bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020–09–20
twenty-two papers selected by
Connor Rogerson, University of Cambridge, MRC Cancer Unit
  1. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation.
  2. Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.
  3. Temporal expression of MOF acetyltransferase primes transcription factor networks for erythroid fate.
  4. Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.
  5. Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion.
  6. NuRD mediates mitochondrial stress-induced longevity via chromatin remodeling in response to acetyl-CoA level.
  7. TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis.
  8. ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.
  9. Functional definition of a transcription factor hierarchy regulating T cell lineage commitment.
  10. TET2 directs mammary luminal cell differentiation and endocrine response.
  11. Context-dependent functional compensation between Ythdf m6A reader proteins.
  12. Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity.
  13. Nucleated transcriptional condensates amplify gene expression.
  14. Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development.
  15. Extensive SUMO Modification of Repressive Chromatin Factors Distinguishes Pluripotent from Somatic Cells.
  16. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.
  17. Prediction of transcription factors binding events based on epigenetic modifications in different human cells.
  18. Deregulated immune cell recruitment orchestrated by FOXM1 impairs human diabetic wound healing.
  19. DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands.
  20. ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer.
  21. Reprogramming roadmap reveals route to human induced trophoblast stem cells.
  22. Androgen receptor modulates metastatic routes of VHL wild-type clear cell renal cell carcinoma in an oxygen-dependent manner.
  1. Genome Biol. 2020 Sep 15. 21(1): 247
    Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation.
    Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L Safgren, Kathryn A Helmin, Emmalee R Adelman, Valentina Serafin, Giuseppe Basso, Kyle P Eagen, Alexandre Gaspar-Maia, Maria E Figueroa, Benjamin D Singer, Aakrosh Ratan, Panagiotis Ntziachristos, Chongzhi Zang.
       BACKGROUND: The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human cancers.
    RESULTS: To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions, partially with DNA methylation changes, and rarely with sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events exhibit enhancer activities and are induced by oncogenic transcription factors. We validate these findings in T cell acute lymphoblastic leukemia cell lines and patient samples and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena.
    CONCLUSIONS: Specific CTCF binding events occur in human cancers. Cancer-specific CTCF binding can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.
    Keywords:  3D genome organization; CTCF; Enhancer; Gene regulation; Integrative analysis; NOTCH1; T cell lymphoblastic leukemia; Transcription factor
    DOI:  https://doi.org/10.1186/s13059-020-02152-7
  2. Sci Adv. 2020 Jun;pii: eaaz6699. [Epub ahead of print]6(25):
    Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.
    Hiroshi Ochiai, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Akihito Harada, Yukiko Shimizu, Kenta Nakano, Noriko Saitoh, Zhe Liu, Takashi Yamamoto, Tadashi Okamura, Yasuyuki Ohkawa, Hiroshi Kimura, Itoshi Nikaido.
      Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.
    DOI:  https://doi.org/10.1126/sciadv.aaz6699
  3. Sci Adv. 2020 May;pii: eaaz4815. [Epub ahead of print]6(21):
    Temporal expression of MOF acetyltransferase primes transcription factor networks for erythroid fate.
    Cecilia Pessoa Rodrigues, Josip Stefan Herman, Benjamin Herquel, Claudia Isabelle Keller Valsecchi, Thomas Stehle, Dominic Grün, Asifa Akhtar.
      Self-renewal and differentiation of hematopoietic stem cells (HSCs) are orchestrated by the combinatorial action of transcription factors and epigenetic regulators. Here, we have explored the mechanism by which histone H4 lysine 16 acetyltransferase MOF regulates erythropoiesis. Single-cell RNA sequencing and chromatin immunoprecipitation sequencing uncovered that MOF influences erythroid trajectory by dynamic recruitment to chromatin and its haploinsufficiency causes accumulation of a transient HSC population. A regulatory network consisting of MOF, RUNX1, and GFI1B is critical for erythroid fate commitment. GFI1B acts as a Mof activator which is necessary and sufficient for cell type-specific induction of Mof expression. Plasticity of Mof-depleted HSCs can be rescued by expression of a downstream effector, Gata1, or by rebalancing acetylation via a histone deacetylase inhibitor. Accurate timing and dosage of Mof expression act as a rheostat for the feedforward transcription factor network that safeguards progression along the erythroid fate.
