
    Ram Prakash Yadav, Vamsi Krishna Polavarapu, Pengwei Xing, Xingqi Chen.
      In basic and translational cancer research, the majority of biopsies are stored in formalin-fixed paraffin-embedded (FFPE) samples. Chromatin accessibility reflects the degree to which nuclear macromolecules can physically interact with chromatinized DNA and plays a key role in gene regulation in different physiological conditions. As such, the profiling of chromatin accessibility in archived FFPE tissue can be critical to understanding gene regulation in health and disease. Due to the high degree of DNA damage in FFPE samples, accurate mapping of chromatin accessibility in these specimens is extremely difficult. To address this issue, we recently established FFPE-ATAC, a highly sensitive method based on T7-Tn5-mediated transposition followed by in vitro transcription (IVT), to generate high-quality chromatin accessibility profiles with 500-50,000 nuclei from a single FFPE tissue section. In FFPE-ATAC, which we describe here, the T7-Tn5 adaptors are inserted into the genome after FFPE sample preparation and are unlikely to sustain the DNA breakage that occurs during reverse cross-linking of these samples. It should, therefore, remain at the ends of broken accessible chromatin sites after reverse cross-linking. IVT is then used to convert the two ends of the broken DNA fragments to RNA molecules before making sequencing libraries from the IVT RNAs and further decoding Tn5 adaptor insertion sites in the genome. Through this strategy, users can decode the flanking sequences of the accessible chromatin even if there are breaks between adjacent pairs of T7-T5 adaptor insertion sites. This method is applicable to dissecting chromatin profiles of a small section of the tissue sample, characterizing stage and region-specific gene regulation and disease-associated chromatin regulation in FFPE tissues. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation from FFPE tissue samples Basic Protocol 2: T7-Tn5 transposase tagmentation, reverse-crosslinking, and in vitro transcription Basic Protocol 3: Preparation of libraries for high-throughput sequencing.
    Keywords:  T7-Tn5-mediated transposition; chromatin accessibility; formalin-fixed paraffin-embedded (FFPE) sample; in vitro transcription
    DOI:  https://doi.org/10.1002/cpz1.535
  14. Nucleic Acids Res. 2022 Aug 26. pii: gkac707. [Epub ahead of print]
    Enhancer looping protein LDB1 regulates hepatocyte gene expression by cooperating with liver transcription factors.
    Guoyou Liu, Lei Wang, Jürgen Wess, Ann Dean.
      Enhancers establish proximity with distant target genes to regulate temporospatial gene expression and specify cell identity. Lim domain binding protein 1 (LDB1) is a conserved and widely expressed protein that functions as an enhancer looping factor. Previous studies in erythroid cells and neuronal cells showed that LDB1 forms protein complexes with different transcription factors to regulate cell-specific gene expression. Here, we show that LDB1 regulates expression of liver genes by occupying enhancer elements and cooperating with hepatic transcription factors HNF4A, FOXA1, TCF7 and GATA4. Using the glucose transporter SLC2A2 gene, encoding GLUT2, as an example, we find that LDB1 regulates gene expression by mediating enhancer-promoter interactions. In vivo, we find that LDB1 deficiency in primary mouse hepatocytes dysregulates metabolic gene expression and changes the enhancer landscape. Conditional deletion of LDB1 in adult mouse liver induces glucose intolerance. However, Ldb1 knockout hepatocytes show improved liver pathology under high-fat diet conditions associated with increased expression of genes related to liver fatty acid metabolic processes. Thus, LDB1 is linked to liver metabolic functions under normal and obesogenic conditions.
    DOI:  https://doi.org/10.1093/nar/gkac707
  15. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01057-9. [Epub ahead of print]40(8): 111240
    Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency.
    Zhipeng Ai, Xinyu Xiang, Yangquan Xiang, Iwona Szczerbinska, Yuli Qian, Xiao Xu, Chenyang Ma, Yaqi Su, Bing Gao, Hao Shen, Muhammad Nadzim Bin Ramli, Di Chen, Yue Liu, Jia-Jie Hao, Huck Hui Ng, Dan Zhang, Yun-Shen Chan, Wanlu Liu, Hongqing Liang.
      Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.
    Keywords:  CP: stem cell research; ERVs; KLFs; cell potency; naive and primed pluripotency; transcription control; trophectoderm
    DOI:  https://doi.org/10.1016/j.celrep.2022.111240
  16. Genes Dev. 2022 Aug 25.
    KLF5 governs sphingolipid metabolism and barrier function of the skin.
    Ying Lyu, Yinglu Guan, Lisa Deliu, Ericka Humphrey, Joanna K Frontera, Youn Joo Yang, Daniel Zamler, Kun Hee Kim, Vakul Mohanty, Kevin Jin, Vakul Mohanty, Virginia Liu, Jinzhuang Dou, Lucas J Veillon, Shwetha V Kumar, Philip L Lorenzi, Yang Chen, Kathleen M McAndrews, Sergei Grivennikov, Xingzhi Song, Jianhua Zhang, Yuanxin Xi, Jing Wang, Ken Chen, Priyadharsini Nagarajan, Yejing Ge.
