bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020‒09‒06
twenty-two papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit
  1. Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer.
  2. EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data.
  3. Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution.
  4. The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells.
  5. CSynth: An Interactive Modelling and Visualisation Tool for 3D Chromatin Structure.
  6. Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes.
  7. MYEOV increases HES1 expression and promotes pancreatic cancer progression by enhancing SOX9 transactivity.
  8. Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.
  9. Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function.
  10. Interplay of m6A and H3K27 trimethylation restrains inflammation during bacterial infection.
  11. Pioneer Transcription Factors Initiating Gene Network Changes.
  12. Alteration of genome folding via contact domain boundary insertion.
  13. Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions.
  14. The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.
  15. Asymmetric Transcription Factor Partitioning During Yeast Cell Division Requires the FACT Chromatin Remodeler and Cell Cycle Progression.
  16. SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks.
  17. FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer.
  18. Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107.
  19. Measuring Genome-Wide Nascent Nucleosome Assembly Using ReIN-Map.
  20. Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma.
  21. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis.
  22. Phosphorylation control of p53 DNA binding cooperativity balances tumorigenesis and aging.
  1. Nat Genet. 2020 Aug 31.
    Chromatin binding of FOXA1 is promoted by LSD1-mediated demethylation in prostate cancer.
    Shuai Gao, Sujun Chen, Dong Han, Zifeng Wang, Muqing Li, Wanting Han, Anna Besschetnova, Mingyu Liu, Feng Zhou, David Barrett, My Phu Luong, Jude Owiredu, Yi Liang, Musaddeque Ahmed, Jessica Petricca, Susan Patalano, Jill A Macoska, Eva Corey, Sen Chen, Steven P Balk, Housheng Hansen He, Changmeng Cai.
      FOXA1 functions as a pioneer transcription factor by facilitating the access to chromatin for steroid hormone receptors, such as androgen receptor and estrogen receptor1-4, but mechanisms regulating its binding to chromatin remain elusive. LSD1 (KDM1A) acts as a transcriptional repressor by demethylating mono/dimethylated histone H3 lysine 4 (H3K4me1/2)5,6, but also acts as a steroid hormone receptor coactivator through mechanisms that are unclear. Here we show, in prostate cancer cells, that LSD1 associates with FOXA1 and active enhancer markers, and that LSD1 inhibition globally disrupts FOXA1 chromatin binding. Mechanistically, we demonstrate that LSD1 positively regulates FOXA1 binding by demethylating lysine 270, adjacent to the wing2 region of the FOXA1 DNA-binding domain. Acting through FOXA1, LSD1 inhibition broadly disrupted androgen-receptor binding and its transcriptional output, and dramatically decreased prostate cancer growth alone and in synergy with androgen-receptor antagonist treatment in vivo. These mechanistic insights suggest new therapeutic strategies in steroid-driven cancers.
    DOI:  https://doi.org/10.1038/s41588-020-0681-7
  2. Genome Biol. 2020 Sep 04. 21(1): 221
    EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data.
    Andrew E Teschendorff, Tianyu Zhu, Charles E Breeze, Stephan Beck.
      Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and samples. We present EPISCORE, a computational algorithm that performs virtual microdissection of bulk tissue DNA methylation data at single cell-type resolution for any solid tissue. EPISCORE applies a probabilistic epigenetic model of gene regulation to a single-cell RNA-seq tissue atlas to generate a tissue-specific DNA methylation reference matrix, allowing quantification of cell-type proportions and cell-type-specific differential methylation signals in bulk tissue data. We validate EPISCORE in multiple epigenome studies and tissue types.
    Keywords:  DNA methylation; EWAS; Single-cell RNA-Seq
    DOI:  https://doi.org/10.1186/s13059-020-02126-9
  3. Cell Res. 2020 Sep 03.
    Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution.
    Li Li, Lin Li, Qingqing Li, Xixi Liu, Xinyi Ma, Jun Yong, Shuai Gao, Xinglong Wu, Yuan Wei, Xiaoye Wang, Wei Wang, Rong Li, Jie Yan, Xiaohui Zhu, Lu Wen, Jie Qiao, Liying Yan, Fuchou Tang.