    DOI:  https://doi.org/10.1126/sciadv.aaz4815
  4. Proc Natl Acad Sci U S A. 2020 Sep 18. pii: 202008013. [Epub ahead of print]
    Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.
    Whitney E Heavner, Shaoyi Ji, James H Notwell, Ethan S Dyer, Alex M Tseng, Johannes Birgmeier, Boyoung Yoo, Gill Bejerano, Susan K McConnell.
      We are only just beginning to catalog the vast diversity of cell types in the cerebral cortex. Such categorization is a first step toward understanding how diversification relates to function. All cortical projection neurons arise from a uniform pool of progenitor cells that lines the ventricles of the forebrain. It is still unclear how these progenitor cells generate the more than 50 unique types of mature cortical projection neurons defined by their distinct gene-expression profiles. Moreover, exactly how and when neurons diversify their function during development is unknown. Here we relate gene expression and chromatin accessibility of two subclasses of projection neurons with divergent morphological and functional features as they develop in the mouse brain between embryonic day 13 and postnatal day 5 in order to identify transcriptional networks that diversify neuron cell fate. We compare these gene-expression profiles with published profiles of single cells isolated from similar populations and establish that layer-defined cell classes encompass cell subtypes and developmental trajectories identified using single-cell sequencing. Given the depth of our sequencing, we identify groups of transcription factors with particularly dense subclass-specific regulation and subclass-enriched transcription factor binding motifs. We also describe transcription factor-adjacent long noncoding RNAs that define each subclass and validate the function of Myt1l in balancing the ratio of the two subclasses in vitro. Our multidimensional approach supports an evolving model of progressive restriction of cell fate competence through inherited transcriptional identities.
    Keywords:  cortical development; gene regulation; next-generation sequencing; transcription
    DOI:  https://doi.org/10.1073/pnas.2008013117
  5. Sci Adv. 2020 Jul;pii: eaaz4012. [Epub ahead of print]6(27):
    Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion.
    Gustavo A Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y Tan, Victor Ythier, Emma L Randall, Ana C Marques, Tuncay Baubec, Rabih Murr, Ioannis Xenarios, Vincent Dion.
      Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.
    DOI:  https://doi.org/10.1126/sciadv.aaz4012
  6. Sci Adv. 2020 Jul;pii: eabb2529. [Epub ahead of print]6(31):
    NuRD mediates mitochondrial stress-induced longevity via chromatin remodeling in response to acetyl-CoA level.
    Di Zhu, Xueying Wu, Jun Zhou, Xinyu Li, Xiahe Huang, Jiasheng Li, Junbo Wu, Qian Bian, Yingchun Wang, Ye Tian.
      Mild mitochondrial stress experienced early in life can have beneficial effects on the life span of organisms through epigenetic regulations. Here, we report that acetyl-coenzyme A (CoA) represents a critical mitochondrial signal to regulate aging through the chromatin remodeling and histone deacetylase complex (NuRD) in Caenorhabditis elegans Upon mitochondrial stress, the impaired tricarboxylic acid cycle results in a decreased level of citrate, which accounts for reduced production of acetyl-CoA and consequently induces nuclear accumulation of the NuRD and a homeodomain-containing transcription factor DVE-1, thereby enabling decreased histone acetylation and chromatin reorganization. The metabolic stress response is thus established during early life and propagated into adulthood to allow transcriptional regulation for life-span extension. Furthermore, adding nutrients to restore acetyl-CoA production is sufficient to counteract the chromatin changes and diminish the longevity upon mitochondrial stress. Our findings uncover the molecular mechanism of the metabolite-mediated epigenome for the regulation of organismal aging.
