bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–10–25
27 papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.
  2. Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development.
  3. Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility.
  4. EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma.
  5. Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis.
  6. Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions.
  7. Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging.
  8. Defining the Functional Targets of Cap'n'collar Transcription Factors NRF1, NRF2, and NRF3.
  9. Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells.
  10. SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity.
  11. ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures.
  12. Pan-cancer analysis of differential DNA methylation patterns.
  13. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.
  14. VARAdb: a comprehensive variation annotation database for human.
  15. Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity.
  16. VGLL4 promotes osteoblast differentiation by antagonizing TEADs-inhibited Runx2 transcription.
  17. MITF is a driver oncogene and potential therapeutic target in kidney angiomyolipoma tumors through transcriptional regulation of CYR61.
  18. A Regulation Loop between YAP and NR4A1 Balances Cell Proliferation and Apoptosis.
  19. Predicting enhancer-promoter interactions by deep learning and matching heuristic.
  20. PCNA antagonizes cohesin-dependent roles in genomic stability.
  21. ARID1A loss in adult hepatocytes activates β-catenin-mediated erythropoietin transcription.
  22. Epigenetic silencing of ZIC4 contributes to cancer progression in hepatocellular carcinoma.
  23. The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
  24. The transcription factor Sox10 is an essential determinant of branching morphogenesis and involution in the mouse mammary gland.
  25. Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1.
  26. Regulation of single-cell genome organization into TADs and chromatin nanodomains.
  27. MARS: discovering novel cell types across heterogeneous single-cell experiments.
  1. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31282-1. [Epub ahead of print]33(3): 108293
    Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.
    Mayinuer Maitituoheti, Emily Z Keung, Ming Tang, Liang Yan, Hunain Alam, Guangchun Han, Anand K Singh, Ayush T Raman, Christopher Terranova, Sharmistha Sarkar, Elias Orouji, Samir B Amin, Sneha Sharma, Maura Williams, Neha S Samant, Mayura Dhamdhere, Norman Zheng, Tara Shah, Amiksha Shah, Jacob B Axelrad, Nazanin E Anvar, Yu-Hsi Lin, Shan Jiang, Edward Q Chang, Davis R Ingram, Wei-Lien Wang, Alexander Lazar, Min Gyu Lee, Florian Muller, Linghua Wang, Haoqiang Ying, Kunal Rai.
      Histone methyltransferase KMT2D harbors frequent loss-of-function somatic point mutations in several tumor types, including melanoma. Here, we identify KMT2D as a potent tumor suppressor in melanoma through an in vivo epigenome-focused pooled RNAi screen and confirm the finding by using a genetically engineered mouse model (GEMM) based on conditional and melanocyte-specific deletion of KMT2D. KMT2D-deficient tumors show substantial reprogramming of key metabolic pathways, including glycolysis. KMT2D deficiency aberrantly upregulates glycolysis enzymes, intermediate metabolites, and glucose consumption rates. Mechanistically, KMT2D loss causes genome-wide reduction of H3K4me1-marked active enhancer chromatin states. Enhancer loss and subsequent repression of IGFBP5 activates IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. Pharmacological inhibition of glycolysis and insulin growth factor (IGF) signaling reduce proliferation and tumorigenesis preferentially in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating an increased use of the glycolysis pathway for enhanced biomass needs via enhancer reprogramming, thus presenting an opportunity for therapeutic intervention through glycolysis or IGF pathway inhibitors.
    Keywords:  2-DG; IGFBP5; KMT2D; Linsitinib; RNAi screen; chromatin; epigenetics; glycolysis; melanoma; mouse model
    DOI:  https://doi.org/10.1016/j.celrep.2020.108293
  2. Nat Commun. 2020 10 19. 11(1): 5275
    Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development.
    Shu Zhang, Yueli Cui, Xinyi Ma, Jun Yong, Liying Yan, Ming Yang, Jie Ren, Fuchou Tang, Lu Wen, Jie Qiao.
      The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. Corticotropes exhibit an early intermediate state prior to full differentiation. Three cell types of the PIT-1 lineage (somatotropes, lactotropes and thyrotropes) segregate from a common progenitor coexpressing lineage-specific transcription factors of different sublineages. Gonadotropes experience two multistep developmental trajectories. Furthermore, we identify a fetal gonadotrope cell subtype expressing the primate-specific hormone chorionic gonadotropin. We also characterize the cellular heterogeneity of pituitary stem cells and identify a hybrid epithelial/mesenchymal state and an early-to-late state transition. Here, our results provide insights into the transcriptional landscape of human pituitary development, defining distinct cell substates and subtypes and illustrating transcription factor dynamics during cell fate commitment.
    DOI:  https://doi.org/10.1038/s41467-020-19012-4
  3. Elife. 2020 Oct 19. pii: e56429. [Epub ahead of print]9
    Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility.
