bims-crepig 2020-10-04 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2020‒10‒04
twenty-six papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.
NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation.
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.
ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis.
Protein arginine methyltransferase 5 promotes pICln-dependent androgen receptor transcription in castration-resistant prostate cancer.
Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder.
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.
The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation.
A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.
Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation.
Histone demethylase JMJD2D activates HIF1 signaling pathway via multiple mechanisms to promote colorectal cancer glycolysis and progression.
STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus.
Activation of CpG-Rich Promoters Mediated by MLL Drives MOZ-Rearranged Leukemia.
Characterization of universal features of partially methylated domains across tissues and species.
PQM-1 controls hypoxic survival via regulation of lipid metabolism.
Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks.
Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases.
Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation.
TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis.
NoPeak: k-mer based motif discovery in ChIP-Seq data without peak calling.
Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen.
tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis.
Role of androgen receptor splice variant-7 (AR-V7) in prostate cancer resistance to 2nd-generation androgen receptor signaling inhibitors.
High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.
Pancreatic Cancer Cells Require the Transcription Factor MYRF to Maintain ER Homeostasis.
BRAF status modulates Interelukin-8 expression through a CHOP-dependent mechanism in colorectal cancer.

Cancers (Basel). 2020 Sep 30. pii: E2823. [Epub ahead of print]12(10):

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.

Ian M Overton, Andrew H Sims, Jeremy A Owen, Bret S E Heale, Matthew J Ford, Alexander L R Lubbock, Erola Pairo-Castineira, Abdelkader Essafi.

  Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted "neutral" (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington's epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.

Keywords:  ChIP-seq; Drosophila melanogaster; EMT; breast cancer; epithelial remodelling; functional gene network; gene regulation; mesoderm; network biology; transcription factors

DOI:  https://doi.org/10.3390/cancers12102823
PLoS Genet. 2020 Sep 29. 16(9): e1009044

NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation.

Yuta Hiraike, Hironori Waki, Kana Miyake, Takahito Wada, Misato Oguchi, Kaede Saito, Shuichi Tsutsumi, Hiroyuki Aburatani, Toshimasa Yamauchi, Takashi Kadowaki.

The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation. Here we show that the C-terminal 17 amino acid residues of NFIA (which we call pro#3 domain) are required for the transcriptional activity of NFIA. Full-length NFIA-but not deletion mutant lacking pro#3 domain-rescued impaired expression of PPARγ, the master transcriptional regulator of adipogenesis and impaired adipocyte differentiation in NFIA-knockout cells. Mechanistically, the ability of NFIA to penetrate chromatin and bind to the crucial Pparg enhancer is mediated through pro#3 domain. However, the deletion mutant still binds to Myod1 enhancer to repress expression of MyoD, the master transcriptional regulator of myogenesis as well as proximally transcribed non-coding RNA called DRReRNA, via competition with KLF5 in terms of enhancer binding, leading to suppression of myogenic gene program. Therefore, the negative effect of NFIA on the myogenic gene program is, at least partly, independent of the positive effect on PPARγ expression and its downstream adipogenic gene program. These results uncover multiple ways of action of NFIA to ensure optimal regulation of brown and beige adipocyte differentiation.

DOI: https://doi.org/10.1371/journal.pgen.1009044
Nat Genet. 2020 Oct;52(10): 1024-1035

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.

Raffaella Nativio, Yemin Lan, Greg Donahue, Simone Sidoli, Amit Berson, Ananth R Srinivasan, Oksana Shcherbakova, Alexandre Amlie-Wolf, Ji Nie, Xiaolong Cui, Chuan He, Li-San Wang, Benjamin A Garcia, John Q Trojanowski, Nancy M Bonini, Shelley L Berger.

Protein aggregation is the hallmark of neurodegeneration, but the molecular mechanisms underlying late-onset Alzheimer's disease (AD) are unclear. Here we integrated transcriptomic, proteomic and epigenomic analyses of postmortem human brains to identify molecular pathways involved in AD. RNA sequencing analysis revealed upregulation of transcription- and chromatin-related genes, including the histone acetyltransferases for H3K27ac and H3K9ac. An unbiased proteomic screening singled out H3K27ac and H3K9ac as the main enrichments specific to AD. In turn, epigenomic profiling revealed gains in the histone H3 modifications H3K27ac and H3K9ac linked to transcription, chromatin and disease pathways in AD. Increasing genome-wide H3K27ac and H3K9ac in a fly model of AD exacerbated amyloid-β42-driven neurodegeneration. Together, these findings suggest that AD involves a reconfiguration of the epigenome, wherein H3K27ac and H3K9ac affect disease pathways by dysregulating transcription- and chromatin-gene feedback loops. The identification of this process highlights potential epigenetic strategies for early-stage disease treatment.

DOI: https://doi.org/10.1038/s41588-020-0696-0
Nucleic Acids Res. 2020 Sep 30. pii: gkaa815. [Epub ahead of print]

ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis.

Shuhei Ishikura, Kazuhiko Nakabayashi, Masayoshi Nagai, Toshiyuki Tsunoda, Senji Shirasawa.