    DOI:  https://doi.org/10.1126/sciadv.abb2529
  7. Sci Adv. 2020 Jun;pii: eaay5872. [Epub ahead of print]6(25):
    TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis.
    Wojciech Rosikiewicz, Xiaowen Chen, Pilar M Dominguez, Hussein Ghamlouch, Said Aoufouchi, Olivier A Bernard, Ari Melnick, Sheng Li.
      The TET2 DNA hydroxymethyltransferase is frequently disrupted by somatic mutations in diffuse large B cell lymphomas (DLBCLs), a tumor that originates from germinal center (GC) B cells. Here, we show that TET2 deficiency leads to DNA hypermethylation of regulatory elements in GC B cells, associated with silencing of the respective genes. This hypermethylation affects the binding of transcription factors including those involved in exit from the GC reaction and involves pathways such as B cell receptor, antigen presentation, CD40, and others. Normal GC B cells manifest a typical hypomethylation signature, which is caused by AID, the enzyme that mediates somatic hypermutation. However, AID-induced demethylation is markedly impaired in TET2-deficient GC B cells, suggesting that AID epigenetic effects are partially dependent on TET2. Last, we find that TET2 mutant DLBCLs also manifest the aberrant TET2-deficient GC DNA methylation signature, suggesting that this epigenetic pattern is maintained during and contributes to lymphomagenesis.
    DOI:  https://doi.org/10.1126/sciadv.aay5872
  8. Sci Adv. 2020 Jul;pii: eaay2078. [Epub ahead of print]6(28):
    ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.
    Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim, Sandeep Namburi, Harianto Tjong, Yuliang Feng, Ping Wang, Zhonghui Tang, Ahmed Abbas, Chia-Lin Wei, Yijun Ruan, Sheng Li.
      ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensional contact map viewing with Juicebox and HiGlass and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. To enable structural interpretation, ChIA-PIPE calls chromatin contact domains, resolves allele-specific peaks and loops, and annotates enhancer-promoter loops. ChIA-PIPE also supports the analysis of other related chromatin-mapping data types.
    DOI:  https://doi.org/10.1126/sciadv.aay2078
  9. Sci Adv. 2020 Jul;pii: eaaw7313. [Epub ahead of print]6(31):
    Functional definition of a transcription factor hierarchy regulating T cell lineage commitment.
    Laura Garcia-Perez, Farbod Famili, Martijn Cordes, Martijn Brugman, Marja van Eggermond, Haoyu Wu, Jihed Chouaref, David San León Granado, Machteld M Tiemessen, Karin Pike-Overzet, Lucia Daxinger, Frank J T Staal.
      T cell factor 1 (Tcf1) is the first T cell-specific protein induced by Notch signaling in the thymus, leading to the activation of two major target genes, Gata3 and Bcl11b Tcf1 deficiency results in partial arrests in T cell development, high apoptosis, and increased development of B and myeloid cells. Phenotypically, seemingly fully T cell-committed thymocytes with Tcf1 deficiency have promiscuous gene expression and an altered epigenetic profile and can dedifferentiate into more immature thymocytes and non-T cells. Restoring Bcl11b expression in Tcf1-deficient cells rescues T cell development but does not strongly suppress the development of non-T cells; in contrast, expressing Gata3 suppresses their development but does not rescue T cell development. Thus, T cell development is controlled by a minimal transcription factor network involving Notch signaling, Tcf1, and the subsequent division of labor between Bcl11b and Gata3, thereby ensuring a properly regulated T cell gene expression program.
    DOI:  https://doi.org/10.1126/sciadv.aaw7313
  10. Nat Commun. 2020 09 15. 11(1): 4642
    TET2 directs mammary luminal cell differentiation and endocrine response.
    Mi Ran Kim, Meng-Ju Wu, Yingsheng Zhang, Jer-Yen Yang, Chun Ju Chang.