    Elizabeth Eck, Jonathan Liu, Maryam Kazemzadeh-Atoufi, Sydney Ghoreishi, Shelby A Blythe, Hernan G Garcia.
      Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes chromatin accessibility and energy expenditure may call for a different framework. Here we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate hunchback transcription. Therefore, we explored a model where DNA accessibility is not the result of thermal fluctuations but is catalyzed by Bicoid and Zelda, possibly through histone acetylation, and found that this model can predict hunchback dynamics. Thus, our theory-experiment dialogue uncovered potential molecular mechanisms of transcriptional regulatory dynamics, a key step toward reaching a predictive understanding of developmental decision-making.
    Keywords:  D. melanogaster; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.56429
  4. Nucleic Acids Res. 2020 Oct 20. pii: gkaa901. [Epub ahead of print]
    EWS-FLI1 regulates and cooperates with core regulatory circuitry in Ewing sarcoma.
    Xianping Shi, Yueyuan Zheng, Liling Jiang, Bo Zhou, Wei Yang, Liyan Li, Lingwen Ding, Moli Huang, Sigal Gery, De-Chen Lin, H Phillip Koeffler.
      Core regulatory circuitry (CRC)-dependent transcriptional network is critical for developmental tumors in children and adolescents carrying few gene mutations. However, whether and how CRC contributes to transcription regulation in Ewing sarcoma is unknown. Here, we identify and functionally validate a CRC 'trio' constituted by three transcription factors (TFs): KLF15, TCF4 and NKX2-2, in Ewing sarcoma cells. Epigenomic analyses demonstrate that EWS-FLI1, the primary fusion driver for this cancer, directly establishes super-enhancers of each of these three TFs to activate their transcription. In turn, KLF15, TCF4 and NKX2-2 co-bind to their own and each other's super-enhancers and promoters, forming an inter-connected auto-regulatory loop. Functionally, CRC factors contribute significantly to cell proliferation of Ewing sarcoma both in vitro and in vivo. Mechanistically, CRC factors exhibit prominent capacity of co-regulating the epigenome in cooperation with EWS-FLI1, occupying 77.2% of promoters and 55.6% of enhancers genome-wide. Downstream, CRC TFs coordinately regulate gene expression networks in Ewing sarcoma, controlling important signaling pathways for cancer, such as lipid metabolism pathway, PI3K/AKT and MAPK signaling pathways. Together, molecular characterization of the oncogenic CRC model advances our understanding of the biology of Ewing sarcoma. Moreover, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.
    DOI:  https://doi.org/10.1093/nar/gkaa901
  5. iScience. 2020 Oct 23. 23(10): 101596
    Unique Epigenetic Programming Distinguishes Regenerative Spermatogonial Stem Cells in the Developing Mouse Testis.
    Keren Cheng, I-Chung Chen, Ching-Hsun Eric Cheng, Kazadi Mutoji, Benjamin J Hale, Brian P Hermann, Christopher B Geyer, Jon M Oatley, John R McCarrey.
      Spermatogonial stem cells (SSCs) both self-renew and give rise to progenitors that initiate spermatogenic differentiation in the mammalian testis. Questions remain regarding the extent to which the SSC and progenitor states are functionally distinct. Here we provide the first multiparametric integrative analysis of mammalian germ cell epigenomes comparable with that done for >100 somatic cell types by the ENCODE Project. Differentially expressed genes distinguishing SSC- and progenitor-enriched spermatogonia showed distinct histone modification patterns, particularly for H3K27ac and H3K27me3. Motif analysis predicted transcription factors that may regulate spermatogonial subtype-specific fate, and immunohistochemistry and gene-specific chromatin immunoprecipitation analyses confirmed subtype-specific differences in target gene binding of a subset of these factors. Taken together, these results show that SSCs and progenitors display distinct epigenetic profiling consistent with these spermatogonial subtypes being differentially programmed to either self-renew and maintain regenerative capacity as SSCs or lose regenerative capacity and initiate lineage commitment as progenitors.
    Keywords:  Developmental Genetics; Omics
    DOI:  https://doi.org/10.1016/j.isci.2020.101596
  6. iScience. 2020 Sep 25. 23(9): 101539
    Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions.
    Irene Salamon, Simone Serio, Simona Bianco, Christina Pagiatakis, Silvia Crasto, Andrea M Chiariello, Mattia Conte, Paola Cattaneo, Luca Fiorillo, Arianna Felicetta, Elisa di Pasquale, Paolo Kunderfranco, Mario Nicodemi, Roberto Papait, Gianluigi Condorelli.
      Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5-a gene specifying a master cardiomyogenic lineage transcription factor (TF)-which we call Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs). The IRENEs are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5: IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription.