      Proper development of fetal germ cells (FGCs) is vital for the precise transmission of genetic and epigenetic information through generations. The transcriptional landscapes of human FGC development have been revealed; however, the epigenetic reprogramming process of FGCs remains elusive. Here, we profiled the genome-wide DNA methylation and chromatin accessibility of human FGCs at different phases as well as gonadal niche cells at single-cell resolution. First, we found that DNA methylation levels of FGCs changed in a temporal manner, whereas FGCs at different phases in the same embryo exhibited comparable DNA methylation levels and patterns. Second, we revealed the phase-specific chromatin accessibility signatures at the promoter regions of a large set of critical transcription factors and signaling pathway genes. We also identified potential distal regulatory elements including enhancers in FGCs. Third, compared with other hominid-specific retrotransposons, SVA_D might have a broad spectrum of binding capacity for transcription factors, including SOX15 and SOX17. Finally, using an in vitro culture system of human FGCs, we showed that the BMP signaling pathway promoted the cell proliferation of FGCs, and regulated the WNT signaling pathway by orchestrating the chromatin accessibility of its ligand genes. Our single-cell epigenomic atlas and functional assays provide valuable insights for understanding the strongly heterogeneous, unsynchronized, yet highly robust nature of human germ cell development.
    DOI:  https://doi.org/10.1038/s41422-020-00401-9
  4. Sci Immunol. 2020 Sep 04. pii: eabb1455. [Epub ahead of print]5(51):
    The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells.
    Kazuko Miyazaki, Hitomi Watanabe, Genki Yoshikawa, Kenian Chen, Reiko Hidaka, Yuki Aitani, Kai Osawa, Rie Takeda, Yotaro Ochi, Shizue Tani-Ichi, Takuya Uehata, Osamu Takeuchi, Koichi Ikuta, Seishi Ogawa, Gen Kondoh, Yin C Lin, Hiroyuki Ogata, Masaki Miyazaki.
      Cell type-specific gene expression is driven by the interplay between lineage-specific transcription factors and cis-regulatory elements to which they bind. Adaptive immunity relies on RAG-mediated assembly of T cell receptor (TCR) and immunoglobulin (Ig) genes. Although Rag1 and Rag2 expression is largely restricted to adaptive lymphoid lineage cells, it remains unclear how Rag gene expression is regulated in a cell lineage-specific manner. Here, we identified three distinct cis-regulatory elements, a T cell lineage-specific enhancer (R-TEn) and the two B cell-specific elements, R1B and R2B By generating mice lacking either R-TEn or R1B and R2B, we demonstrate that these distinct sets of regulatory elements drive the expression of Rag genes in developing T and B cells. What these elements have in common is their ability to bind the transcription factor E2A. By generating a mouse strain that carries a mutation within the E2A binding site of R-TEn, we demonstrate that recruitment of E2A to this site is essential for orchestrating changes in chromatin conformation that drive expression of Rag genes in T cells. By mapping cis-regulatory elements and generating multiple mouse strains lacking distinct enhancer elements, we demonstrate expression of Rag genes in developing T and B cells to be driven by distinct sets of E2A-dependent cis-regulatory modules.
    DOI:  https://doi.org/10.1126/sciimmunol.abb1455
  5. Bioinformatics. 2020 Aug 31. pii: btaa757. [Epub ahead of print]
    CSynth: An Interactive Modelling and Visualisation Tool for 3D Chromatin Structure.
    Stephen Todd, Peter Todd, Simon J McGowan, James R Hughes, Yasutaka Kakui, Frederic Fol Leymarie, William Latham, Stephen Taylor.
      MOTIVATION: The 3D structure of chromatin in the nucleus is important for gene expression and regulation.  Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.RESULTS: We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualise models of any chromosome conformation capture (3C) data. Unlike other modelling systems CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues / cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and public engagement tool.
    AVAILABILITY: CSynth is web based and available to use at https://csynth.org.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa757
  6. Proc Natl Acad Sci U S A. 2020 Sep 02. pii: 202010250. [Epub ahead of print]
    Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes.
    Peter A Crisp, Alexandre P Marand, Jaclyn M Noshay, Peng Zhou, Zefu Lu, Robert J Schmitz, Nathan M Springer.