      Epigenetic regulation plays an important role in governing stem cell fate and tumorigenesis. Lost expression of a key DNA demethylation enzyme TET2 is associated with human cancers and has been linked to stem cell traits in vitro; however, whether and how TET2 regulates mammary stem cell fate and mammary tumorigenesis in vivo remains to be determined. Here, using our recently established mammary specific Tet2 deletion mouse model, the data reveals that TET2 plays a pivotal role in mammary gland development and luminal lineage commitment. We show that TET2 and FOXP1 form a chromatin complex that mediates demethylation of ESR1, GATA3, and FOXA1, three key genes that are known to coordinately orchestrate mammary luminal lineage specification and endocrine response, and also are often silenced by DNA methylation in aggressive breast cancers. Furthermore, Tet2 deletion-PyMT breast cancer mouse model exhibits enhanced mammary tumor development with deficient ERα expression that confers tamoxifen resistance in vivo. As a result, this study elucidates a role for TET2 in governing luminal cell differentiation and endocrine response that underlies breast cancer resistance to anti-estrogen treatments.
    DOI:  https://doi.org/10.1038/s41467-020-18129-w
  11. Genes Dev. 2020 Sep 17.
    Context-dependent functional compensation between Ythdf m6A reader proteins.
    Lior Lasman, Vladislav Krupalnik, Sergey Viukov, Nofar Mor, Alejandro Aguilera-Castrejon, Dan Schneir, Jonathan Bayerl, Orel Mizrahi, Shani Peles, Shadi Tawil, Shashank Sathe, Aharon Nachshon, Tom Shani, Mirie Zerbib, Itay Kilimnik, Stefan Aigner, Archana Shankar, Jasmine R Mueller, Schraga Schwartz, Noam Stern-Ginossar, Gene W Yeo, Shay Geula, Noa Novershtern, Jacob H Hanna.
      The N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is regulated by a set of writer, eraser, and reader proteins. The YTH domain family of proteins, consists of three homologous m6A-binding proteins, Ythdf1, Ythdf2, and Ythdf3, which were suggested to have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer, each of the Ythdf readers, and the three readers together (triple-KO). We then estimated the effect in vivo in mouse gametogenesis, postnatal viability, and in vitro in mouse embryonic stem cells (mESCs). In gametogenesis, Mettl3-KO severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, due to differences in readers' expression pattern across different cell types, both in quantity and in spatial location. Knocking out the three readers together and systematically testing viable offspring genotypes revealed a redundancy in the readers' role during early development that is Ythdf1/2/3 gene dosage-dependent. Finally, in mESCs there is compensation between the three Ythdf reader proteins, since the resistance to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a new model for the Ythdf readers function, in which there is profound dosage-dependent redundancy when all three readers are equivalently coexpressed in the same cell types.
    Keywords:  RNA methylation; m6A; stem cells
    DOI:  https://doi.org/10.1101/gad.340695.120
  12. Nat Commun. 2020 09 15. 11(1): 4639
    Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity.
    Li-Wa Shao, Qi Peng, Mingyue Dong, Kaiyu Gao, Yumei Li, Yi Li, Chuan-Yun Li, Ying Liu.
      The ability to detect, respond and adapt to mitochondrial stress ensures the development and survival of organisms. Caenorhabditis elegans responds to mitochondrial stress by activating the mitochondrial unfolded protein response (UPRmt) to buffer the mitochondrial folding environment, rewire the metabolic state, and promote innate immunity and lifespan extension. Here we show that HDA-1, the C. elegans ortholog of mammalian histone deacetylase (HDAC) is required for mitochondrial stress-mediated activation of UPRmt. HDA-1 interacts and coordinates with the genome organizer DVE-1 to induce the transcription of a broad spectrum of UPRmt, innate immune response and metabolic reprogramming genes. In rhesus monkey and human tissues, HDAC1/2 transcript levels correlate with the expression of UPRmt genes. Knocking down or pharmacological inhibition of HDAC1/2 disrupts the activation of the UPRmt and the mitochondrial network in mammalian cells. Our results underscore an evolutionarily conserved mechanism of HDAC1/2 in modulating mitochondrial homeostasis and regulating longevity.