    Keywords:  Biological Sciences; Molecular Biology; Molecular Mechanism of Gene Regulation
    DOI:  https://doi.org/10.1016/j.isci.2020.101539
  7. Mol Cell. 2020 Oct 14. pii: S1097-2765(20)30684-5. [Epub ahead of print]
    Opposing Effects of Cohesin and Transcription on CTCF Organization Revealed by Super-resolution Imaging.
    Bo Gu, Colin J Comerci, Dannielle G McCarthy, Saumya Saurabh, W E Moerner, Joanna Wysocka.
      CCCTC-binding factor (CTCF) and cohesin play critical roles in organizing mammalian genomes into topologically associating domains (TADs). Here, by combining genetic engineering with quantitative super-resolution stimulated emission depletion (STED) microscopy, we demonstrate that in living cells, CTCF forms clusters typically containing 2-8 molecules. A fraction of CTCF clusters, enriched for those with ≥3 molecules, are coupled with cohesin complexes with a characteristic physical distance suggestive of a defined molecular interaction. Acute degradation of the cohesin unloader WAPL or transcriptional inhibition (TI) result in increased CTCF clustering. Furthermore, the effect of TI on CTCF clusters is alleviated by the acute loss of the cohesin subunit SMC3. Our study provides quantitative characterization of CTCF clusters in living cells, uncovers the opposing effects of cohesin and transcription on CTCF clustering, and highlights the power of quantitative super-resolution microscopy as a tool to bridge the gap between biochemical and genomic methodologies in chromatin research.
    Keywords:  CTCF; Pol II; chromatin; cohesin; quantitative analysis; super-resolution imaging; topological associated domain; transcription
    DOI:  https://doi.org/10.1016/j.molcel.2020.10.001
  8. Antioxidants (Basel). 2020 Oct 21. pii: E1025. [Epub ahead of print]9(10):
    Defining the Functional Targets of Cap'n'collar Transcription Factors NRF1, NRF2, and NRF3.
    Lara Ibrahim, Jaleh Mesgarzadeh, Ian Xu, Evan T Powers, R Luke Wiseman, Michael J Bollong.
      The NRF transcription factors NRF1, NRF2, and NRF3, are a subset of Cap'n'collar transcriptional regulators which modulate the expression of genes harboring antioxidant-response element (ARE) sequences within their genomic loci. Despite the emerging physiological importance of NRF family members, the repertoire of their genetic targets remains incompletely defined. Here we use RNA-sequencing-based transcriptional profiling and quantitative proteomics to delineate the overlapping and differential genetic programs effected by the three NRF transcription factors. We then create consensus target gene sets regulated by NRF1, NRF2, and NRF3 and define the integrity of these gene sets for probing NRF activity in mammalian cell culture and human tissues. Together, our data provide a quantitative assessment of how NRF family members sculpt proteomes and transcriptomes, providing a framework to understand the critical physiological importance of NRF transcription factors and to establish pharmacologic approaches for therapeutically activating these transcriptional programs in disease.
    Keywords:  NRF transcription factors; cellular pathway analysis; oxidative stress response; proteomics; transcriptomics
    DOI:  https://doi.org/10.3390/antiox9101025
  9. Nat Commun. 2020 10 21. 11(1): 5292
    Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells.
    Hiroki Inada, Miyako Udono, Kanae Matsuda-Ito, Kenichi Horisawa, Yasuyuki Ohkawa, Shizuka Miura, Takeshi Goya, Junpei Yamamoto, Masao Nagasaki, Kazuko Ueno, Daisuke Saitou, Mikita Suyama, Yoshihiko Maehara, Wataru Kumamaru, Yoshihiro Ogawa, Sayaka Sekiya, Atsushi Suzuki.
      Recent advances have enabled the direct induction of human tissue-specific stem and progenitor cells from differentiated somatic cells. However, it is not known whether human hepatic progenitor cells (hHepPCs) can be generated from other cell types by direct lineage reprogramming with defined transcription factors. Here, we show that a set of three transcription factors, FOXA3, HNF1A, and HNF6, can induce human umbilical vein endothelial cells to directly acquire the properties of hHepPCs. These induced hHepPCs (hiHepPCs) propagate in long-term monolayer culture and differentiate into functional hepatocytes and cholangiocytes by forming cell aggregates and cystic epithelial spheroids, respectively, under three-dimensional culture conditions. After transplantation, hiHepPC-derived hepatocytes and cholangiocytes reconstitute damaged liver tissues and support hepatic function. The defined transcription factors also induce hiHepPCs from endothelial cells circulating in adult human peripheral blood. These expandable and bipotential hiHepPCs may be useful in the study and treatment of human liver diseases.
    DOI:  https://doi.org/10.1038/s41467-020-19041-z
  10. Hum Mol Genet. 2020 Oct 19. pii: ddaa227. [Epub ahead of print]
    SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity.
