bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2022–03–13
25 papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity.
  2. Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.
  3. Broad domains of histone marks in the highly compact Paramecium macronuclear genome.
  4. Regulation of Chromatin Accessibility by hypoxia and HIF.
  5. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms.
  6. CellWalkR: An R Package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.
  7. Coordinated DNA and histone dynamics drive accurate histone H2A.Z exchange.
  8. Base-resolution prediction of transcription factor binding signals by a deep learning framework.
  9. Prediction of histone post-translational modification patterns based on nascent transcription data.
  10. Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation.
  11. The ACF chromatin remodeling complex is essential for Polycomb repression.
  12. NDF is a transcription factor that stimulates elongation by RNA polymerase II.
  13. THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data.
  14. Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome.
  15. A transcriptional roadblock protects yeast centromeres.
  16. Reversible phase separation of HSF1 is required for an acute transcriptional response during heat shock.
  17. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
  18. Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.
  19. BET proteins are essential for the specification and maintenance of the epiblast lineage in mouse preimplantation embryos.
  20. Chromatin accessibility and transcriptome integrative analysis revealed AP-1-mediated genes potentially modulate histopathology features in psoriasis.
  21. The zinc-finger transcription factor LSL-1 is a major regulator of the germline transcriptional program in C. elegans.
  22. Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets.
  23. An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression.
  24. CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.
  25. Nucleolar-based Dux repression is essential for embryonic two-cell stage exit.
  1. Nat Commun. 2022 Mar 11. 13(1): 1293
    Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity.
    Mingsen Li, Huaxing Huang, Bofeng Wang, Shaoshuai Jiang, Huizhen Guo, Liqiong Zhu, Siqi Wu, Jiafeng Liu, Li Wang, Xihong Lan, Wang Zhang, Jin Zhu, Fuxi Li, Jieying Tan, Zhen Mao, Chunqiao Liu, Jianping Ji, Junjun Ding, Kang Zhang, Jin Yuan, Yizhi Liu, Hong Ouyang.
      The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia.
    DOI:  https://doi.org/10.1038/s41467-022-28966-6
  2. NAR Genom Bioinform. 2022 Mar;4(1): lqac021
    Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification.
    Silvia Galan, François Serra, Marc A Marti-Renom.
      Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored. Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using self-organizing feature maps and their functionality characterized by their epigenetic states. The resulting clusters were then input to a convolutional neural network aiming at the de novo detecting chromatin loops from Hi-C interaction matrices. Our new method, called LOOPbit, is able to automatically detect significant interactions with a higher proportion of enhancer-promoter loops compared to other callers. Our highly specific loop caller adds a new layer of detail to the link between chromatin structure and function.
    DOI:  https://doi.org/10.1093/nargab/lqac021
  3. Genome Res. 2022 Mar 09. pii: gr.276126.121. [Epub ahead of print]
    Broad domains of histone marks in the highly compact Paramecium macronuclear genome.
    Franzisa Drews, Abdulraham Salhab, Sivarajan Karunanithi, Miriam Cheaib, Martin Jung, Marcel Schulz, Martin Simon.
      The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) revealed no narrow peaks but broad domains along gene bodies, whereas intergenic regions were devoid of nucleosomes. Our data implicates H3K4me3 levels inside ORFs to be the main factor to associate with gene expression and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Due to a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different to other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data implies that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.
    DOI:  https://doi.org/10.1101/gr.276126.121
  4. Biochem J. 2022 Mar 08. pii: BCJ20220008. [Epub ahead of print]
    Regulation of Chromatin Accessibility by hypoxia and HIF.
    Michael Batie, Julianty Frost, Dilem Shakir, Sonia Rocha.
      Reduced oxygen availability (hypoxia) can act as a signalling cue in physiological processes such as development, but also in pathological conditions such as cancer or ischaemic disease. As such, understanding how cells and organisms respond to hypoxia is of great importance. The family of transcription factors called Hypoxia Inducible Factors (HIFs) coordinate a transcriptional programme required for survival and adaptation to hypoxia. The effects of HIF on chromatin accessibility landscape are still unclear. Here, using genome wide mapping of chromatin accessibility via ATAC-seq, we find hypoxia induces loci specific changes in chromatin accessibility are enriched at a subset hypoxia transcriptionally responsive genes, agreeing with previous data using other models. We show for the first time that hypoxia inducible changes in chromatin accessibility across the genome are predominantly HIF dependent, rapidly reversible upon reoxygenation and partially mimicked by HIF-α stabilisation independent of molecular dioxygenase inhibition. This work demonstrates that HIF is central to chromatin accessibility alterations in hypoxia, and has implications for our understanding of gene expression regulation by hypoxia and HIF.