      Stem cells are fundamental units of tissue remodeling whose functions are dictated by lineage-specific transcription factors. Home to epidermal stem cells and their upward-stratifying progenies, skin relies on its secretory functions to form the outermost protective barrier, of which a transcriptional orchestrator has been elusive. KLF5 is a Krüppel-like transcription factor broadly involved in development and regeneration whose lineage specificity, if any, remains unclear. Here we report KLF5 specifically marks the epidermis, and its deletion leads to skin barrier dysfunction in vivo. Lipid envelopes and secretory lamellar bodies are defective in KLF5-deficient skin, accompanied by preferential loss of complex sphingolipids. KLF5 binds to and transcriptionally regulates genes encoding rate-limiting sphingolipid metabolism enzymes. Remarkably, skin barrier defects elicited by KLF5 ablation can be rescued by dietary interventions. Finally, we found that KLF5 is widely suppressed in human diseases with disrupted epidermal secretion, and its regulation of sphingolipid metabolism is conserved in human skin. Altogether, we established KLF5 as a disease-relevant transcription factor governing sphingolipid metabolism and barrier function in the skin, likely representing a long-sought secretory lineage-defining factor across tissue types.
    Keywords:  barrier; secretory; skin epidermis; sphingolipid metabolism; stem cells; transcription factors
    DOI:  https://doi.org/10.1101/gad.349662.122
  17. Dev Cell. 2022 08 22. pii: S1534-5807(22)00531-7. [Epub ahead of print]57(16): 1922-1936.e9
    Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster.
    Irene Miguel-Escalada, Miguel Ángel Maestro, Diego Balboa, Anamaria Elek, Aina Bernal, Edgar Bernardo, Vanessa Grau, Javier García-Hurtado, Arnau Sebé-Pedrós, Jorge Ferrer.
      Sequence variants in cis-acting enhancers are important for polygenic disease, but their role in Mendelian disease is poorly understood. Redundancy between enhancers that regulate the same gene is thought to mitigate the pathogenic impact of enhancer mutations. Recent findings, however, have shown that loss-of-function mutations in a single enhancer near PTF1A cause pancreas agenesis and neonatal diabetes. Using mouse and human genetic models, we show that this enhancer activates an entire PTF1A enhancer cluster in early pancreatic multipotent progenitors. This leading role, therefore, precludes functional redundancy. We further demonstrate that transient expression of PTF1A in multipotent progenitors sets in motion an epigenetic cascade that is required for duct and endocrine differentiation. These findings shed insights into the genome regulatory mechanisms that drive pancreas differentiation. Furthermore, they reveal an enhancer that acts as a regulatory master key and is thus vulnerable to pathogenic loss-of-function mutations.
    Keywords:  Mendelian disease; NEUROG3; PTF1A; diabetes mellitus; endocrine differentiation; enhancers; non-coding mutations; pancreas development; stem cell differentiation
    DOI:  https://doi.org/10.1016/j.devcel.2022.07.014
  18. Nucleic Acids Res. 2022 Aug 26. pii: gkac708. [Epub ahead of print]
    DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.
    Sandro Barissi, Alba Sala, Miłosz Wieczór, Federica Battistini, Modesto Orozco.
      We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any non-coding nucleobases. When complemented with chromatin structure information, our in vitro trained method provides also good estimates of in vivo binding sites in yeast.
    DOI:  https://doi.org/10.1093/nar/gkac708
  19. iScience. 2022 Aug 19. 25(8): 104839
    Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression.
    Alla V Tsytsykova, Graham Wiley, Chuang Li, Richard C Pelikan, Lori Garman, Francis A Acquah, Blaine H M Mooers, Erdyni N Tsitsikov, Ian F Dunn.
      Krüppel-like factor 4 (KLF4) is a transcription factor that has been proven necessary for both induction and maintenance of pluripotency and self-renewal. Whole-genome sequencing defined a unique mutation in KLF4 (KLF4K409Q) in human meningiomas. However, the molecular mechanism of this tumor-specific KLF4 mutation is unknown. Using genome-wide high-throughput and focused quantitative transcriptional approaches in human cell lines, primary meningeal cells, and meningioma tumor tissue, we found that a change in the evolutionarily conserved DNA-binding domain of KLF4 alters its DNA recognition preference, resulting in a shift in downstream transcriptional activity. In the KLF4K409Q-specific targets, the normally silent fibroblast growth factor 3 (FGF3) is activated. We demonstrated a neomorphic function of KLF4K409Q in stimulating FGF3 transcription through binding to its promoter and in using short tandem repeats (STRs) located within the locus as enhancers.
    Keywords:  Cancer; Molecular biology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2022.104839
  20. Mol Cell. 2022 Aug 18. pii: S1097-2765(22)00706-7. [Epub ahead of print]
    RAD51 protects human cells from transcription-replication conflicts.
    Rahul Bhowmick, Mads Lerdrup, Sampath Amitash Gadi, Giacomo G Rossetti, Manika I Singh, Ying Liu, Thanos D Halazonetis, Ian D Hickson.
      Oncogene activation during tumorigenesis promotes DNA replication stress (RS), which subsequently drives the formation of cancer-associated chromosomal rearrangements. Many episodes of physiological RS likely arise due to conflicts between the DNA replication and transcription machineries operating simultaneously at the same loci. One role of the RAD51 recombinase in human cells is to protect replication forks undergoing RS. Here, we have identified a key role for RAD51 in preventing transcription-replication conflicts (TRCs) from triggering replication fork breakage. The genomic regions most affected by RAD51 deficiency are characterized by being replicated and transcribed in early S-phase and show significant overlap with loci prone to cancer-associated amplification. Consistent with a role for RAD51 in protecting against transcription-replication conflicts, many of the adverse effects of RAD51 depletion are ameliorated by inhibiting early S-phase transcription. We propose a model whereby RAD51 suppresses fork breakage and subsequent inadvertent amplification of genomic loci prone to experiencing TRCs.
    Keywords:  common fragile sites; gene amplification in cancer; mitotic DNA synthesis; oncogene-induced DNA replication stress; replication fork protection
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.010
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