    Jake J Reske, Mike R Wilson, Jeanne Holladay, Marc Wegener, Marie Adams, Ronald L Chandler.
      Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of BRG1 (SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than 1/3 of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
    DOI:  https://doi.org/10.1093/hmg/ddaa227
  11. Nucleic Acids Res. 2020 Oct 19. pii: gkaa872. [Epub ahead of print]
    ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures.
    Tiantian Ye, Wenxiu Ma.
      The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations. The ASHIC software is publicly available at https://github.com/wmalab/ASHIC.
    DOI:  https://doi.org/10.1093/nar/gkaa872
  12. BMC Med Genomics. 2020 Oct 22. 13(Suppl 10): 154
    Pan-cancer analysis of differential DNA methylation patterns.
    Mai Shi, Stephen Kwok-Wing Tsui, Hao Wu, Yingying Wei.
       BACKGROUND: DNA methylation is a key epigenetic regulator contributing to cancer development. To understand the role of DNA methylation in tumorigenesis, it is important to investigate and compare differential methylation (DM) patterns between normal and case samples across different cancer types. However, current pan-cancer analyses call DM separately for each cancer, which suffers from lower statistical power and fails to provide a comprehensive view for patterns across cancers.
    METHODS: In this work, we propose a rigorous statistical model, PanDM, to jointly characterize DM patterns across diverse cancer types. PanDM uses the hidden correlations in the combined dataset to improve statistical power through joint modeling. PanDM takes summary statistics from separate analyses as input and performs methylation site clustering, differential methylation detection, and pan-cancer pattern discovery. We demonstrate the favorable performance of PanDM using simulation data. We apply our model to 12 cancer methylome data collected from The Cancer Genome Atlas (TCGA) project. We further conduct ontology- and pathway-enrichment analyses to gain new biological insights into the pan-cancer DM patterns learned by PanDM.
    RESULTS: PanDM outperforms two types of separate analyses in the power of DM calling in the simulation study. Application of PanDM to TCGA data reveals 37 pan-cancer DM patterns in the 12 cancer methylomes, including both common and cancer-type-specific patterns. These 37 patterns are in turn used to group cancer types. Functional ontology and biological pathways enriched in the non-common patterns not only underpin the cancer-type-specific etiology and pathogenesis but also unveil the common environmental risk factors shared by multiple cancer types. Moreover, we also identify PanDM-specific DM CpG sites that the common strategy fails to detect.
    CONCLUSIONS: PanDM is a powerful tool that provides a systematic way to investigate aberrant methylation patterns across multiple cancer types. Results from real data analyses suggest a novel angle for us to understand the common and specific DM patterns in different cancers. Moreover, as PanDM works on the summary statistics for each cancer type, the same framework can in principle be applied to pan-cancer analyses of other functional genomic profiles. We implement PanDM as an R package, which is freely available at http://www.sta.cuhk.edu.hk/YWei/PanDM.html .
    Keywords:  Cancer epigenomics; DNA methylation; Differential methylation; Pan-cancer
    DOI:  https://doi.org/10.1186/s12920-020-00780-3
  13. Nat Genet. 2020 Oct 19.
    CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction.
    Silvia Galan, Nick Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, Juan M Vaquerizas.
      Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
    DOI:  https://doi.org/10.1038/s41588-020-00712-y
  14. Nucleic Acids Res. 2020 Oct 23. pii: gkaa922. [Epub ahead of print]
    VARAdb: a comprehensive variation annotation database for human.
    Qi Pan, Yue-Juan Liu, Xue-Feng Bai, Xiao-Le Han, Yong Jiang, Bo Ai, Shan-Shan Shi, Fan Wang, Ming-Cong Xu, Yue-Zhu Wang, Jun Zhao, Jia-Xin Chen, Jian Zhang, Xue-Cang Li, Jiang Zhu, Guo-Rui Zhang, Qiu-Yu Wang, Chun-Quan Li.
      With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.
    DOI:  https://doi.org/10.1093/nar/gkaa922
  15. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31262-6. [Epub ahead of print]33(3): 108273
    Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity.
    Nicholas Pervolarakis, Quy H Nguyen, Justice Williams, Yanwen Gong, Guadalupe Gutierrez, Peng Sun, Darisha Jhutty, Grace X Y Zheng, Corey M Nemec, Xing Dai, Kazuhide Watanabe, Kai Kessenbrock.
      The mammary epithelial cell (MEC) system is a bilayered ductal epithelium of luminal and basal cells, maintained by a lineage of stem and progenitor populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define differentiation states within the secretory type of luminal cells, which forms a continuous spectrum of general luminal progenitor and lactation-committed progenitor cells. By integrating single-cell transcriptomics and chromatin accessibility landscapes, we identify cis- and trans-regulatory elements that are differentially activated in the specific epithelial cell types and our newly defined luminal differentiation states. Our work provides a resource to reveal cis/trans-regulatory elements associated with MEC identity and differentiation that will serve as a reference to determine how the chromatin accessibility landscape changes during breast cancer.