    Keywords:  ATAC-seq; Hypoxia; JmjC-histone demethylases; chromatin; hypoxia inducible factors; transcription
    DOI:  https://doi.org/10.1042/BCJ20220008
  5. Cell Rep. 2022 Mar 08. pii: S2211-1247(22)00200-5. [Epub ahead of print]38(10): 110467
    Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms.
    Zidong Zhang, Michel Zamojski, Gregory R Smith, Thea L Willis, Val Yianni, Natalia Mendelev, Hanna Pincas, Nitish Seenarine, Mary Anne S Amper, Mital Vasoya, Wan Sze Cheng, Elena Zaslavsky, Venugopalan D Nair, Judith L Turgeon, Daniel J Bernard, Olga G Troyanskaya, Cynthia L Andoniadou, Stuart C Sealfon, Frederique Ruf-Zamojski.
      Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource from pediatric, adult, and aged postmortem pituitaries (snpituitaryatlas.princeton.edu) and characterize cell-type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early-life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors that are significantly associated with gene expression in PSCs compared with other cell types and within PSCs. We identify distinct deterministic mechanisms that contribute to heterogeneous marker expression within PSCs. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes and cell type identity.
    Keywords:  chromatin accessibility; multiomics; pituitary; single nucleus analysis; stem cells; transcriptome
    DOI:  https://doi.org/10.1016/j.celrep.2022.110467
  6. Bioinformatics. 2022 Mar 11. pii: btac150. [Epub ahead of print]
    CellWalkR: An R Package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.
    Pawel F Przytycki, Katherine S Pollard.
        : CellWalkR is an R package that integrates single-cell open chromatin (scATAC-seq) data with cell type labels and bulk epigenetic data to identify cell type-specific regulatory regions. A GPU implementation and downsampling strategies enable thousands of cells to be processed in seconds. CellWalkR's user-friendly interface provides interactive analysis and visualization of cell labels and regulatory region mappings.
    AVAILABILITY: CellWalkR is freely available as an R package under a GNU GPL-2.0 License and can be accessed from https://github.com/PFPrzytycki/CellWalkR with an accompanying vignette.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btac150
  7. Sci Adv. 2022 Mar 11. 8(10): eabj5509
    Coordinated DNA and histone dynamics drive accurate histone H2A.Z exchange.
    Matthew F Poyton, Xinyu A Feng, Anand Ranjan, Qin Lei, Feng Wang, Jasmin S Zarb, Robert K Louder, Giho Park, Myung Hyun Jo, Joseph Ye, Sheng Liu, Taekjip Ha, Carl Wu.
      Nucleosomal histone H2A is exchanged for its variant H2A.Z by the SWR1 chromatin remodeler, but the mechanism and timing of histone exchange remain unclear. Here, we quantify DNA and histone dynamics during histone exchange in real time using a three-color single-molecule FRET assay. We show that SWR1 operates with timed precision to unwrap DNA with large displacement from one face of the nucleosome, remove H2A-H2B from the same face, and rewrap DNA, all within 2.3 s. This productive DNA unwrapping requires full SWR1 activation and differs from unproductive, smaller-scale DNA unwrapping caused by SWR1 binding alone. On an asymmetrically positioned nucleosome, SWR1 intrinsically senses long-linker DNA to preferentially exchange H2A.Z on the distal face as observed in vivo. The displaced H2A-H2B dimer remains briefly associated with the SWR1-nucleosome complex and is dissociated by histone chaperones. These findings reveal how SWR1 coordinates DNA unwrapping with histone dynamics to rapidly and accurately place H2A.Z at physiological sites on chromatin.
    DOI:  https://doi.org/10.1126/sciadv.abj5509
  8. PLoS Comput Biol. 2022 Mar 09. 18(3): e1009941
    Base-resolution prediction of transcription factor binding signals by a deep learning framework.
    Qinhu Zhang, Ying He, Siguo Wang, Zhanheng Chen, Zhenhao Guo, Zhen Cui, Qi Liu, De-Shuang Huang.
