bims-crepig Biomed News
on Chromatin regulation and epigenetics in cell fate and cancer
Issue of 2020‒08‒30
27 papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit


  1. Nat Metab. 2020 Aug 24.
    Li L, Chen K, Wang T, Wu Y, Xing G, Chen M, Hao Z, Zhang C, Zhang J, Ma B, Liu Z, Yuan H, Liu Z, Long Q, Zhou Y, Qi J, Zhao D, Gao M, Pei D, Nie J, Ye D, Pan G, Liu X.
      Somatic cell reprogramming provides insight into basic principles of cell fate determination, which remain poorly understood. Here we show that the transcription factor Glis1 induces multi-level epigenetic and metabolic remodelling in stem cells that facilitates the induction of pluripotency. We find that Glis1 enables reprogramming of senescent cells into pluripotent cells and improves genome stability. During early phases of reprogramming, Glis1 directly binds to and opens chromatin at glycolytic genes, whereas it closes chromatin at somatic genes to upregulate glycolysis. Subsequently, higher glycolytic flux enhances cellular acetyl-CoA and lactate levels, thereby enhancing acetylation (H3K27Ac) and lactylation (H3K18la) at so-called 'second-wave' and pluripotency gene loci, opening them up to facilitate cellular reprogramming. Our work highlights Glis1 as a powerful reprogramming factor, and reveals an epigenome-metabolome-epigenome signalling cascade that involves the glycolysis-driven coordination of histone acetylation and lactylation in the context of cell fate determination.
    DOI:  https://doi.org/10.1038/s42255-020-0267-9
  2. Epigenetics. 2020 Aug 25. 1-20
    Theisen ER, Selich-Anderson J, Miller KR, Tanner JM, Taslim C, Pishas KI, Sharma S, Lessnick SL.
      Paediatric cancers commonly harbour quiet mutational landscapes and are instead characterized by single driver events such as the mutation of critical chromatin regulators, expression of oncohistones, or expression of oncogenic fusion proteins. These events ultimately promote malignancy through disruption of normal gene regulation and development. The driver protein in Ewing sarcoma, EWS/FLI, is an oncogenic fusion and transcription factor that reshapes the enhancer landscape, resulting in widespread transcriptional dysregulation. Lysine-specific demethylase 1 (LSD1) is a critical functional partner for EWS/FLI as inhibition of LSD1 reverses the transcriptional activity of EWS/FLI. However, how LSD1 participates in fusion-directed epigenomic regulation and aberrant gene activation is unknown. We now show EWS/FLI causes dynamic rearrangement of LSD1 and we uncover a role for LSD1 in gene activation through colocalization at EWS/FLI binding sites throughout the genome. LSD1 is integral to the establishment of Ewing sarcoma super-enhancers at GGAA-microsatellites, which ubiquitously overlap non-microsatellite loci bound by EWS/FLI. Together, we show that EWS/FLI induces widespread changes to LSD1 distribution in a process that impacts the enhancer landscape throughout the genome.
    Keywords:  Chromatin; EWS/FLI; Ewing sarcoma; LSD1; epigenetics; super-enhancers
    DOI:  https://doi.org/10.1080/15592294.2020.1805678
  3. Front Bioeng Biotechnol. 2020 ;8 886
    Xu S, Feng W, Lu Z, Yu CY, Shao W, Nakshatri H, Reiter JL, Gao H, Chu X, Wang Y, Liu Y.