      The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
    Keywords:  DNA methylation; chromatin accessibility; cis-regulatory elements
    DOI:  https://doi.org/10.1073/pnas.2010250117
  7. Oncogene. 2020 Sep 02.
    MYEOV increases HES1 expression and promotes pancreatic cancer progression by enhancing SOX9 transactivity.
    Erbo Liang, Yishi Lu, Yanqiang Shi, Qian Zhou, Fachao Zhi.
      Emerging evidence indicates that myeloma overexpressed (MYEOV) is an oncogene and plays crucial roles in multiple human cancers. However, its roles in the development of pancreatic ductal adenocarcinoma (PDAC) remain elusive. Here, we provide evidence of essential roles of MYEOV in the development and progression of PDAC. In tumor specimens derived from pancreatic cancer patients, MYEOV was overexpressed and associated with poor prognosis. In addition, MYEOV expression in PDAC was upregulated through promoter hypomethylation. MYEOV depletion impaired metastatic ability and proliferation of PDAC cells both in vitro and in vivo, whereas its overexpression had the opposite effect. Mechanistic investigations revealed that MYEOV interacted with SRY-Box Transcription Factor 9 (SOX9), a well-known oncogenic transcription factor in PDAC. This interaction occurred mainly in the nuclei of PDAC cells and increased transcriptional activity of SOX9. Furthermore, MYEOV promoted the expression of Hairy and enhancer of split homolog-1 (HES1), a SOX9 target gene, by enhancing SOX9 DNA-binding ability to the HES1 enhancer without affecting the protein level and subcellular localization of SOX9. HES1 knockdown partly abrogated the oncogenic effect of MYEOV. Our findings suggest that MYEOV could be a potential prognostic biomarker and therapeutic target for PDAC.
    DOI:  https://doi.org/10.1038/s41388-020-01443-4
  8. Nat Immunol. 2020 Aug 31.
    Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development.
    Natalie Burrows, Rachael J M Bashford-Rogers, Vijesh J Bhute, Ana Peñalver, John R Ferdinand, Benjamin J Stewart, Joscelin E G Smith, Mukta Deobagkar-Lele, Girolamo Giudice, Thomas M Connor, Akimichi Inaba, Laura Bergamaschi, Sam Smith, Maxine G B Tran, Evangelia Petsalaki, Paul A Lyons, Marion Espeli, Brian J P Huntly, Kenneth G C Smith, Richard J Cornall, Menna R Clatworthy, Patrick H Maxwell.
      B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF activity is high in human and murine bone marrow pro-B and pre-B cells and decreases at the immature B cell stage. This stage-specific HIF suppression is required for normal B cell development because genetic activation of HIF-1α in murine B cells led to reduced repertoire diversity, decreased BCR editing and developmental arrest of immature B cells, resulting in reduced peripheral B cell numbers. HIF-1α activation lowered surface BCR, CD19 and B cell-activating factor receptor and increased expression of proapoptotic BIM. BIM deletion rescued the developmental block. Administration of a HIF activator in clinical use markedly reduced bone marrow and transitional B cells, which has therapeutic implications. Together, our work demonstrates that dynamic regulation of HIF-1α is essential for normal B cell development.
    DOI:  https://doi.org/10.1038/s41590-020-0772-8
  9. PeerJ. 2020 ;8 e9566
    Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function.
    Margarita D Samborskaia, Aleksandra Galitsyna, Ilya Pletenev, Anna Trofimova, Andrey A Mironov, Mikhail S Gelfand, Ekaterina E Khrameeva.
      Regulation of gene transcription is a complex process controlled by many factors, including the conformation of chromatin in the nucleus. Insights into chromatin conformation on both local and global scales can be provided by the Hi-C (high-throughput chromosomes conformation capture) method. One of the drawbacks of Hi-C analysis and interpretation is the presence of systematic biases, such as different accessibility to enzymes, amplification, and mappability of DNA regions, which all result in different visibility of the regions. Iterative correction (IC) is one of the most popular techniques developed for the elimination of these systematic biases. IC is based on the assumption that all chromatin regions have an equal number of observed contacts in Hi-C. In other words, the IC procedure is equalizing the experimental visibility approximated by the cumulative contact frequency (CCF) for all genomic regions. However, the differences in experimental visibility might be explained by biological factors such as chromatin openness, which is characteristic of distinct chromatin states. Here we show that CCF is positively correlated with active transcription. It is associated with compartment organization, since compartment A demonstrates higher CCF and gene expression levels than compartment B. Notably, this observation holds for a wide range of species, including human, mouse, and Drosophila. Moreover, we track the CCF state for syntenic blocks between human and mouse and conclude that active state assessed by CCF is an intrinsic property of the DNA region, which is independent of local genomic and epigenomic context. Our findings establish a missing link between Hi-C normalization procedures removing CCF from the data and poorly investigated and possibly relevant biological factors contributing to CCF.