      Transcription factors (TFs) play an important role in regulating gene expression, thus the identification of the sites bound by them has become a fundamental step for molecular and cellular biology. In this paper, we developed a deep learning framework leveraging existing fully convolutional neural networks (FCN) to predict TF-DNA binding signals at the base-resolution level (named as FCNsignal). The proposed FCNsignal can simultaneously achieve the following tasks: (i) modeling the base-resolution signals of binding regions; (ii) discriminating binding or non-binding regions; (iii) locating TF-DNA binding regions; (iv) predicting binding motifs. Besides, FCNsignal can also be used to predict opening regions across the whole genome. The experimental results on 53 TF ChIP-seq datasets and 6 chromatin accessibility ATAC-seq datasets show that our proposed framework outperforms some existing state-of-the-art methods. In addition, we explored to use the trained FCNsignal to locate all potential TF-DNA binding regions on a whole chromosome and predict DNA sequences of arbitrary length, and the results show that our framework can find most of the known binding regions and accept sequences of arbitrary length. Furthermore, we demonstrated the potential ability of our framework in discovering causal disease-associated single-nucleotide polymorphisms (SNPs) through a series of experiments.
    DOI:  https://doi.org/10.1371/journal.pcbi.1009941
  9. Nat Genet. 2022 Mar 10.
    Prediction of histone post-translational modification patterns based on nascent transcription data.
    Zhong Wang, Alexandra G Chivu, Lauren A Choate, Edward J Rice, Donald C Miller, Tinyi Chu, Shao-Pei Chou, Nicole B Kingsley, Jessica L Petersen, Carrie J Finno, Rebecca R Bellone, Douglas F Antczak, John T Lis, Charles G Danko.
      The role of histone modifications in transcription remains incompletely understood. Here, we examine the relationship between histone modifications and transcription using experimental perturbations combined with sensitive machine-learning tools. Transcription predicted the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. Blocking transcription rapidly removed two punctate marks, H3K4me3 and H3K27ac, from chromatin indicating that transcription is required for active histone modifications. Transcription was also required for maintenance of H3K27me3, consistent with a role for RNA in recruiting PRC2. A subset of DNase-I-hypersensitive sites were refractory to prediction, precluding models where transcription initiates pervasively at any open chromatin. Our results, in combination with past literature, support a model in which active histone modifications serve a supportive, rather than an essential regulatory, role in transcription.
    DOI:  https://doi.org/10.1038/s41588-022-01026-x
  10. PLoS One. 2022 ;17(3): e0265027
    Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation.
    Petri Rummukainen, Kati Tarkkonen, Amel Dudakovic, Rana Al-Majidi, Vappu Nieminen-Pihala, Cristina Valensisi, R David Hawkins, Andre J van Wijnen, Riku Kiviranta.
      Epigenetic mechanisms regulate osteogenic lineage differentiation of mesenchymal stromal cells. Histone methylation is controlled by multiple lysine demethylases and is an important step in controlling local chromatin structure and gene expression. Here, we show that the lysine-specific histone demethylase Kdm1A/Lsd1 is abundantly expressed in osteoblasts and that its suppression impairs osteoblast differentiation and bone nodule formation in vitro. Although Lsd1 knockdown did not affect global H3K4 methylation levels, genome-wide ChIP-Seq analysis revealed high levels of Lsd1 at gene promoters and its binding was associated with di- and tri-methylation of histone 3 at lysine 4 (H3K4me2 and H3K4me3). Lsd1 binding sites in osteoblastic cells were enriched for the Runx2 consensus motif suggesting a functional link between the two proteins. Importantly, inhibition of Lsd1 activity decreased osteoblast activity in vivo. In support, mesenchymal-targeted knockdown of Lsd1 led to decreased osteoblast activity and disrupted primary spongiosa ossification and reorganization in vivo. Together, our studies demonstrate that Lsd1 occupies Runx2-binding cites at H3K4me2 and H3K4me3 and its activity is required for proper bone formation.
    DOI:  https://doi.org/10.1371/journal.pone.0265027
  11. Elife. 2022 Mar 08. pii: e77595. [Epub ahead of print]11
    The ACF chromatin remodeling complex is essential for Polycomb repression.
    Elizabeth T Wiles, Colleen C Mumford, Kevin J McNaught, Hideki Tanizawa, Eric U Selker.