      Expression quantitative trait loci (eQTL) analysis is useful for identifying genetic variants correlated with gene expression, however, it cannot distinguish between causal and nearby non-functional variants. Because the majority of disease-associated SNPs are located in regulatory regions, they can impact allele-specific binding (ASB) of transcription factors and result in differential expression of the target gene alleles. In this study, our aim was to identify functional single-nucleotide polymorphisms (SNPs) that alter transcriptional regulation and thus, potentially impact cellular function. Here, we present regSNPs-ASB, a generalized linear model-based approach to identify regulatory SNPs that are located in transcription factor binding sites. The input for this model includes ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) raw read counts from heterozygous loci, where differential transposase-cleavage patterns between two alleles indicate preferential transcription factor binding to one of the alleles. Using regSNPs-ASB, we identified 53 regulatory SNPs in human MCF-7 breast cancer cells and 125 regulatory SNPs in human mesenchymal stem cells (MSC). By integrating the regSNPs-ASB output with RNA-seq experimental data and publicly available chromatin interaction data from MCF-7 cells, we found that these 53 regulatory SNPs were associated with 74 potential target genes and that 32 (43%) of these genes showed significant allele-specific expression. By comparing all of the MCF-7 and MSC regulatory SNPs to the eQTLs in the Genome-Tissue Expression (GTEx) Project database, we found that 30% (16/53) of the regulatory SNPs in MCF-7 and 43% (52/122) of the regulatory SNPs in MSC were also in eQTL regions. The enrichment of regulatory SNPs in eQTLs indicated that many of them are likely responsible for allelic differences in gene expression (chi-square test, p-value < 0.01). In summary, we conclude that regSNPs-ASB is a useful tool for identifying causal variants from ATAC-seq data. This new computational tool will enable efficient prioritization of genetic variants identified as eQTL for further studies to validate their causal regulatory function. Ultimately, identifying causal genetic variants will further our understanding of the underlying molecular mechanisms of disease and the eventual development of potential therapeutic targets.
    Keywords:  ATAC-seq; allele-specific binding; bioinformatics; computational biology; expression quantitative trait loci; functional single-nucleotide polymorphisms; transcription factor; transcriptional regulation
    DOI:  https://doi.org/10.3389/fbioe.2020.00886
  4. Mol Cancer Res. 2020 Aug 27. pii: molcanres.0082.2020. [Epub ahead of print]
    Song S, Nguyen V, Schrank T, Mulvaney K, Walter V, Wei D, Orvis T, Desai N, Zhang J, Hayes DN, Zheng Y, Major MB, Weissman BE.
      The NF-E2-related factor 2 (referred to as NRF2) transcription factor binds antioxidant responsive elements within the promoters of cytoprotective genes to induce their expression. Next-generation sequencing studies in lung cancer have shown a significant number of activating mutations within the NRF2 signaling pathway. Mutations in components of the SWI/SNF chromatin-remodeling complex, a general regulator of transcription employing either BRG1 or BRM as the catalytic subunit, also frequently occur in lung cancers. Importantly, low BRG1 expression levels in primary human NSCLC correlated with increased NRF2-target gene expression. Here, we show that loss of SWI/SNF complex function activated a subset of NRF2-mediated transcriptional targets. Using a series of isogenic NSCLC lines with reduced or depleted BRG1 and/or BRM expression, we observed significantly increased expression of the NRF2-target genes HMOX1 and GSTM4. In contrast, expression of the NRF2 target genes NQO1 and GCLM modestly increased following BRM reduction. Chromatin immunoprecipitation showed that BRG1 knockdown led to increased NRF2 binding at its respective ARE sites in the HMOX1 promoter but not in NQO1 and GCLM. Our data demonstrate that loss of BRG1 or BRM in lung cancer results in activation of the NRF2/KEAP1 pathway and HMOX1 expression. Therefore, we provide an additional molecular explanation for why patients harboring BRG1 or BRM mutations show poor prognoses. A better understanding of this mechanism may yield novel insights into the design of targeted treatment modalities. Implications: Our study identifies a novel mechanism for how mutations in the SMARCA4 gene may drive progression of human lung adenocarcinomas.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-20-0082
  5. PLoS One. 2020 ;15(8): e0238076
    Oda Y, Nguyen T, Hata A, Meyer MB, Pike JW, Bikle DD.