    Keywords:  cellular heterogeneity; chromatin accessibility; mammary stem cells; single-cell genomics; transcriptomics
    DOI:  https://doi.org/10.1016/j.celrep.2020.108273
  16. Sci Adv. 2020 Oct;pii: eaba4147. [Epub ahead of print]6(43):
    VGLL4 promotes osteoblast differentiation by antagonizing TEADs-inhibited Runx2 transcription.
    Jinlong Suo, Xue Feng, Jiayi Li, Jinghui Wang, Zuoyun Wang, Lei Zhang, Weiguo Zou.
      VGLL4 has been identified as a YAP inhibitor. However, the exact function of VGLL4 in bone development and bone homeostasis remains unclear. In this study, we demonstrated that VGLL4 breaks TEADs-mediated transcriptional inhibition of RUNX2 to promote osteoblast differentiation and bone development. We found that knockout of VGLL4 in mesenchymal stem cells and preosteoblasts showed osteoporosis and a cleidocranial dysplasia-like phenotype due to osteoblast differentiation disorders. Mechanistically, we showed that the TEAD transcriptional factors severely inhibited osteoblast differentiation in a YAP binding-independent manner. TEADs interacted with RUNX2 to repress RUNX2 transcriptional activity. Furthermore, VGLL4 relieved the transcriptional inhibition of TEADs by directly competing with RUNX2 to bind TEADs through its two TDU domains. Collectively, our studies demonstrate that VGLL4 plays an important role in regulating osteoblast differentiation and bone development, and that TEADs regulate the transcriptional activity of RUNX2, which may shed light on treatment of cleidocranial dysplasia and osteoporosis.
    DOI:  https://doi.org/10.1126/sciadv.aba4147
  17. Oncogene. 2020 Oct 20.
    MITF is a driver oncogene and potential therapeutic target in kidney angiomyolipoma tumors through transcriptional regulation of CYR61.
    Mahsa Zarei, Krinio Giannikou, Heng Du, Heng-Jia Liu, Melissa Duarte, Sneha Johnson, Amin H Nassar, Hans R Widlund, Elizabeth P Henske, Henry W Long, David J Kwiatkowski.
      Tuberous sclerosis complex (TSC) is an autosomal dominant tumor suppressor syndrome, characterized by tumor development in multiple organs, including renal angiomyolipoma. Biallelic loss of TSC1 or TSC2 is a known genetic driver of angiomyolipoma development, however, whether an altered transcriptional repertoire contributes to TSC-associated tumorigenesis is unknown. RNA-seq analyses showed that MITF A isoform (MITF-A) was consistently highly expressed in angiomyolipoma, immunohistochemistry showed microphthalmia-associated transcription factor nuclear localization, and Chromatin immuno-Precipitation Sequencing analysis showed that the MITF-A transcriptional start site was highly enriched with H3K27ac marks. Using the angiomyolipoma cell line 621-101, MITF knockout (MITF.KO) and MITF-A overexpressing (MITF.OE) cell lines were generated. MITF.KO cells showed markedly reduced growth and invasion in vitro, and were unable to form xenografted tumors. In contrast, MITF.OE cells grew faster in vitro and as xenografted tumors compared to control cells. RNA-Seq analysis showed that both ID2 and Cysteine-rich angiogenic inducer 61 (CYR61) expression levels were increased in the MITF.OE cells and reduced in the MITF.KO cells, and luciferase assays showed this was due to transcriptional effects. Importantly, CYR61 overexpression rescued MITF.KO cell growth in vitro and tumor growth in vivo. These findings suggest that MITF-A is a transcriptional oncogenic driver of angiomyolipoma tumor development, acting through regulation of CYR61.
    DOI:  https://doi.org/10.1038/s41388-020-01504-8
  18. Cell Rep. 2020 Oct 20. pii: S2211-1247(20)31273-0. [Epub ahead of print]33(3): 108284
    A Regulation Loop between YAP and NR4A1 Balances Cell Proliferation and Apoptosis.
    Lingli He, Liang Yuan, Wentao Yu, Yang Sun, Dan Jiang, Xiaodong Wang, Xue Feng, Zuoyun Wang, Jinjin Xu, Ruizeng Yang, Wenxiang Zhang, Hua Feng, Hang-Zi Chen, Yi Arial Zeng, Lijian Hui, Qiao Wu, Yonglong Zhang, Lei Zhang.