      Establishing and maintaining appropriate gene repression is critical for the health and development of multicellular organisms. Histone H3 lysine 27 (H3K27) methylation is a chromatin modification associated with repressed facultative heterochromatin, but the mechanism of this repression remains unclear. We used a forward genetic approach to identify genes involved in transcriptional silencing of H3K27-methylated chromatin in the filamentous fungus Neurospora crassa. We found that the N. crassa homologs of ISWI (NCU03875) and ACF1 (NCU00164) are required for repression of a subset of H3K27- methylated genes and that they form an ACF chromatin remodeling complex. This ACF complex interacts with chromatin throughout the genome, yet association with facultative heterochromatin is specifically promoted by the H3K27 methyltransferase, SET-7. H3K27-methylated genes that are upregulated when iswi or acf1 are deleted show a downstream shift of the +1 nucleosome, suggesting that proper nucleosome positioning is critical for repression of facultative heterochromatin. Our findings support a direct role for the ACF complex in Polycomb repression.
    Keywords:  N. crassa; chromosomes; gene expression; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.77595
  12. Genes Dev. 2022 Mar 10.
    NDF is a transcription factor that stimulates elongation by RNA polymerase II.
    Jia Fei, Jun Xu, Ziwei Li, Kevin Xu, Dong Wang, George A Kassavetis, James T Kadonaga.
      RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than that used by transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.
    Keywords:  NDF; RNA polymerase II; TFIIS; elongation; gene expression; transcription
    DOI:  https://doi.org/10.1101/gad.349150.121
  13. PLoS Genet. 2022 Mar 08. 18(3): e1010102
    THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data.
    Bryce Rowland, Ruth Huh, Zoey Hou, Cheynna Crowley, Jia Wen, Yin Shen, Ming Hu, Paola Giusti-Rodríguez, Patrick F Sullivan, Yun Li.
      Hi-C data provide population averaged estimates of three-dimensional chromatin contacts across cell types and states in bulk samples. Effective analysis of Hi-C data entails controlling for the potential confounding factor of differential cell type proportions across heterogeneous bulk samples. We propose a novel unsupervised deconvolution method for inferring cell type composition from bulk Hi-C data, the Two-step Hi-c UNsupervised DEconvolution appRoach (THUNDER). We conducted extensive simulations to test THUNDER based on combining two published single-cell Hi-C (scHi-C) datasets. THUNDER more accurately estimates the underlying cell type proportions compared to reference-free methods (e.g., TOAST, and NMF) and is more robust than reference-dependent methods (e.g. MuSiC). We further demonstrate the practical utility of THUNDER to estimate cell type proportions and identify cell-type-specific interactions in Hi-C data from adult human cortex tissue samples. THUNDER will be a useful tool in adjusting for varying cell type composition in population samples, facilitating valid and more powerful downstream analysis such as differential chromatin organization studies. Additionally, THUNDER estimated contact profiles provide a useful exploratory framework to investigate cell-type-specificity of the chromatin interactome while experimental data is still rare.
    DOI:  https://doi.org/10.1371/journal.pgen.1010102
  14. iScience. 2022 Mar 18. 25(3): 103937
    Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome.
    Ayako Furukawa, Masatoshi Wakamori, Yasuhiro Arimura, Hideaki Ohtomo, Yasuo Tsunaka, Hitoshi Kurumizaka, Takashi Umehara, Yoshifumi Nishimura.
      The nucleosome core particle (NCP) comprises a histone octamer, wrapped around by ∼146-bp DNA, while the nucleosome additionally contains linker DNA. We previously showed that, in the nucleosome, H4 N-tail acetylation enhances H3 N-tail acetylation by altering their mutual dynamics. Here, we have evaluated the roles of linker DNA and/or linker histone on H3 N-tail dynamics and acetylation by using the NCP and the chromatosome (i.e., linker histone H1.4-bound nucleosome). In contrast to the nucleosome, H3 N-tail acetylation and dynamics are greatly suppressed in the NCP regardless of H4 N-tail acetylation because the H3 N-tail is strongly bound between two DNA gyres. In the chromatosome, the asymmetric H3 N-tail adopts two conformations: one contacts two DNA gyres, as in the NCP; and one contacts linker DNA, as in the nucleosome. However, the rate of H3 N-tail acetylation is similar in the chromatosome and nucleosome. Thus, linker DNA and linker histone both regulate H3-tail dynamics and acetylation.
    Keywords:  Cell biology; Molecular biology; Structural biology
    DOI:  https://doi.org/10.1016/j.isci.2022.103937
  15. Nucleic Acids Res. 2022 Mar 07. pii: gkac117. [Epub ahead of print]
    A transcriptional roadblock protects yeast centromeres.