      Epidermal lineages and injury induced regeneration are controlled by transcriptional programs coordinating cellular signaling and epigenetic regulators, but the mechanism remains unclear. Previous studies showed that conditional deletion of the transcriptional coactivator Mediator 1 (Med1) changes epidermal lineages and accelerates wound re-epithelialization. Here, we studied a molecular mechanism by which Med1 facilitates these processes, in particular, by focusing on TGFβ signaling through genome wide transcriptome analysis. The expression of the TGF ligands (Tgfβ1/β2) and their downstream target genes is decreased in both normal and wounded Med1 null skin. Med1 silencing in cultured keratinocytes likewise reduces the expression of the ligands (TGFβ1/β2) and diminishes activity of TGFβ signaling as shown by decreased p-Smad2/3. Silencing Med1 increases keratinocyte proliferation and migration in vitro. Epigenetic studies using chromatin immuno-precipitation and next generation DNA sequencing reveals that Med1 regulates transcription of TGFβ components by forming large clusters of enhancers called super-enhancers at the regulatory regions of the TGFβ ligand and SMAD3 genes. These results demonstrate that Med1 is required for the maintenance of the TGFβ signaling pathway. Finally, we show that pharmacological inhibition of TGFβ signaling enhances epidermal lineages and accelerates wound re-epithelialization in skin similar to that seen in the Med1 null mice, providing new insights into epidermal regeneration.
    DOI:  https://doi.org/10.1371/journal.pone.0238076
  6. Sci Adv. 2020 Jul;6(29): eaba1593
    Zhang M, Lai Y, Krupalnik V, Guo P, Guo X, Zhou J, Xu Y, Yu Z, Liu L, Jiang A, Li W, Abdul MM, Ma G, Li N, Fu X, Lv Y, Jiang M, Tariq M, Kanwal S, Liu H, Xu X, Zhang H, Huang Y, Wang L, Chen S, Babarinde IA, Luo Z, Wang D, Zhou T, Ward C, He M, Ibañez DP, Li Y, Zhou J, Yuan J, Feng Y, Arumugam K, Di Vicino U, Bao X, Wu G, Schambach A, Wang H, Sun H, Gao F, Qin B, Hutchins AP, Doble BW, Hartmann C, Cosma MP, Qin Y, Xu GL, Chen R, Volpe G, Chen L, Hanna JH, Esteban MA.
      Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.
    DOI:  https://doi.org/10.1126/sciadv.aba1593
  7. Nat Biotechnol. 2020 Aug 24.
    You Q, Cheng AY, Gu X, Harada BT, Yu M, Wu T, Ren B, Ouyang Z, He C.
      Determining the spatial organization of chromatin in cells mainly relies on crosslinking-based chromosome conformation capture techniques, but resolution and signal-to-noise ratio of these approaches is limited by interference from DNA-bound proteins. Here we introduce chemical-crosslinking assisted proximity capture (CAP-C), a method that uses multifunctional chemical crosslinkers with defined sizes to capture chromatin contacts. CAP-C generates chromatin contact maps at subkilobase (sub-kb) resolution with low background noise. We applied CAP-C to formaldehyde prefixed mouse embryonic stem cells (mESCs) and investigated loop domains (median size of 200 kb) and nonloop domains (median size of 9 kb). Transcription inhibition caused a greater loss of contacts in nonloop domains than loop domains. We uncovered conserved, transcription-state-dependent chromatin compartmentalization at high resolution that is shared from Drosophila to human, and a transcription-initiation-dependent nuclear subcompartment that brings multiple nonloop domains in close proximity. We also showed that CAP-C could be used to detect native chromatin conformation without formaldehyde prefixing.
    DOI:  https://doi.org/10.1038/s41587-020-0643-8
  8. Elife. 2020 Aug 26. pii: e56980. [Epub ahead of print]9
    Xi L, Carroll T, Matos I, Luo JD, Polak L, Pasolli HA, Brüning JC, Jaffrey SR, Fuchs E.
      N6-methyladenosine is the most prominent RNA modification in mammals. Here we study mouse skin embryogenesis to tackle m6A's functions and physiological importance. We first landscape the m6A modifications on skin epithelial progenitor mRNAs. Contrasting with in vivo ribosomal profiling, we unearth a correlation between m6A-modification in coding sequences and enhanced translation, particularly of key morphogenetic signaling pathways. Tapping physiological relevance, we show that m6A loss profoundly alters these cues and perturbs cellular fate choices and tissue architecture in all skin lineages. By single-cell transcriptomics and bioinformatics, both signaling and canonical translation pathways show significant downregulation after m6A loss. Interestingly, however, many highly m6A-modified mRNAs are markedly upregulated upon m6A loss, and they encode RNA-methylation, RNA-processing and RNA-metabolism factors. Together, our findings suggest that m6A functions to enhance translation of key morphogenetic regulators, while also destabilizing sentinel mRNAs that are primed to activate rescue pathways when m6A levels drop.