    DOI:  https://doi.org/10.1038/s41467-020-18501-w
  13. Nat Cell Biol. 2020 Sep 14.
    Nucleated transcriptional condensates amplify gene expression.
    Ming-Tzo Wei, Yi-Che Chang, Shunsuke F Shimobayashi, Yongdae Shin, Amy R Strom, Clifford P Brangwynne.
      Membraneless organelles or condensates form through liquid-liquid phase separation1-4, which is thought to underlie gene transcription through condensation of the large-scale nucleolus5-7 or in smaller assemblies known as transcriptional condensates8-11. Transcriptional condensates have been hypothesized to phase separate at particular genomic loci and locally promote the biomolecular interactions underlying gene expression. However, there have been few quantitative biophysical tests of this model in living cells, and phase separation has not yet been directly linked with dynamic transcriptional outputs12,13. Here, we apply an optogenetic approach to show that FET-family transcriptional regulators exhibit a strong tendency to phase separate within living cells, a process that can drive localized RNA transcription. We find that TAF15 has a unique charge distribution among the FET family members that enhances its interactions with the C-terminal domain of RNA polymerase II. Nascent C-terminal domain clusters at primed genomic loci lower the energetic barrier for nucleation of TAF15 condensates, which in turn further recruit RNA polymerase II to drive transcriptional output. These results suggest that positive feedback between interacting transcriptional components drives localized phase separation to amplify gene expression.
    DOI:  https://doi.org/10.1038/s41556-020-00578-6
  14. Sci Adv. 2020 Aug;pii: eaaz2978. [Epub ahead of print]6(34):
    Single-cell transcriptome analysis reveals cell lineage specification in temporal-spatial patterns in human cortical development.
    Xiaoying Fan, Yuanyuan Fu, Xin Zhou, Le Sun, Ming Yang, Mengdi Wang, Ruiguo Chen, Qian Wu, Jun Yong, Ji Dong, Lu Wen, Jie Qiao, Xiaoqun Wang, Fuchou Tang.
      Neurogenesis processes differ in different areas of the cortex in many species, including humans. Here, we performed single-cell transcriptome profiling of the four cortical lobes and pons during human embryonic and fetal development. We identified distinct subtypes of neural progenitor cells (NPCs) and their molecular signatures, including a group of previously unidentified transient NPCs. We specified the neurogenesis path and molecular regulations of the human deep-layer, upper-layer, and mature neurons. Neurons showed clear spatial and temporal distinctions, while glial cells of different origins showed development patterns similar to those of mice, and we captured the developmental trajectory of oligodendrocyte lineage cells until the human mid-fetal stage. Additionally, we verified region-specific characteristics of neurons in the cortex, including their distinct electrophysiological features. With systematic single-cell analysis, we decoded human neuronal development in temporal and spatial dimensions from GW7 to GW28, offering deeper insights into the molecular regulations underlying human neurogenesis and cortical development.
    DOI:  https://doi.org/10.1126/sciadv.aaz2978
  15. Cell Rep. 2020 Sep 15. pii: S2211-1247(20)31135-9. [Epub ahead of print]32(11): 108146
    Extensive SUMO Modification of Repressive Chromatin Factors Distinguishes Pluripotent from Somatic Cells.
    Ilan Theurillat, Ivo A Hendriks, Jack-Christophe Cossec, Alexandra Andrieux, Michael L Nielsen, Anne Dejean.
      Post-translational modification by SUMO is a key regulator of cell identity. In mouse embryonic fibroblasts (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct substrates to preserve somatic and pluripotent states. Using MS-based proteomics, we show that the composition of endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMO2/3 targets proteins associated with canonical SUMO functions, such as splicing, and transcriptional regulators driving somatic enhancer selection. In contrast, in ESCs, SUMO2/3 primarily modifies highly interconnected repressive chromatin complexes, thereby preventing chromatin opening and transitioning to totipotent-like states. We also characterize several SUMO-modified pluripotency factors and show that SUMOylation of Dppa2 and Dppa4 impedes the conversion to 2-cell-embryo-like states. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate decision during embryonic development.