    Sabrine Hedouin, Glennis A Logsdon, Jason G Underwood, Sue Biggins.
      Centromeres are the chromosomal loci essential for faithful chromosome segregation during cell division. Although centromeres are transcribed and produce non-coding RNAs (cenRNAs) that affect centromere function, we still lack a mechanistic understanding of how centromere transcription is regulated. Here, using a targeted RNA isoform sequencing approach, we identified the transcriptional landscape at and surrounding all centromeres in budding yeast. Overall, cenRNAs are derived from transcription readthrough of pericentromeric regions but rarely span the entire centromere and are a complex mixture of molecules that are heterogeneous in abundance, orientation, and sequence. While most pericentromeres are transcribed throughout the cell cycle, centromere accessibility to the transcription machinery is restricted to S-phase. This temporal restriction is dependent on Cbf1, a centromere-binding transcription factor, that we demonstrate acts locally as a transcriptional roadblock. Cbf1 deletion leads to an accumulation of cenRNAs at all phases of the cell cycle which correlates with increased chromosome mis-segregation that is partially rescued when the roadblock activity is restored. We propose that a Cbf1-mediated transcriptional roadblock protects yeast centromeres from untimely transcription to ensure genomic stability.
    DOI:  https://doi.org/10.1093/nar/gkac117
  16. Nat Cell Biol. 2022 Mar 07.
    Reversible phase separation of HSF1 is required for an acute transcriptional response during heat shock.
    Hongchen Zhang, Shipeng Shao, Yong Zeng, Xiaotian Wang, Yizhi Qin, Qiunan Ren, Shengqi Xiang, Yuxin Wang, Junyu Xiao, Yujie Sun.
      Heat-shock transcription factor 1 (HSF1) orchestrates the fast and vast cellular response to heat shock through increased expression of heat-shock proteins. However, how HSF1 rapidly and reversibly regulates transcriptional reprogramming remains poorly defined. Here by combining super-resolution imaging, in vitro reconstitution and high-throughput sequencing, we reveal that HSF1 forms small nuclear condensates via liquid-liquid phase separation at heat-shock-protein gene loci and enriches multiple transcription apparatuses through co-phase separation to promote the transcription of target genes. Furthermore, the phase-separation capability of HSF1 is fine-tuned through phosphorylation at specific sites within the regulatory domain. Last, we discovered that HSP70 disperses HSF1 condensates to attenuate transcription following the cessation of heat shock and further prevents the gel-like phase transition of HSF1 under extended heat-shock stress. Our work reveals an inducible and reversible phase-separation feedback mechanism for dynamic regulation of HSF1 activity to drive the transcriptional response and maintain protein homeostasis during acute stress.
    DOI:  https://doi.org/10.1038/s41556-022-00846-7
  17. Nat Methods. 2022 Mar;19(3): 296-306
    A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
    Tianyu Zhu, Jacklyn Liu, Stephan Beck, Sun Pan, David Capper, Matt Lechner, Chrissie Thirlwell, Charles E Breeze, Andrew E Teschendorff.
      Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.
    DOI:  https://doi.org/10.1038/s41592-022-01412-7
  18. Nat Commun. 2022 Mar 10. 13(1): 1246
    Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data.
    Aleksandr Ianevski, Anil K Giri, Tero Aittokallio.
      Identification of cell populations often relies on manual annotation of cell clusters using established marker genes. However, the selection of marker genes is a time-consuming process that may lead to sub-optimal annotations as the markers must be informative of both the individual cell clusters and various cell types present in the sample. Here, we developed a computational platform, ScType, which enables a fully-automated and ultra-fast cell-type identification based solely on a given scRNA-seq data, along with a comprehensive cell marker database as background information. Using six scRNA-seq datasets from various human and mouse tissues, we show how ScType provides unbiased and accurate cell type annotations by guaranteeing the specificity of positive and negative marker genes across cell clusters and cell types. We also demonstrate how ScType distinguishes between healthy and malignant cell populations, based on single-cell calling of single-nucleotide variants, making it a versatile tool for anticancer applications. The widely applicable method is deployed both as an interactive web-tool ( https://sctype.app ), and as an open-source R-package.
    DOI:  https://doi.org/10.1038/s41467-022-28803-w
  19. BMC Biol. 2022 Mar 09. 20(1): 64
    BET proteins are essential for the specification and maintenance of the epiblast lineage in mouse preimplantation embryos.