    Keywords:  developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.56980
  9. Mol Cell Biol. 2020 Aug 24. pii: MCB.00224-20. [Epub ahead of print]
    Lazar SB, Pongor L, Li XL, Grammatikakis I, Muys BR, Dangelmaier EA, Redon CE, Jang SM, Walker RL, Tang W, Ambs S, Harris CC, Meltzer PS, Aladjem MI, Lal A.
      Differentiation status of tumors is correlated with metastatic potential and malignancy. FOXA1 (forkhead box A1) is a transcription factor known to regulate differentiation in certain tissues. Here, we investigate FOXA1 function in human colorectal cancer (CRC). We found that FOXA1 is robustly expressed in the normal human colon but significantly downregulated in colon adenocarcinoma (COAD). Applying FOXA1 ChIP-seq and RNA-seq upon FOXA1 knockdown in well-differentiated colon-like cells, and FOXA1 overexpression in poorly differentiated CRC cells, we identified novel protein-coding and lncRNA genes regulated by FOXA1. Among the numerous novel FOXA1 targets we identified, we focused on CEACAM5, a tumor marker and facilitator of cell adhesion. We show that FOXA1 binds to a distal enhancer downstream of CEACAM5 and strongly activates its expression. Consistent with these data, we show that FOXA1 inhibits anoikis in CRC cells. Collectively, our results uncover novel protein-coding and non-coding targets of FOXA1 and suggest a vital role of FOXA1 in enhancing CEACAM5 expression and anoikis resistance in CRC cells.
    DOI:  https://doi.org/10.1128/MCB.00224-20
  10. Cancer Lett. 2020 Aug 25. pii: S0304-3835(20)30448-1. [Epub ahead of print]
    Hu H, Chen Z, Ji L, Wang Y, Yang M, Lai R, Zhong Y, Zhang X, Wang L.
      Estrogen receptor α (ER) acts as an oncogenic signal in endometrial endometrioid carcinoma. ER binding activity largely depends on chromatin remodeling and recruitment of transcription factors to estrogen response elements. A deeper understanding of these regulatory mechanisms may uncover therapeutic targets for ER-dependent endometrial cancers. We show that estrogen induces accessible chromatin and ER binding at a subset of enhancers, which form higher-order super enhancers that are vital for ER signaling. ER positively correlates with active enhancers in primary tumors, and tumors were effectively classified into molecular subtypes with chromatin accessibility dynamics and ER-dependent gene signature. ARID1A binds within ER-bound enhancers and regulates ER-dependent transcription. Knockdown of ARID1A or fulvestrant treatment profoundly affects the gene-expression program, and inhibits cell growth phenotype by affecting the chromatin environment. Importantly, we found dysregulated expression of circadian rhythms genes by estrogen in cancer cells and in primary tumors. Knockdown of ARID1A reduces the chromatin accessibility and ER binding at enhancers of the circadian gene ARNTL and BHLHE41, leading to a decreased expression of these genes. Altogether, we uncover a critical role for ARID1A in ER signaling and therapeutic target in ER-positive endometrial cancer.
    Keywords:  ARID1A; Chromatin accessibility; Endometrial cancer; Estrogen-receptor; Super enhancer
    DOI:  https://doi.org/10.1016/j.canlet.2020.08.034
  11. Nat Commun. 2020 Aug 27. 11(1): 4281
    Sohn BK, Basu U, Lee SW, Cho H, Shen J, Deshpande A, Johnson LC, Das K, Patel SS, Kim H.
      Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription.
    DOI:  https://doi.org/10.1038/s41467-020-17793-2
  12. Nat Commun. 2020 Aug 26. 11(1): 4267
    Bentsen M, Goymann P, Schultheis H, Klee K, Petrova A, Wiegandt R, Fust A, Preussner J, Kuenne C, Braun T, Kim J, Looso M.