    Keywords:  2C-like cells; Dppa2/4; SUMO; cell differentiation; embryonic stem cells; heterochromatin; pluripotency; proteomics; somatic cells; totipotency
    DOI:  https://doi.org/10.1016/j.celrep.2020.108146
  16. PLoS Genet. 2020 Sep 14. 16(9): e1009023
    TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.
    Daniel J Mullen, Chunli Yan, Diane S Kang, Beiyun Zhou, Zea Borok, Crystal N Marconett, Peggy J Farnham, Ite A Offringa, Suhn Kyong Rhie.
      Lung cancer is the leading cause of cancer-related death and lung adenocarcinoma is its most common subtype. Although genetic alterations have been identified as drivers in subsets of lung adenocarcinoma, they do not fully explain tumor development. Epigenetic alterations have been implicated in the pathogenesis of tumors. To identify epigenetic alterations driving lung adenocarcinoma, we used an improved version of the Tracing Enhancer Networks using Epigenetic Traits method (TENET 2.0) in primary normal lung and lung adenocarcinoma cells. We found over 32,000 enhancers that appear differentially activated between normal lung and lung adenocarcinoma. Among the identified transcriptional regulators inactivated in lung adenocarcinoma vs. normal lung, NKX2-1 was linked to a large number of silenced enhancers. Among the activated transcriptional regulators identified, CENPA, FOXM1, and MYBL2 were linked to numerous cancer-specific enhancers. High expression of CENPA, FOXM1, and MYBL2 is particularly observed in a subgroup of lung adenocarcinomas and is associated with poor patient survival. Notably, CENPA, FOXM1, and MYBL2 are also key regulators of cancer-specific enhancers in breast adenocarcinoma of the basal subtype, but they are associated with distinct sets of activated enhancers. We identified individual lung adenocarcinoma enhancers linked to CENPA, FOXM1, or MYBL2 that were associated with poor patient survival. Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. For example, we found that expression of TK1, a potential target gene of a MYBL2-linked enhancer, is associated with poor patient survival. Identification and characterization of key transcriptional regulators and associated enhancers in lung adenocarcinoma provides important insights into the deregulation of lung adenocarcinoma epigenomes, highlighting novel potential targets for clinical intervention.
    DOI:  https://doi.org/10.1371/journal.pgen.1009023
  17. Epigenomics. 2020 Aug;12(16): 1443-1456
    Prediction of transcription factors binding events based on epigenetic modifications in different human cells.
    Yan Huang, Dianshuang Zhou, Yihan Wang, Xingda Zhang, Mu Su, Cong Wang, Zhongyi Sun, Qinghua Jiang, Baoqing Sun, Yan Zhang.
      Aim: We aim to predict transcription factor (TF) binding events from knowledge of gene expression and epigenetic modifications. Materials & methods: TF-binding events based on the Encode project and The Cancer Genome Atlas data were analyzed by the random forest method. Results: We showed the high performance of TF-binding predictive models in GM12878, HeLa, HepG2 and K562 cell lines and applied them to other cell lines and tissues. The genes bound by the top TFs (MAX and MAZ) were significantly associated with cancer-related processes such as cell proliferation and DNA repair. Conclusion: We successfully constructed TF-binding predictive models in cell lines and applied them in tissues.
    Keywords:  binding state; epigenetic modifications; gene expression; transcription factors
    DOI:  https://doi.org/10.2217/epi-2019-0321
  18. Nat Commun. 2020 09 16. 11(1): 4678
    Deregulated immune cell recruitment orchestrated by FOXM1 impairs human diabetic wound healing.
    Andrew P Sawaya, Rivka C Stone, Stephen R Brooks, Irena Pastar, Ivan Jozic, Kowser Hasneen, Katelyn O'Neill, Spencer Mehdizadeh, Cheyanne R Head, Natasa Strbo, Maria I Morasso, Marjana Tomic-Canic.