    Keywords:  Chromatin; Compartments; Conformation capture; Hi-C
    DOI:  https://doi.org/10.7717/peerj.9566
  10. Sci Adv. 2020 Aug;6(34): eaba0647
    Interplay of m6A and H3K27 trimethylation restrains inflammation during bacterial infection.
    Chenglei Wu, Weixin Chen, Jincan He, Shouheng Jin, Yukun Liu, Yang Yi, Zhuoxing Gao, Jiayan Yang, Jianhua Yang, Jun Cui, Wei Zhao.
      While N 6-methyladenosine (m6A) is the most prevalent modification of eukaryotic messenger RNA (mRNA) involved in various cellular responses, its role in modulating bacteria-induced inflammatory response remains elusive. Here, we showed that loss of the m6A reader YTH-domain family 2 (YTHDF2) promoted demethylation of histone H3 lysine-27 trimethylation (H3K27me3), which led to enhanced production of proinflammatory cytokines and facilitated the deposition of m6A cotranscriptionally. Mechanistically, the mRNA of lysine demethylase 6B (KDM6B) was m6A-modified and its decay mediated by YTHDF2. YTHDF2 deficiency stabilized KDM6B to promote H3K27me3 demethylation of multiple proinflammatory cytokines and subsequently enhanced their transcription. Furthermore, we identified H3K27me3 as a barrier for m6A modification during transcription. KDM6B recruits the m6A methyltransferase complex to facilitate the methylation of m6A in transcribing mRNA by removing adjacent H3K27me3 barriers. These results revealed cross-talk between m6A and H3K27me3 during bacterial infection, which has broader implications for deciphering epitranscriptomics in immune homeostasis.
    DOI:  https://doi.org/10.1126/sciadv.aba0647
  11. Annu Rev Genet. 2020 Sep 04.
    Pioneer Transcription Factors Initiating Gene Network Changes.
    Kenneth S Zaret.
      Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will. Expected final online publication date for the Annual Review of Genetics, Volume 54 is November 23, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-genet-030220-015007
  12. Nat Genet. 2020 Aug 31.
    Alteration of genome folding via contact domain boundary insertion.
    Di Zhang, Peng Huang, Malini Sharma, Cheryl A Keller, Belinda Giardine, Haoyue Zhang, Thomas G Gilgenast, Jennifer E Phillips-Cremins, Ross C Hardison, Gerd A Blobel.
      Animal chromosomes are partitioned into contact domains. Pathogenic domain disruptions can result from chromosomal rearrangements or perturbation of architectural factors. However, such broad-scale alterations are insufficient to define the minimal requirements for domain formation. Moreover, to what extent domains can be engineered is just beginning to be explored. In an attempt to create contact domains, we inserted a 2-kb DNA sequence underlying a tissue-invariant domain boundary-containing a CTCF-binding site (CBS) and a transcription start site (TSS)-into 16 ectopic loci across 11 chromosomes, and characterized its architectural impact. Depending on local constraints, this fragment variably formed new domains, partitioned existing ones, altered compartmentalization and initiated contacts reflecting chromatin loop extrusion. Deletions of the CBS or the TSS individually or in combination within inserts revealed its distinct contributions to genome folding. Altogether, short DNA insertions can suffice to shape the spatial genome in a manner influenced by chromatin context.
    DOI:  https://doi.org/10.1038/s41588-020-0680-8
  13. Nucleic Acids Res. 2020 Sep 04. pii: gkaa705. [Epub ahead of print]
    Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions.
    Gongcheng Hu, Xiaotao Dong, Shixin Gong, Yawei Song, Andrew P Hutchins, Hongjie Yao.
      CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.
    DOI:  https://doi.org/10.1093/nar/gkaa705
  14. Nat Commun. 2020 08 31. 11(1): 4360
    The cellular and molecular landscape of hypothalamic patterning and differentiation from embryonic to late postnatal development.
    Dong Won Kim, Parris Whitney Washington, Zoe Qianyi Wang, Sonia Hao Lin, Changyu Sun, Basma Taleb Ismail, Hong Wang, Lizhi Jiang, Seth Blackshaw.
      The hypothalamus is a central regulator of many innate behaviors essential for survival, but the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control hypothalamic development, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across 12 developmental time points between embryonic day 10 and postnatal day 45. This identified genes that delineated clear developmental trajectories for all major hypothalamic cell types, and readily distinguished major regional subdivisions of the developing hypothalamus. By using our developmental dataset, we were able to rapidly annotate previously unidentified clusters from existing scRNA-Seq datasets collected during development and to identify the developmental origins of major neuronal populations of the ventromedial hypothalamus. We further show that our approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, identifying Nkx2.1 as a negative regulator of prethalamic identity. These data serve as a resource for further studies of hypothalamic development, physiology, and dysfunction.
    DOI:  https://doi.org/10.1038/s41467-020-18231-z
  15. Genetics. 2020 Sep 02. pii: genetics.303439.2020. [Epub ahead of print]
    Asymmetric Transcription Factor Partitioning During Yeast Cell Division Requires the FACT Chromatin Remodeler and Cell Cycle Progression.
    Eva Herrero, Sonia Stinus, Eleanor Bellows, Lisa K Berry, Henry Wood, Peter H Thorpe.
      The polarized partitioning of proteins in cells underlies asymmetric cell division, which is an important driver of development and cellular diversity. The budding yeast Saccharomyces cerevisiae divides asymmetrically, like many other cells, to generate two distinct progeny cells. A well-known example of an asymmetric protein is the transcription factor Ace2, which localizes specifically to the daughter nucleus, where it drives a daughter-specific transcriptional network. We screened a collection of essential genes to analyze the effect of core cellular processes in asymmetric cell division based on Ace2 localization. This screen identified mutations that affect progression through the cell cycle, suggesting that cell cycle delay is sufficient to disrupt Ace2 asymmetry. To test this model, we blocked cells from progressing through mitosis and found that prolonged metaphase delay is sufficient to disrupt Ace2 asymmetry after release, and that Ace2 asymmetry is restored after cytokinesis. We also demonstrate that members of the evolutionarily conserved FACT chromatin-reorganizing complex are required for both asymmetric and cell cycle-regulated localization of Ace2 and for localization of the RAM network components.
    Keywords:  Ace2; Asymmetry; cell cycle
    DOI:  https://doi.org/10.1534/genetics.120.303439
  16. Cell Syst. 2020 Aug 25. pii: S2405-4712(20)30287-8. [Epub ahead of print]
    SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks.
    Payam Dibaeinia, Saurabh Sinha.
      A common approach to benchmarking of single-cell transcriptomics tools is to generate synthetic datasets that statistically resemble experimental data. However, most existing single-cell simulators do not incorporate transcription factor-gene regulatory interactions that underlie expression dynamics. Here, we present SERGIO, a simulator of single-cell gene expression data that models the stochastic nature of transcription as well as regulation of genes by multiple transcription factors according to a user-provided gene regulatory network. SERGIO can simulate any number of cell types in steady state or cells differentiating to multiple fates. We show that datasets generated by SERGIO are statistically comparable to experimental data generated by Illumina HiSeq2000, Drop-seq, Illumina 10X chromium, and Smart-seq. We use SERGIO to benchmark several single-cell analysis tools, including GRN inference methods, and identify Tcf7, Gata3, and Bcl11b as key drivers of T cell differentiation by performing in silico knockout experiments. SERGIO is freely available for download here: https://github.com/PayamDiba/SERGIO.
    Keywords:  RNA velocity; benchmarking single-cell analysis tools; differentiation trajectories; gene regulatory networks; simulations; single-cell RNA-seq
    DOI:  https://doi.org/10.1016/j.cels.2020.08.003
  17. Cancer Cell. 2020 Aug 25. pii: S1535-6108(20)30414-1. [Epub ahead of print]
    FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer.