      While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.
    DOI:  https://doi.org/10.1038/s41467-020-18035-1
  13. Elife. 2020 Aug 26. pii: e57757. [Epub ahead of print]9
    Hildreth AE, Ellison MA, Francette AM, Seraly JM, Lotka LM, Arndt KM.
      Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. We performed a genetic screen in Saccharomyces cerevisiae to identify histone mutants that exhibit transcriptional readthrough of terminators. Amino acid substitutions identified by the screen map to the nucleosome DNA entry-exit site. The strongest H3 mutants revealed widespread genomic changes, including increased sense-strand transcription upstream and downstream of genes, increased antisense transcription overlapping gene bodies, and reduced nucleosome occupancy particularly at the 3' ends of genes. Replacement of the native sequence downstream of a gene with a sequence that increases nucleosome occupancy in vivo reduced readthrough transcription and suppressed the effect of a DNA entry-exit site substitution. Our results suggest that nucleosomes can facilitate termination by serving as a barrier to transcription and highlight the importance of the DNA entry-exit site in broadly maintaining the integrity of the transcriptome.
    Keywords:  DNA entry-exit site; RNA polymerase II; S. cerevisiae; chromatin; chromosomes; gene expression; noncoding RNA; nucleosome; transcription termination
    DOI:  https://doi.org/10.7554/eLife.57757
  14. Sci Adv. 2020 Jul;6(28): eaay2078
    Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei CL, Ruan Y, Li S.
      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
  15. Cell. 2020 Aug 18. pii: S0092-8674(20)30938-7. [Epub ahead of print]
    Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE.
      Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors. This reorganization is accompanied by compartment-specific hypomethylation and chromatin changes. Additionally, we identify a compartment at the interface between the canonical A and B compartments that is reorganized in tumors. Remarkably, similar shifts were evident in non-malignant cells that have accumulated excess divisions. Our analyses suggest that these topological changes repress stemness and invasion programs while inducing anti-tumor immunity genes and may therefore restrain malignant progression. Our findings call into question the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.
    Keywords:  DNA methylation; chromatin; colon cancer; compartment; epigenetics; genome topology; nuclear architecture
    DOI:  https://doi.org/10.1016/j.cell.2020.07.030
  16. Genome Biol. 2020 Aug 27. 21(1): 218
    Hou W, Ji Z, Ji H, Hicks SC.
      BACKGROUND: The rapid development of single-cell RNA-sequencing (scRNA-seq) technologies has led to the emergence of many methods for removing systematic technical noises, including imputation methods, which aim to address the increased sparsity observed in single-cell data. Although many imputation methods have been developed, there is no consensus on how methods compare to each other.RESULTS: Here, we perform a systematic evaluation of 18 scRNA-seq imputation methods to assess their accuracy and usability. We benchmark these methods in terms of the similarity between imputed cell profiles and bulk samples and whether these methods recover relevant biological signals or introduce spurious noise in downstream differential expression, unsupervised clustering, and pseudotemporal trajectory analyses, as well as their computational run time, memory usage, and scalability. Methods are evaluated using data from both cell lines and tissues and from both plate- and droplet-based single-cell platforms.
    CONCLUSIONS: We found that the majority of scRNA-seq imputation methods outperformed no imputation in recovering gene expression observed in bulk RNA-seq. However, the majority of the methods did not improve performance in downstream analyses compared to no imputation, in particular for clustering and trajectory analysis, and thus should be used with caution. In addition, we found substantial variability in the performance of the methods within each evaluation aspect. Overall, MAGIC, kNN-smoothing, and SAVER were found to outperform the other methods most consistently.
    Keywords:  Benchmark; Gene expression; Imputation; Single-cell RNA-sequencing
    DOI:  https://doi.org/10.1186/s13059-020-02132-x
  17. Genome Biol. 2020 Aug 28. 21(1): 220
    Hop PJ, Luijk R, Daxinger L, van Iterson M, Dekkers KF, Jansen R, , van Meurs JBJ, 't Hoen PAC, Ikram MA, van Greevenbroek MMJ, Boomsma DI, Slagboom PE, Veldink JH, van Zwet EW, Heijmans BT.