    Mami Tsume-Kajioka, Chiharu Kimura-Yoshida, Kyoko Mochida, Yoko Ueda, Isao Matsuo.
       BACKGROUND: During mammalian preimplantation development, as the fertilized egg develops and differentiates, three cell lineages become specified: trophectoderm (TE), epiblast, and primitive endoderm (PrE). Through two steps of cell fate decisions, 16-cell blastomeres develop into TE and an inner cell mass (ICM), and thereafter, the latter differentiates into pluripotent epiblast and PrE. Although bromodomain and extra-terminal domain (BET) proteins, such as BRD4, are necessary for the transcriptional activation of genes involved in the maintenance of mouse embryonic stem cells by occupying their enhancers, their roles in the development of mouse preimplantation are unknown.
    RESULTS: To evaluate the effect of BET protein deficiency on cell lineage formation, we cultured preimplantation embryos in the presence of JQ1, which blocks the binding of BET bromodomains to acetylated-histones. We found BET inhibition blocked the transcriptional activation of genes, such as Nanog, Otx2, and Sox2, important for the formation of the epiblast lineage in blastocysts. Expression studies with lineage-specific markers in morulae and blastocysts revealed BET proteins were essential for the specification and maintenance of the epiblast lineage but were dispensable for the formation of primarily extraembryonic TE and PrE lineages. Additional Ingenuity Pathway Analysis and expression studies with a transcriptionally active form of signal transducer and activator of the transcription 3 (STAT3) suggested BET-dependent activation was partly associated with the STAT3-dependent pathway to maintain the epiblast lineage. To identify BET proteins involved in the formation of the epiblast lineage, we analyzed mutant embryos deficient in Brd4, Brd2, and double mutants. Abolishment of NANOG-positive epiblast cells was only evident in Brd4/Brd2 double-deficient morulae. Thus, the phenotype of JQ1-treated embryos is reproduced not by a Brd4- or Brd2-single deficiency, but only Brd4/Brd2-double deficiency, demonstrating the redundant roles of BRD2 and BRD4 in the specification of the epiblast lineage.
    CONCLUSIONS: BET proteins are essential to the specification and maintenance of the epiblast lineage by activating lineage-specific core transcription factors during mouse preimplantation development. Among BET proteins, BRD4 plays a central role and BRD2 a complementary role in the specification and maintenance of epiblast lineages. Additionally, BET-dependent maintenance of the epiblast lineage may be partly associated with the STAT3-dependent pathway.
    Keywords:  BET; Blastocyst; Brd2; Brd4; Bromodomain; Epiblast; Inner cell mass; JQ1; Mouse; Nanog
    DOI:  https://doi.org/10.1186/s12915-022-01251-0
  20. Clin Epigenetics. 2022 Mar 11. 14(1): 38
    Chromatin accessibility and transcriptome integrative analysis revealed AP-1-mediated genes potentially modulate histopathology features in psoriasis.
    Xiaoqing Xu, Xianfa Tang, Yuxi Zhang, Zhaobing Pan, Qingping Wang, Lili Tang, Caihong Zhu, Hui Cheng, Fusheng Zhou.
       BACKGROUND: Psoriasis is a chronic and hyperproliferative skin disease featured by hyperkeratosis with parakeratosis, Munro micro-abscess, elongation of rete pegs, granulosa thinning, and lymphocyte infiltration. We previously profiled gene expression and chromatin accessibility of psoriatic skins by transcriptome sequencing and ATAC-seq. However, integrating both of these datasets to unravel gene expression regulation is lacking. Here, we integrated transcriptome and ATAC-seq of the same psoriatic and normal skin tissues, trying to leverage the potential role of chromatin accessibility and their function in histopathology features.
    RESULTS: By inducing binding and expression target analysis (BETA) algorithms, we explored the target prediction of transcription factors binding in 15 psoriatic and 19 control skins. BETA identified 408 upregulated genes (rank product < 0.01) and 133 downregulated genes linked with chromatin accessibility. We noticed that cumulative fraction of genes in upregulation group was statistically higher than background, while that of genes in downregulation group was not significant. KEGG pathway analysis showed that the upregulated 408 genes were enriched in TNF, NOD, and IL-17 signaling pathways. In addition, the motif module in BETA suggested the 57 upregulated genes are targeted by transcription factor AP-1, indicating that increased chromatin accessibility facilitated the binding of AP-1 to the target regions and further induced expression of relevant genes. Among these genes, SQLE, STRN, EIF4, and MYO1B expression was increased in patients with hyperkeratosis, parakeratosis, and acanthosis thickening.