    Amaia Arruabarrena-Aristorena, Jesper L V Maag, Srushti Kittane, Yanyan Cai, Wouter R Karthaus, Erik Ladewig, Jane Park, Srinivasaraghavan Kannan, Lorenzo Ferrando, Emiliano Cocco, Sik Y Ho, Daisylyn S Tan, Mirna Sallaku, Fan Wu, Barbara Acevedo, Pier Selenica, Dara S Ross, Matthew Witkin, Charles L Sawyers, Jorge S Reis-Filho, Chandra S Verma, Ralf Jauch, Richard Koche, José Baselga, Pedram Razavi, Eneda Toska, Maurizio Scaltriti.
      Mutations in the pioneer transcription factor FOXA1 are a hallmark of estrogen receptor-positive (ER+) breast cancers. Examining FOXA1 in ∼5,000 breast cancer patients identifies several hotspot mutations in the Wing2 region and a breast cancer-specific mutation SY242CS, located in the third β strand. Using a clinico-genomically curated cohort, together with breast cancer models, we find that FOXA1 mutations associate with a lower response to aromatase inhibitors. Mechanistically, Wing2 mutations display increased chromatin binding at ER loci upon estrogen stimulation, and an enhanced ER-mediated transcription without changes in chromatin accessibility. In contrast, SY242CS shows neomorphic properties that include the ability to open distinct chromatin regions and activate an alternative cistrome and transcriptome. Structural modeling predicts that SY242CS confers a conformational change that mediates stable binding to a non-canonical DNA motif. Taken together, our results provide insights into how FOXA1 mutations perturb its function to dictate cancer progression and therapeutic response.
    Keywords:  ESR1 mutations; FOXA1 mutations; breast cancer; chromatin accessibility; endocrine therapy; epigenomics; estrogen receptor; pioneer transcription factor; transcription; transcriptomics
    DOI:  https://doi.org/10.1016/j.ccell.2020.08.003
  18. Mol Cell Endocrinol. 2020 Aug 29. pii: S0303-7207(20)30309-9. [Epub ahead of print] 111007
    Hypoxia regulates GR function through multiple mechanisms involving microRNAs 103 and 107.
    Nan Yang, Andrew Berry, Carolin Sauer, Matthew Baxter, Ian J Donaldson, Karen Forbes, Rachelle Donn, Laura Matthews, David Ray.
      Glucocorticoids (Gcs) potently inhibit inflammation, and regulate liver energy metabolism, often acting in a hypoxic environment. We now show hypoxic conditions open a specific GR cistrome, and prevent access of GR to part of the normoxic GR cistrome. Motif analysis identified enrichment of KLF4 binding sites beneath those peaks of GR binding exclusive to normoxia, implicating KLF4 as a pioneer, or co-factor under these conditions. Hypoxia reduced KLF4 expression, however, knockdown of KLF4 did not impair GR recruitment. KLF4 is a known target of microRNAs 103 and 107, both of which are induced by hypoxia. Expression of mimics to either microRNA103, or microRNA107 inhibited GR transactivation of normoxic target genes, thereby replicating the hypoxic effect. Therefore, studies in hypoxia reveal that microRNAs 103 and 107 are potent regulators of GR function. We have now identified a new pathway linking hypoxia through microRNAs 103 and 107 to regulation of GR function.
    Keywords:  Glucocorticoid receptor; Glucocorticoids; HIF-1α; Hypoxia; MicroRNAs
    DOI:  https://doi.org/10.1016/j.mce.2020.111007
  19. Methods Mol Biol. 2021 ;2196 117-141
    Measuring Genome-Wide Nascent Nucleosome Assembly Using ReIN-Map.
    Zhiyun Xu, Jianxun Feng, Qing Li.