      BACKGROUND: DNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation. Here, we identify 818 genes that affect DNA methylation patterns in blood using large-scale population genomics data.RESULTS: By employing genetic instruments as causal anchors, we establish directed associations between gene expression and distant DNA methylation levels, while ensuring specificity of the associations by correcting for linkage disequilibrium and pleiotropy among neighboring genes. The identified genes are enriched for transcription factors, of which many consistently increased or decreased DNA methylation levels at multiple CpG sites. In addition, we show that a substantial number of transcription factors affected DNA methylation at their experimentally determined binding sites. We also observe genes encoding proteins with heterogenous functions that have widespread effects on DNA methylation, e.g., NFKBIE, CDCA7(L), and NLRC5, and for several examples, we suggest plausible mechanisms underlying their effect on DNA methylation.
    CONCLUSION: We report hundreds of genes that affect DNA methylation and provide key insights in the principles underlying epigenetic regulation.
    Keywords:  Causal inference; Chromatin; DNA methylation; Epigenetic regulation; Functional genomics; Genetic instrumental variable; Pleiotropy; Transcription factor
    DOI:  https://doi.org/10.1186/s13059-020-02114-z
  18. Nat Commun. 2020 Aug 27. 11(1): 4313
    Damal Villivalam S, You D, Kim J, Lim HW, Xiao H, Zushin PH, Oguri Y, Amin P, Kang S.
      It has been suggested that beige fat thermogenesis is tightly controlled by epigenetic regulators that sense environmental cues such as temperature. Here, we report that subcutaneous adipose expression of the DNA demethylase TET1 is suppressed by cold and other stimulators of beige adipocyte thermogenesis. TET1 acts as an autonomous repressor of key thermogenic genes, including Ucp1 and Ppargc1a, in beige adipocytes. Adipose-selective Tet1 knockout mice generated by using Fabp4-Cre improves cold tolerance and increases energy expenditure and protects against diet-induced obesity and insulin resistance. Moreover, the suppressive role of TET1 in the thermogenic gene regulation of beige adipocytes is largely DNA demethylase-independent. Rather, TET1 coordinates with HDAC1 to mediate the epigenetic changes to suppress thermogenic gene transcription. Taken together, TET1 is a potent beige-selective epigenetic breaker of the thermogenic gene program. Our findings may lead to a therapeutic strategy to increase energy expenditure in obesity and related metabolic disorders.
    DOI:  https://doi.org/10.1038/s41467-020-18054-y
  19. Sci Adv. 2020 Aug;6(33): eaaz8850
    Qiu X, Ma F, Zhao M, Cao Y, Shipp L, Liu A, Dutta A, Singh A, Braikia FZ, De S, Wood WH, Becker KG, Zhou W, Ji H, Zhao K, Atchison ML, Sen R.
      Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombination activating gene products (RAG) 1 and 2. Diversity (DH) gene segments rearrange first, followed by variable (VH) gene rearrangements. Here, we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, which recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on wild-type IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by distinct mechanisms from those that apply to DH gene segments. These distinctions may underlie differential allelic choice associated with each step of IgH gene assembly.
    DOI:  https://doi.org/10.1126/sciadv.aaz8850
  20. Genomics Proteomics Bioinformatics. 2020 Aug 25. pii: S1672-0229(20)30095-4. [Epub ahead of print]
    Zhang Q, Liu W, Zhang HM, Xie GY, Miao YR, Xia M, Guo AY.
      Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples of 659 TFs and high-confidence binding sites of 699 TFs) and epigenetic modification information to predict accurate TF-target regulations. hTFtarget offers the following functions for users to explore TF-target regulations: 1) browse or search general targets of a query TF across datasets; 2) browse TF-target regulations for a query TF in a specific dataset or tissue; 3) search potential TFs for a given target gene or non-coding RNA; 4) investigate co-association between TFs in cell lines; 5) explore potential co-regulations for given target genes or TFs; 6) predict candidate TF binding sites on given DNA sequences; 7) visualize ChIP-seq peaks for different TFs and conditions in a genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF-target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.