      Diabetic foot ulcers (DFUs) are a life-threatening disease that often result in lower limb amputations and a shortened lifespan. However, molecular mechanisms contributing to the pathogenesis of DFUs remain poorly understood. We use next-generation sequencing to generate a human dataset of pathogenic DFUs to compare to transcriptional profiles of human skin and oral acute wounds, oral as a model of "ideal" adult tissue repair due to accelerated closure without scarring. Here we identify major transcriptional networks deregulated in DFUs that result in decreased neutrophils and macrophages recruitment and overall poorly controlled inflammatory response. Transcription factors FOXM1 and STAT3, which function to activate and promote survival of immune cells, are inhibited in DFUs. Moreover, inhibition of FOXM1 in diabetic mouse models (STZ-induced and db/db) results in delayed wound healing and decreased neutrophil and macrophage recruitment in diabetic wounds in vivo. Our data underscore the role of a perturbed, ineffective inflammatory response as a major contributor to the pathogenesis of DFUs, which is facilitated by FOXM1-mediated deregulation of recruitment of neutrophils and macrophages, revealing a potential therapeutic strategy.
    DOI:  https://doi.org/10.1038/s41467-020-18276-0
  19. Sci Adv. 2020 Aug;6(35): eabb5820
    DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands.
    Zhiming Li, Xu Hua, Albert Serra-Cardona, Xiaowei Xu, Songlin Gan, Hui Zhou, Wen-Si Yang, Chun-Long Chen, Rui-Ming Xu, Zhiguo Zhang.
      How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we describe the eSPAN method (enrichment and sequencing of protein-associated nascent DNA) in mouse embryonic stem (ES) cells and use it to detect histone deposition onto replicating DNA strands with a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes short primers for DNA synthesis, binds histone H3-H4 preferentially. A Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strands in both yeast and mouse ES cells. Last, dysregulation of both coding genes and noncoding endogenous retroviruses is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication-linked processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.
    DOI:  https://doi.org/10.1126/sciadv.abb5820
  20. Cancer Res. 2020 Sep 15. pii: canres.2044.2020. [Epub ahead of print]
    ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer.
    Neel Shah, Nikolas Kesten, Alba Font-Tello, Matthew E K Chang, Raga Vadhi, Klothilda Lim, Mark R Flory, Paloma Cejas, Hisham Mohammed, Henry W Long, Myles Brown.
      The TMPRSS2-ERG fusion is the most common genomic rearrangement in human prostate cancer. However, in established adenocarcinoma, it is unknown how the ERG oncogene promotes a cancerous phenotype and maintains downstream androgen receptor (AR) signaling pathways. In this study, we utilized a murine prostate organoid system to explore the effects of ERG on tumorigenesis and determined the mechanism underlying prostate cancer dependence on ERG. Prostate organoids lacking PTEN and overexpressing ERG (Pten-/- R26-ERG) faithfully recapitulated distinct stages of prostate cancer disease progression. In this model, deletion of ERG significantly dampened AR-dependent gene expression. While ERG was able to reprogram the AR cistrome in the process of prostate carcinogenesis, ERG knockout in established prostate cancer organoids did not drastically alter AR binding, H3K27ac enhancer, or open-chromatin profiles at these reprogrammed sites. Proteomic analysis of DNA-bound AR complexes demonstrated that ERG deletion causes a loss of recruitment of critical AR coregulators and basal transcriptional machinery, including NCOA3 and RNA polymerase II, but does not alter AR binding itself. Together these data reveal a novel mechanism of ERG oncogene addiction in prostate cancer whereby ERG facilitates AR signaling by maintaining coregulator complexes at AR-bound sites across the genome.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2044
  21. Nature. 2020 Sep 16.
    Reprogramming roadmap reveals route to human induced trophoblast stem cells.