      The successful assembly of nucleosomes following DNA replication is critically important for both the inheritance of epigenetic information and the maintenance of genome integrity. This process, termed DNA replication-coupled (RC) nucleosome assembly, requires that DNA replication and nucleosome assembly function in a highly coordinated fashion to transmit both genetic and epigenetic information. In this chapter, we describe a genome-wide method for measuring nucleosome occupancy patterns on nascent strands, which we have termed Replication-Intermediate Nucleosome Mapping (ReIN-Map), to monitor the RC nucleosome assembly level genome-wide in vivo. This method takes advantage of next-generation sequencing and in vivo labeling of newly synthesized DNA using a thymidine analogue, 5-bromo-2'-deoxyuridine (BrdU), and involves parallel analyses of the nucleosome formation using micrococcal nuclease (MNase) digestion of chromatin (MNase-seq) and of the newly synthesized DNA levels using sonication shearing of chromatin s (Sonication-seq). Replicated chromatin was enriched by immunoprecipitation using antibodies against BrdU (BrdU-IP), which is incorporated into DNA during DNA synthesis; the DNA is then subjected to strand-specific sequencing.
    Keywords:  BrdU-IP-seq; MNase-seq; Next-generation sequencing; Replication-coupled nucleosome assembly; Sonication-seq
    DOI:  https://doi.org/10.1007/978-1-0716-0868-5_10
  20. Elife. 2020 Sep 03. pii: e57189. [Epub ahead of print]9
    Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma.
    Connor Rogerson, Samuel Ogden, Edward Britton, , Yeng Ang, Andrew D Sharrocks.
      Oesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths. Barrett's oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the molecular events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin to directly regulate cell cycle genes specifically in OAC cells. This new KLF5 target gene programme has potential prognostic significance as high levels correlate with poorer patient survival. Thus, the repurposing of KLF5 for novel regulatory activity in OAC provides new insights into the mechanisms behind disease progression.
    Keywords:  cancer biology; human
    DOI:  https://doi.org/10.7554/eLife.57189
  21. Mol Cell. 2020 Aug 04. pii: S1097-2765(20)30515-3. [Epub ahead of print]
    Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis.
    Abeer Prakash Singh, Roger Salvatori, Wasim Aftab, Andreas Aufschnaiter, Andreas Carlström, Ignasi Forne, Axel Imhof, Martin Ott.
      Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BioID, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.
    Keywords:  assembly; co-factor acquisition; gene expression; mitochondria; network; proximity interactions; respiratory chain; ribosome; translation; tunnel exit
    DOI:  https://doi.org/10.1016/j.molcel.2020.07.024
  22. Cancer Res. 2020 Sep 01. pii: canres.2002.2020. [Epub ahead of print]
    Phosphorylation control of p53 DNA binding cooperativity balances tumorigenesis and aging.
    Oleg Timofeev, Lukas Koch, Constantin Niederau, Alina Tscherne, Jean Schneikert, Maria Klimovich, Sabrina Elmshäuser, Marie Zeitlinger, Marco Mernberger, Andrea Nist, Christian Osterburg, Volker Dötsch, German Mouse Clinic Consortium, Martin Hrabé de Angelis, Thorsten Stiewe.
      Post-translational modifications are essential for regulating the transcription factor p53 which binds DNA in a highly cooperative manner to control expression of a plethora of tumor suppressive programs. Here we show at the biochemical, cellular, and organismal level that the cooperative nature of DNA binding is reduced by phosphorylation of highly conserved serine residues (human S183/S185, mouse S180) in the DNA binding domain. To explore the role of this inhibitory phosphorylation in vivo, new phosphorylation-deficient p53-S180A knock-in mice were generated. ChIP-seq and RNA-seq studies of S180A knock-in cells demonstrated enhanced DNA binding and increased target gene expression. In vivo, this translated into a tissue-specific vulnerability of the bone marrow that caused depletion of hematopoietic stem cells and impaired proper regeneration of hematopoiesis after DNA damage. Median lifespan was significantly reduced by 20% from 709 days in wild-type to only 568 days in S180A littermates. Importantly, lifespan was reduced by a loss of general fitness and increased susceptibility to age-related diseases, not by increased cancer incidence as often seen in other p53 mutant mouse models. For example, S180A knock-in mice showed markedly reduced spontaneous tumorigenesis and increased resistance to Myc-driven lymphoma and Eml4-Alk-driven lung cancer. Preventing phosphorylation of S183/S185 in human cells boosted p53 activity and allowed tumor cells to be killed more efficiently. Together out data identify p53 DNA binding domain phosphorylation as a druggable mechanism that balances tumorigenesis and aging.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2002
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