    Keywords:  ChIP-seq; Database; Human; Transcription factor; Transcriptional regulation
    DOI:  https://doi.org/10.1016/j.gpb.2019.09.006
  21. Nat Cancer. 2020 Mar;1(3): 345-358
    Tran TQ, Hanse EA, Habowski AN, Li H, Gabra MBI, Yang Y, Lowman XH, Ooi AM, Liao SY, Edwards RA, Waterman ML, Kong M.
      Genetic-driven deregulation of the Wnt pathway is crucial but not sufficient for colorectal cancer (CRC) tumourigenesis. Here, we show that environmental glutamine restriction further augments Wnt signaling in APC mutant intestinal organoids to promote stemness and leads to adenocarcinoma formation in vivo via decreasing intracellular alpha-ketoglutarate (aKG) levels. aKG supplementation is sufficient to rescue low-glutamine induced stemness and Wnt hyperactivation. Mechanistically, we found that aKG promotes hypomethylation of DNA and histone H3K4me3, leading to an upregulation of differentiation-associated genes and downregulation of Wnt target genes, respectively. Using CRC patient-derived organoids and several in vivo CRC tumour models, we show that aKG supplementation suppresses Wnt signaling and promotes cellular differentiation, thereby significantly restricting tumour growth and extending survival. Together, our results reveal how metabolic microenvironment impacts Wnt signaling and identify aKG as a potent antineoplastic metabolite for potential differentiation therapy for CRC patients.
    Keywords:  Wnt signaling; cancer metabolism; colon cancer; epigenetics; glutamine
    DOI:  https://doi.org/10.1038/s43018-020-0035-5
  22. Sci Adv. 2020 Jul;6(29): eaaz3440
    Shi H, Tao T, Abraham BJ, Durbin AD, Zimmerman MW, Kadoch C, Look AT.
      Mutations in genes encoding SWI/SNF chromatin remodeling complexes are found in approximately 20% of all human cancers, with ARID1A being the most frequently mutated subunit. Here, we show that disruption of ARID1A homologs in a zebrafish model accelerates the onset and increases the penetrance of MYCN-driven neuroblastoma by increasing cell proliferation in the sympathoadrenal lineage. Depletion of ARID1A in human NGP neuroblastoma cells promoted the adrenergic-to-mesenchymal transition with changes in enhancer-mediated gene expression due to alterations in the genomic occupancies of distinct SWI/SNF assemblies, BAF and PBAF. Our findings indicate that ARID1A is a haploinsufficient tumor suppressor in MYCN-driven neuroblastoma, whose depletion enhances tumor development and promotes the emergence of the more drug-resistant mesenchymal cell state.
    DOI:  https://doi.org/10.1126/sciadv.aaz3440
  23. Nat Commun. 2020 Aug 27. 11(1): 4158
    Han L, Chaturvedi P, Kishimoto K, Koike H, Nasr T, Iwasawa K, Giesbrecht K, Witcher PC, Eicher A, Haines L, Lee Y, Shannon JM, Morimoto M, Wells JM, Takebe T, Zorn AM.
      Visceral organs, such as the lungs, stomach and liver, are derived from the fetal foregut through a series of inductive interactions between the definitive endoderm (DE) and the surrounding splanchnic mesoderm (SM). While DE patterning is fairly well studied, the paracrine signaling controlling SM regionalization and how this is coordinated with epithelial identity is obscure. Here, we use single cell transcriptomics to generate a high-resolution cell state map of the embryonic mouse foregut. This identifies a diversity of SM cell types that develop in close register with the organ-specific epithelium. We infer a spatiotemporal signaling network of endoderm-mesoderm interactions that orchestrate foregut organogenesis. We validate key predictions with mouse genetics, showing the importance of endoderm-derived signals in mesoderm patterning. Finally, leveraging these signaling interactions, we generate different SM subtypes from human pluripotent stem cells (hPSCs), which previously have been elusive. The single cell data can be explored at: https://research.cchmc.org/ZornLab-singlecell .