      The Hippo signaling pathway maintains organ size and tissue homeostasis via orchestration of cell proliferation and apoptosis. How this pathway triggers cell apoptosis remains largely unexplored. Here, we identify NR4A1 as a target of the Hippo pathway that mediates the pro-apoptotic and anti-tumor effects of the Hippo pathway whereby YAP regulates the transcription, phosphorylation, and mitochondrial localization of NR4A1. NR4A1, in turn, functions as a feedback inhibitor of YAP to promote its degradation, thereby inhibiting the function of YAP during liver regeneration and tumorigenesis. Our studies elucidate a regulatory loop between NR4A1 and YAP to coordinate Hippo signaling activity during liver regeneration and tumorigenesis and highlight NR4A1 as a marker of Hippo signaling, as well as a therapeutic target for hepatocellular carcinoma.
    Keywords:  Hippo signaling pathway; NR4A1; apoptosis; hepatocellular carcinoma (HCC); liver regeneration
    DOI:  https://doi.org/10.1016/j.celrep.2020.108284
  19. Brief Bioinform. 2020 Oct 24. pii: bbaa254. [Epub ahead of print]
    Predicting enhancer-promoter interactions by deep learning and matching heuristic.
    Xiaoping Min, Congmin Ye, Xiangrong Liu, Xiangxiang Zeng.
      Enhancer-promoter interactions (EPIs) play an important role in transcriptional regulation. Recently, machine learning-based methods have been widely used in the genome-scale identification of EPIs due to their promising predictive performance. In this paper, we propose a novel method, termed EPI-DLMH, for predicting EPIs with the use of DNA sequences only. EPI-DLMH consists of three major steps. First, a two-layer convolutional neural network is used to learn local features, and an bidirectional gated recurrent unit network is used to capture long-range dependencies on the sequences of promoters and enhancers. Second, an attention mechanism is used for focusing on relatively important features. Finally, a matching heuristic mechanism is introduced for the exploration of the interaction between enhancers and promoters. We use benchmark datasets in evaluating and comparing the proposed method with existing methods. Comparative results show that our model is superior to currently existing models in multiple cell lines. Specifically, we found that the matching heuristic mechanism introduced into the proposed model mainly contributes to the improvement of performance in terms of overall accuracy. Additionally, compared with existing models, our model is more efficient with regard to computational speed.
    Keywords:  DNA sequence; deep learning; enhancer-promoter interactions; matching heuristic; pretraining
    DOI:  https://doi.org/10.1093/bib/bbaa254
  20. PLoS One. 2020 ;15(10): e0235103
    PCNA antagonizes cohesin-dependent roles in genomic stability.
    Caitlin M Zuilkoski, Robert V Skibbens.
      PCNA sliding clamp binds factors through which histone deposition, chromatin remodeling, and DNA repair are coupled to DNA replication. PCNA also directly binds Eco1/Ctf7 acetyltransferase, which in turn activates cohesins and establishes cohesion between nascent sister chromatids. While increased recruitment thus explains the mechanism through which elevated levels of chromatin-bound PCNA rescue eco1 mutant cell growth, the mechanism through which PCNA instead worsens cohesin mutant cell growth remains unknown. Possibilities include that elevated levels of long-lived chromatin-bound PCNA reduce either cohesin deposition onto DNA or cohesin acetylation. Instead, our results reveal that PCNA increases the levels of both chromatin-bound cohesin and cohesin acetylation. Beyond sister chromatid cohesion, PCNA also plays a critical role in genomic stability such that high levels of chromatin-bound PCNA elevate genotoxic sensitivities and recombination rates. At a relatively modest increase of chromatin-bound PCNA, however, fork stability and progression appear normal in wildtype cells. Our results reveal that even a moderate increase of PCNA indeed sensitizes cohesin mutant cells to DNA damaging agents and in a process that involves the DNA damage response kinase Mec1(ATR), but not Tel1(ATM). These and other findings suggest that PCNA mis-regulation results in genome instabilities that normally are resolved by cohesin. Elevating levels of chromatin-bound PCNA may thus help target cohesinopathic cells linked that are linked to cancer.
    DOI:  https://doi.org/10.1371/journal.pone.0235103
  21. Elife. 2020 Oct 21. pii: e53550. [Epub ahead of print]9
    ARID1A loss in adult hepatocytes activates β-catenin-mediated erythropoietin transcription.
    Rozenn Riou, Meriem Ladli, Sabine Gerbal-Chaloin, Pascale Bossard, Angélique Gougelet, Cécile Godard, Robin Loesch, Isabelle Lagoutte, Franck Lager, Julien Calderaro, Alexandre Dos Santos, Zhong Wang, Frédérique Verdier, Sabine Colnot.