    Xiaodong Liu, John F Ouyang, Fernando J Rossello, Jia Ping Tan, Kathryn C Davidson, Daniela S Valdes, Jan Schröder, Yu B Y Sun, Joseph Chen, Anja S Knaupp, Guizhi Sun, Hun S Chy, Ziyi Huang, Jahnvi Pflueger, Jaber Firas, Vincent Tano, Sam Buckberry, Jacob M Paynter, Michael R Larcombe, Daniel Poppe, Xin Yi Choo, Carmel M O'Brien, William A Pastor, Di Chen, Anna L Leichter, Haroon Naeem, Pratibha Tripathi, Partha P Das, Alexandra Grubman, David R Powell, Andrew L Laslett, Laurent David, Susan K Nilsson, Amander T Clark, Ryan Lister, Christian M Nefzger, Luciano G Martelotto, Owen J L Rackham, Jose M Polo.
      The reprogramming of human somatic cells to primed or naive induced pluripotent stem cells recapitulates the stages of early embryonic development1-6. The molecular mechanism that underpins these reprogramming processes remains largely unexplored, which impedes our understanding and limits rational improvements to reprogramming protocols. Here, to address these issues, we reconstruct molecular reprogramming trajectories of human dermal fibroblasts using single-cell transcriptomics. This revealed that reprogramming into primed and naive pluripotency follows diverging and distinct trajectories. Moreover, genome-wide analyses of accessible chromatin showed key changes in the regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets revealed a role for transcription factors associated with the trophectoderm lineage, and the existence of a subpopulation of cells that enter a trophectoderm-like state during reprogramming. Furthermore, this trophectoderm-like state could be captured, which enabled the derivation of induced trophoblast stem cells. Induced trophoblast stem cells are molecularly and functionally similar to trophoblast stem cells derived from human blastocysts or first-trimester placentas7. Our results provide a high-resolution roadmap for the transcription-factor-mediated reprogramming of human somatic cells, indicate a role for the trophectoderm-lineage-specific regulatory program during this process, and facilitate the direct reprogramming of somatic cells into induced trophoblast stem cells.
    DOI:  https://doi.org/10.1038/s41586-020-2734-6
  22. Oncogene. 2020 Sep 17.
    Androgen receptor modulates metastatic routes of VHL wild-type clear cell renal cell carcinoma in an oxygen-dependent manner.
    Qingbo Huang, Yin Sun, Wei Zhai, Xin Ma, Donglai Shen, Songliang Du, Bosen You, Yuanjie Niu, Chi-Ping Huang, Xu Zhang, Chawnshang Chang.
      Recent studies indicated that the androgen receptor (AR) plays important roles in modulating metastasis of VHL-mutant clear cell renal cell carcinoma (ccRCC). However, the precise mechanisms of AR roles in VHL wild-type (VHL-wt) ccRCC, remain unclear. Here we found that AR interacted with VHL to modulate the metastasis of VHL-wt ccRCC via an oxygen-dependent manner. Mechanism dissection revealed that AR could transcriptionally suppress the miR-185-5p expression in the presence of functional VHL-wt protein under a normoxic condition, which might then result in increasing the expression of VEGF-A and VEGF-C via targeting the 3'UTR of mRNAs at a post-transcriptional level. In contrast, under a hypoxic condition, AR could increase miR-185-5p expression to suppress VEGF-C expression, yet this miR-185-5p effect on VEGF-A was reversed via AR's positive regulation on the HIF2α-increased VEGF-A expression that resulted in increasing VEGF-A in the VHL-wt RCC cells. These distinct AR functions under different oxygen conditions may involve the VHL-impacted ubiquitination and nuclear localization of AR. The differential regulation of VEGF-A vs VEGF-C by AR may then result in differential impacts on the ccRCC metastatic destinations of VHL-wt ccRCC cells under different oxygen conditions. These finer mechanisms may help in the development of a novel therapy to better suppress the ccRCC progression under different oxygenization conditions.
    DOI:  https://doi.org/10.1038/s41388-020-01455-0
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