    CONCLUSIONS: In summary, with the advantage of BETA, we identified a series of genes that contribute to the disease pathogenesis, especially in modulating histopathology features, providing us with new clues in treating psoriasis.
    Keywords:  AP-1; ATAC-seq; BETA; Gene expression; Histopathology; Integrated analysis; Psoriasis
    DOI:  https://doi.org/10.1186/s13148-022-01250-6
  21. Genetics. 2022 Mar 09. pii: iyac039. [Epub ahead of print]
    The zinc-finger transcription factor LSL-1 is a major regulator of the germline transcriptional program in C. elegans.
    David Rodriguez-Crespo, Magali Nanchen, Shweta Rajopadhye, Chantal Wicky.
      Specific gene transcriptional programs are required to ensure proper proliferation and differentiation processes underlying the production of specialized cells during development. Gene activity is mainly regulated by the concerted action of transcription factors and chromatin proteins. In the nematode C. elegans, mechanisms that silence improper transcriptional programs in germline and somatic cells have been well studied, however, how are tissue specific sets of genes turned on is less known. LSL-1 is herein defined as a novel crucial transcriptional regulator of germline genes in C. elegans. LSL-1 is first detected in the P4 blastomere and remains present at all stages of germline development, from primordial germ cell proliferation to the end of meiotic prophase. lsl-1 loss-of-function mutants exhibit many defects including meiotic prophase progression delay, a high level of germline apoptosis, and production of almost no functional gametes. Transcriptomic analysis and ChIP-seq data show that LSL-1 binds to promoters and acts as a transcriptional activator of germline genes involved in various processes, including homologous chromosome pairing, recombination, and genome stability. Furthermore, we show that LSL-1 functions by antagonizing the action of the heterochromatin proteins HPL-2/HP1 and LET-418/Mi2 known to be involved in the repression of germline genes in somatic cells. Based on our results, we propose LSL-1 to be a major regulator of the germline transcriptional program during development.
    Keywords:   Caenorhabditis elegans ; ChIP-seq; RNA-seq; chromatin; germline; meiosis; transcription regulation
    DOI:  https://doi.org/10.1093/genetics/iyac039
  22. Sci Rep. 2022 Mar 09. 12(1): 3826
    Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets.
    Catherine Cerutti, Ling Zhang, Violaine Tribollet, Jing-Ru Shi, Riwan Brillet, Benjamin Gillet, Sandrine Hughes, Christelle Forcet, Tie-Liu Shi, Jean-Marc Vanacker.
      Estrogen related receptors are orphan members of the nuclear receptor superfamily acting as transcription factors (TFs). In contrast to classical nuclear receptors, the activities of the ERRs are not controlled by a natural ligand. Regulation of their activities thus relies on availability of transcriptional co-regulators. In this paper, we focus on ERRα, whose involvement in cancer progression has been broadly demonstrated. We propose a new approach to identify potential co-activators, starting from previously identified ERRα-activated genes in a breast cancer (BC) cell line. Considering mRNA gene expression from two sets of human BC cells as major endpoint, we used sparse partial least squares modeling to uncover new transcriptional regulators associated with ERRα. Among them, DDX21, MYBBP1A, NFKB1, and SETD7 are functionally relevant in MDA-MB-231 cells, specifically activating the expression of subsets of ERRα-activated genes. We studied SET7 in more details and showed its co-localization with ERRα and its ERRα-dependent transcriptional and phenotypic effects. Our results thus demonstrate the ability of a modeling approach to identify new transcriptional partners from gene expression. Finally, experimental results show that ERRα cooperates with distinct co-regulators to control the expression of distinct sets of target genes, thus reinforcing the combinatorial specificity of transcription.
    DOI:  https://doi.org/10.1038/s41598-022-07744-w
  23. Nat Commun. 2022 Mar 09. 13(1): 1232
    An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression.
    Ting Shen, Ting Ni, Jiaxuan Chen, Haitao Chen, Xiaopin Ma, Guangwen Cao, Tianzhi Wu, Haisheng Xie, Bin Zhou, Gang Wei, Hexige Saiyin, Suqin Shen, Peng Yu, Qianyi Xiao, Hui Liu, Yuzheng Gao, Xidai Long, Jianhua Yin, Yanfang Guo, Jiaxue Wu, Gong-Hong Wei, Jinlin Hou, De-Ke Jiang.