      Erythropoietin (EPO) is a key regulator of erythropoiesis. The embryonic liver is the main site of erythropoietin synthesis, after which the kidney takes over. The adult liver retains the ability to express EPO, and we discovered here new players of this transcription, distinct from the classical hypoxia-inducible factor pathway. In mice genetically-invalidated in hepatocytes for the chromatin remodeler Arid1a, and for Apc, the major silencer of Wnt pathway, chromatin was more accessible and histone marks turned into active ones at the Epo downstream enhancer. Activating β-catenin signaling increased binding of Tcf4/β-catenin complex and upregulated its enhancer function. The loss of Arid1a together with β-catenin signaling, resulted in cell-autonomous EPO transcription in mouse and human hepatocytes. In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. Thus, we identified new hepatic EPO regulation mechanism stimulating erythropoiesis.
    Keywords:  chromosomes; developmental biology; gene expression; human; mouse
    DOI:  https://doi.org/10.7554/eLife.53550
  22. Cell Death Dis. 2020 Oct 23. 11(10): 906
    Epigenetic silencing of ZIC4 contributes to cancer progression in hepatocellular carcinoma.
    Wenbiao Chen, Donge Tang, Dongxin Tang, Yong Dai.
      Inactivation of tumor suppressor gene played critical roles in the development and progression of human hepatocellular carcinoma (HCC). Zic family member 4 (ZIC4) is transcription factor and plays an important role in the developmental process. However, the expression and biological role of ZIC4 in HCC is poorly understood. Here, bioinformatics analysis based on The Cancer Genome Atlas (TCGA) database revealed an aberrant hypermethylation of ZIC4 in HCC. ZIC4 is frequently hypermethylated in promoter region and down expressed in HCC cells and tissues. Functionally, ZIC4 inhibition facilitated the proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and in vivo. Conversely, ZIC4 overexpression reduced proliferation and invasiveness of HCC cells. In addition, ZIC4 inhibition rescued the antitumor effect induced by enhancer of zeste homolog 2 (EZH2) knockdown or EZH2 inhibitor. Mechanistically, EZH2 knockdown or EZH2 inhibitor reduced the enrichment of EZH2 and H3K27me3 in ZIC4 promoter region and leading to the upregulation of ZIC4. Altogether, these data indicate that epigenetic silencing of ZIC4 by EZH2 mediated H3K27me3 is an important mechanism in HCC and provide a new therapeutic target for the treatment of hepatocellular carcinoma disease.
    DOI:  https://doi.org/10.1038/s41419-020-03109-1
  23. Cell Death Dis. 2020 Oct 17. 11(10): 873
    The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
    Florian Wegwitz, Evangelos Prokakis, Anastasija Pejkovska, Robyn Laura Kosinsky, Markus Glatzel, Klaus Pantel, Harriet Wikman, Steven A Johnsen.
      The HER2-positive breast cancer subtype (HER2+-BC) displays a particularly aggressive behavior. Anti-HER2 therapies have significantly improved the survival of patients with HER2+-BC. However, a large number of patients become refractory to current targeted therapies, necessitating the development of new treatment strategies. Epigenetic regulators are commonly misregulated in cancer and represent attractive molecular therapeutic targets. Monoubiquitination of histone 2B (H2Bub1) by the heterodimeric ubiquitin ligase complex RNF20/RNF40 has been described to have tumor suppressor functions and loss of H2Bub1 has been associated with cancer progression. In this study, we utilized human tumor samples, cell culture models, and a mammary carcinoma mouse model with tissue-specific Rnf40 deletion and identified an unexpected tumor-supportive role of RNF40 in HER2+-BC. We demonstrate that RNF40-driven H2B monoubiquitination is essential for transcriptional activation of RHO/ROCK/LIMK pathway components and proper actin-cytoskeleton dynamics through a trans-histone crosstalk with histone 3 lysine 4 trimethylation (H3K4me3). Collectively, this work demonstrates a previously unknown essential role of RNF40 in HER2+-BC, revealing the H2B monoubiquitination axis as a possible tumor context-dependent therapeutic target in breast cancer.
    DOI:  https://doi.org/10.1038/s41419-020-03081-w
  24. Sci Rep. 2020 Oct 20. 10(1): 17807
    The transcription factor Sox10 is an essential determinant of branching morphogenesis and involution in the mouse mammary gland.
    Svenja Mertelmeyer, Matthias Weider, Tina Baroti, Simone Reiprich, Franziska Fröb, C Claus Stolt, Kay-Uwe Wagner, Michael Wegner.
      The high mobility group-domain containing transcription factor Sox10 is an essential regulator of developmental processes and homeostasis in the neural crest, several neural crest-derived lineages and myelinating glia. Recent studies have also implicated Sox10 as an important factor in mammary stem and precursor cells. Here we employ a series of mouse mutants with constitutive and conditional Sox10 deficiencies to show that Sox10 has multiple functions in the developing mammary gland. While there is no indication for a requirement of Sox10 in the specification of the mammary placode or descending mammary bud, it is essential for both the prenatal hormone-independent as well as the pubertal hormone-dependent branching of the mammary epithelium and for proper alveologenesis during pregnancy. It furthermore acts in a dosage-dependent manner. Sox10 also plays a role during the involution process at the end of the lactation period. Whereas its effect on epithelial branching and alveologenesis are likely causally related to its function in mammary stem and precursor cells, this is not the case for its function during involution where Sox10 seems to work at least in part through regulation of the miR-424(322)/503 cluster.