    DOI:  https://doi.org/10.1038/s41467-020-17968-x
  24. Elife. 2020 Aug 26. pii: e59810. [Epub ahead of print]9
    Geisberg JV, Moqtaderi Z, Struhl K.
      Yeast cells undergoing the diauxic response show a striking upstream shift in poly(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3' mRNA isoforms for most genes. This altered poly(A) pattern is extremely similar to that observed in cells containing Pol II derivatives with slow elongation rates. Conversely, cells containing derivatives with fast elongation rates show a subtle downstream shift in poly(A) sites. Polyadenylation patterns of many genes are sensitive to both fast and slow elongation rates, and a global shift of poly(A) utilization is strongly linked to increased purine content of sequences flanking poly(A) sites. Pol II processivity is impaired in diauxic cells, but strains with reduced processivity and normal Pol II elongation rates have normal polyadenylation profiles. Thus, Pol II elongation speed is important for poly(A) site selection and for regulating poly(A) patterns in response to environmental conditions.
    Keywords:  S. cerevisiae; chromosomes; gene expression
    DOI:  https://doi.org/10.7554/eLife.59810
  25. Nat Commun. 2020 Aug 28. 11(1): 4338
    Parua PK, Kalan S, Benjamin B, Sansó M, Fisher RP.
      Reversible phosphorylation of Pol II and accessory factors helps order the transcription cycle. Here, we define two kinase-phosphatase switches that operate at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3' and 5' ends of genes, respectively, and have overlapping but distinct specificities for Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between Kyrpides-Ouzounis-Woese (KOW) motifs 4 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation decreases as transcription complexes pass the cleavage and polyadenylation signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in termination first uncovered in yeast. Depletion of PP4-complex subunits increases phosphorylation of both Ser666 and the CTR, and promotes redistribution of promoter-proximally paused Pol II into gene bodies. These results suggest that switches comprising Cdk9 and either PP4 or PP1 govern pause release and the elongation-termination transition, respectively.
    DOI:  https://doi.org/10.1038/s41467-020-18173-6
  26. Genome Biol. 2020 Aug 28. 21(1): 219
    Fernandez LR, Gilgenast TG, Phillips-Cremins JE.
      An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Computational tools for rigorous assessment of cell type-specific loops across multiple biological conditions are needed. We present 3DeFDR, a simple and effective statistical tool for classifying dynamic loops across biological conditions from Chromosome-Conformation-Capture-Carbon-Copy (5C) and Hi-C data. Our work provides a statistical framework and open-source coding libraries for sensitive detection of cell type-specific loops in high-resolution 5C and Hi-C data from multiple cellular conditions.
    Keywords:  3D chromatin looping interactions; Chromatin dynamics; Chromosome-conformation-capture; Epigenetics; False discovery rate; Higher-order chromatin architecture
    DOI:  https://doi.org/10.1186/s13059-020-02061-9
  27. Nat Commun. 2020 Aug 28. 11(1): 4345
    Castellano-Pozo M, Pacheco S, Sioutas G, Jaso-Tamame AL, Dore MH, Karimi MM, Martinez-Perez E.
      Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Meiotic progression involves checkpoint-controlled termination of these events when all homologue pairs achieve synapsis and form crossover precursors. Exploiting the temporo-spatial organisation of the C. elegans germline and time-resolved methods of protein removal, we show that surveillance of the synaptonemal complex (SC) controls meiotic progression. In nuclei with fully synapsed homologues and crossover precursors, removing different meiosis-specific cohesin complexes, which are individually required for SC stability, or a SC central region component causes functional redeployment of the chromosome movement and DSB machinery, triggering whole-nucleus reorganisation. This apparent reversal of the meiotic programme requires CHK-2 kinase reactivation via signalling from chromosome axes containing HORMA proteins, but occurs in the absence of transcriptional changes. Our results uncover an unexpected plasticity of the meiotic programme and show how chromosome signalling orchestrates nuclear organisation and meiotic progression.
    DOI:  https://doi.org/10.1038/s41467-020-18219-9