      Most cancer causal variants are found in gene regulatory elements, e.g., enhancers. However, enhancer variants predisposing to hepatocellular carcinoma (HCC) remain unreported. Here we conduct a genome-wide survey of HCC-susceptible enhancer variants through a three-stage association study in 11,958 individuals and identify rs73613962 (T > G) within the intronic region of PRMT7 at 16q22.1 as a susceptibility locus of HCC (OR = 1.41, P = 6.02 × 10-10). An enhancer dual-luciferase assay indicates that the rs73613962-harboring region has allele-specific enhancer activity. CRISPR-Cas9/dCas9 experiments further support the enhancer activity of this region to regulate PRMT7 expression. Mechanistically, transcription factor HNF4A binds to this enhancer region, with preference to the risk allele G, to promote PRMT7 expression. PRMT7 upregulation contributes to in vitro, in vivo, and clinical HCC-associated phenotypes, possibly by affecting the p53 signaling pathway. This concept of HCC pathogenesis may open a promising window for HCC prevention/treatment.
    DOI:  https://doi.org/10.1038/s41467-022-28861-0
  24. Cell Genom. 2022 Feb 09. pii: 100098. [Epub ahead of print]2(2):
    CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.
    David Bray, Heather Hook, Rose Zhao, Jessica L Keenan, Ashley Penvose, Yemi Osayame, Nima Mohaghegh, Xiaoting Chen, Sreeja Parameswaran, Leah C Kottyan, Matthew T Weirauch, Trevor Siggers.
      Non-coding DNA variants (NCVs) impact gene expression by altering binding sites for regulatory complexes. New high-throughput methods are needed to characterize the impact of NCVs on regulatory complexes. We developed CASCADE (Customizable Approach to Survey Complex Assembly at DNA Elements), an array-based high-throughput method to profile cofactor (COF) recruitment. CASCADE identifies DNA-bound transcription factor-cofactor (TF-COF) complexes in nuclear extracts and quantifies the impact of NCVs on their binding. We demonstrate CASCADE sensitivity in characterizing condition-specific recruitment of COFs p300 and RBBP5 (MLL subunit) to the CXCL10 promoter in lipopolysaccharide (LPS)-stimulated human macrophages and quantify the impact of all possible NCVs. To demonstrate applicability to NCV screens, we profile TF-COF binding to ~1,700 single-nucleotide polymorphism quantitative trait loci (SNP-QTLs) in human macrophages and identify perturbed ETS domain-containing complexes. CASCADE will facilitate high-throughput testing of molecular mechanisms of NCVs for diverse biological applications.
    DOI:  https://doi.org/10.1016/j.xgen.2022.100098
  25. Genes Dev. 2022 Mar 10.
    Nucleolar-based Dux repression is essential for embryonic two-cell stage exit.
    Sheila Q Xie, Bryony J Leeke, Chad Whilding, Ryan T Wagner, Ferran Garcia-Llagostera, YiXuan Low, Paul Chammas, Nathan T-F Cheung, Dirk Dormann, Michael T McManus, Michelle Percharde.
      Upon fertilization, the mammalian embryo must switch from dependence on maternal transcripts to transcribing its own genome, and in mice this involves the transient up-regulation of MERVL transposons and MERVL-driven genes at the two-cell stage. The mechanisms and requirement for MERVL and two-cell (2C) gene up-regulation are poorly understood. Moreover, this MERVL-driven transcriptional program must be rapidly shut off to allow two-cell exit and developmental progression. Here, we report that robust ribosomal RNA (rRNA) synthesis and nucleolar maturation are essential for exit from the 2C state. 2C-like cells and two-cell embryos show similar immature nucleoli with altered structure and reduced rRNA output. We reveal that nucleolar disruption via blocking RNA polymerase I activity or preventing nucleolar phase separation enhances conversion to a 2C-like state in embryonic stem cells (ESCs) by detachment of the MERVL activator Dux from the nucleolar surface. In embryos, nucleolar disruption prevents proper nucleolar maturation and Dux silencing and leads to two- to four-cell arrest. Our findings reveal an intriguing link between rRNA synthesis, nucleolar maturation, and gene repression during early development.
    Keywords:  2C-like state; Dux; MERVL; nucleolus; totipotency
    DOI:  https://doi.org/10.1101/gad.349172.121
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