    DOI:  https://doi.org/10.1038/s41598-020-74664-y
  25. Nat Metab. 2020 Oct 19.
    Cytosolic pH regulates proliferation and tumour growth by promoting expression of cyclin D1.
    Lisa Maria Koch, Eivind Salmorin Birkeland, Stefania Battaglioni, Xiao Helle, Mayura Meerang, Stefanie Hiltbrunner, Alfredo J Ibáñez, Matthias Peter, Alessandra Curioni-Fontecedro, Isabelle Opitz, Reinhard Dechant.
      Enhanced growth and proliferation of cancer cells are accompanied by profound changes in cellular metabolism. These metabolic changes are also common under physiological conditions, and include increased glucose fermentation accompanied by elevated cytosolic pH (pHc)1,2. However, how these changes contribute to enhanced cell growth and proliferation is unclear. Here, we show that elevated pHc specifically orchestrates an E2F-dependent transcriptional programme to drive cell proliferation by promoting cyclin D1 expression. pHc-dependent transcription of cyclin D1 requires the transcription factors CREB1, ATF1 and ETS1, and the histone acetyltransferases p300 and CBP. Biochemical characterization revealed that the CREB1-p300/CBP interaction acts as a pH sensor and coincidence detector, integrating different mitotic signals to regulate cyclin D1 transcription. We also show that elevated pHc contributes to increased cyclin D1 expression in malignant pleural mesotheliomas (MPMs), and renders these cells hypersensitive to pharmacological reduction of pHc. Taken together, these data demonstrate that elevated pHc is a critical cellular signal regulating G1 progression, and provide a mechanism linking elevated pHc to oncogenic activation of cyclin D1 in MPMs, and possibly other cyclin D1~dependent tumours. Thus, an increase of pHc may represent a functionally important, early event in the aetiology of cancer that is amenable to therapeutic intervention.
    DOI:  https://doi.org/10.1038/s42255-020-00297-0
  26. Nat Genet. 2020 Oct 19.
    Regulation of single-cell genome organization into TADs and chromatin nanodomains.
    Quentin Szabo, Axelle Donjon, Ivana Jerković, Giorgio L Papadopoulos, Thierry Cheutin, Boyan Bonev, Elphège P Nora, Benoit G Bruneau, Frédéric Bantignies, Giacomo Cavalli.
      The genome folds into a hierarchy of three-dimensional structures within the nucleus. At the sub-megabase scale, chromosomes form topologically associating domains (TADs)1-4. However, how TADs fold in single cells is elusive. Here, we reveal TAD features inaccessible to cell population analysis by using super-resolution microscopy. TAD structures and physical insulation associated with their borders are variable between individual cells, yet chromatin intermingling is enriched within TADs compared to adjacent TADs in most cells. The spatial segregation of TADs is further exacerbated during cell differentiation. Favored interactions within TADs are regulated by cohesin and CTCF through distinct mechanisms: cohesin generates chromatin contacts and intermingling while CTCF prevents inter-TAD contacts. Furthermore, TADs are subdivided into discrete nanodomains, which persist in cells depleted of CTCF or cohesin, whereas disruption of nucleosome contacts alters their structural organization. Altogether, these results provide a physical basis for the folding of individual chromosomes at the nanoscale.
    DOI:  https://doi.org/10.1038/s41588-020-00716-8
  27. Nat Methods. 2020 Oct 19.
    MARS: discovering novel cell types across heterogeneous single-cell experiments.
    Maria Brbić, Marinka Zitnik, Sheng Wang, Angela O Pisco, Russ B Altman, Spyros Darmanis, Jure Leskovec.
      Although tremendous effort has been put into cell-type annotation, identification of previously uncharacterized cell types in heterogeneous single-cell RNA-seq data remains a challenge. Here we present MARS, a meta-learning approach for identifying and annotating known as well as new cell types. MARS overcomes the heterogeneity of cell types by transferring latent cell representations across multiple datasets. MARS uses deep learning to learn a cell embedding function as well as a set of landmarks in the cell embedding space. The method has a unique ability to discover cell types that have never been seen before and annotate experiments that are as yet unannotated. We apply MARS to a large mouse cell atlas and show its ability to accurately identify cell types, even when it has never seen them before. Further, MARS automatically generates interpretable names for new cell types by probabilistically defining a cell type in the embedding space.
    DOI:  https://doi.org/10.1038/s41592-020-00979-3
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