Centromeres are genomic regions essential for faithful chromosome segregation. Transcription of noncoding RNA (ncRNA) at centromeres is important for their formation and functions. Here, we report the molecular mechanism by which the transcriptional regulator ZFAT controls the centromeric ncRNA transcription in human and mouse cells. Chromatin immunoprecipitation with high-throughput sequencing analysis shows that ZFAT binds to centromere regions at every chromosome. We find a specific 8-bp DNA sequence for the ZFAT-binding motif that is highly conserved and widely distributed at whole centromere regions of every chromosome. Overexpression of ZFAT increases the centromeric ncRNA levels at specific chromosomes, whereas its silencing reduces them, indicating crucial roles of ZFAT in centromeric transcription. Overexpression of ZFAT increases the centromeric levels of both the histone acetyltransferase KAT2B and the acetylation at the lysine 8 in histone H4 (H4K8ac). siRNA-mediated knockdown of KAT2B inhibits the overexpressed ZFAT-induced increase in centromeric H4K8ac levels, suggesting that ZFAT recruits KAT2B to centromeres to induce H4K8ac. Furthermore, overexpressed ZFAT recruits the bromodomain-containing protein BRD4 to centromeres through KAT2B-mediated H4K8ac, leading to RNA polymerase II-dependent ncRNA transcription. Thus, ZFAT binds to centromeres to control ncRNA transcription through the KAT2B-H4K8ac-BRD4 axis.

DOI: https://doi.org/10.1093/nar/gkaa815
Cancer Res. 2020 Sep 30. pii: canres.1228.2020. [Epub ahead of print]

Protein arginine methyltransferase 5 promotes pICln-dependent androgen receptor transcription in castration-resistant prostate cancer.

Elena Beketova, Shuyi Fang, Jake L Owens, Sheng Liu, Xufeng Chen, Qingfu Zhang, Andrew M Asberry, Xuehong Deng, Jonathan Malola, Jiaoti Huang, Chenglong Li, Roberto Pili, Bennett D Elzey, Timothy L Ratliff, Jun Wan, Chang-Deng Hu.

The majority of advanced prostate cancer therapies aim to inhibit androgen receptor (AR) signaling. However, AR reactivation inevitably drives disease progression to castration-resistant prostate cancer (CRPC). Here we demonstrate that protein arginine methyltransferase 5 (PRMT5) functions as an epigenetic activator of AR transcription in CRPC, requiring cooperation with a methylosome subunit pICln. In vitro and in xenograft tumors in mice, targeting PRMT5 or pICln suppressed growth of CRPC cells. Full-length AR and AR-V7 transcription activation required both PRMT5 and pICln but not MEP50. This activation of transcription was accompanied by PRMT5-mediated symmetric dimethylation of H4R3 at the proximal AR promoter. Further, knockdown of PRMT5 abolished the binding of pICln (but not vice versa) to the AR proximal promoter region, suggesting that PRMT5 recruits pICln to the AR promoter to activate AR transcription. Differential gene expression analysis in 22Rv1 cells confirmed that PRMT5 and pICln both regulate the androgen signaling pathway. Additionally, PRMT5 and pICln protein expression positively correlated with AR and AR-V7 protein expression in CRPC tissues and their expression was highly correlated at the mRNA level across multiple publicly available CRPC datasets. Our results suggest that targeting PRMT5 or pICln may be explored as a novel therapy for CRPC treatment by suppressing expression of AR and AR splice variants to circumvent AR reactivation.

DOI: https://doi.org/10.1158/0008-5472.CAN-20-1228
Cell Stem Cell. 2020 Sep 22. pii: S1934-5909(20)30447-1. [Epub ahead of print]

Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder.

Hannah K Long, Marco Osterwalder, Ian C Welsh, Karissa Hansen, James O J Davies, Yiran E Liu, Mervenaz Koska, Alexander T Adams, Robert Aho, Neha Arora, Kazuya Ikeda, Ruth M Williams, Tatjana Sauka-Spengler, Matthew H Porteus, Tim Mohun, Diane E Dickel, Tomek Swigut, Jim R Hughes, Douglas R Higgs, Axel Visel, Licia Selleri, Joanna Wysocka.

  Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.

Keywords:  Pierre Robin sequence; SOX9; craniofacial; enhancer; enhanceropathy; gene dosage; long-range regulation; neural crest; non-coding mutation; transcription

DOI:  https://doi.org/10.1016/j.stem.2020.09.001
Genome Biol. 2020 Sep 30. 21(1): 256

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.

Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi, Ferhat Ay.

  We present MUSTACHE, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. MUSTACHE employs scale-space theory, a technical advance in computer vision, to detect blob-shaped objects in contact maps. MUSTACHE is scalable to kilobase-resolution maps and reports loops that are highly consistent between replicates and between Hi-C and Micro-C datasets. Compared to other loop callers, such as HiCCUPS and SIP, MUSTACHE recovers a higher number of published ChIA-PET and HiChIP loops as well as loops linking promoters to regulatory elements. Overall, MUSTACHE enables an efficient and comprehensive analysis of chromatin loops. Available at: https://github.com/ay-lab/mustache .

Keywords:  CTCF; ChIA-PET; Chromatin loops; Cohesin; Contact maps; Genome architecture; Hi-C; HiChIP; Micro-C; Promoter-enhancer interactions

DOI:  https://doi.org/10.1186/s13059-020-02167-0
Genes Dev. 2020 Oct 01.

The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation.

Yang Zeng, Ren Ren, Gundeep Kaur, Swanand Hardikar, Zhengzhou Ying, Lance Babcock, Esha Gupta, Xing Zhang, Taiping Chen, Xiaodong Cheng.

  The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments in Dnmt3a/3b/3l triple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.

Keywords:  DNA cytosine methylation; Dnmt3a; Dnmt3b; Dnmt3b3; de novo methylation

DOI:  https://doi.org/10.1101/gad.341925.120
Cancer Cell. 2020 Sep 22. pii: S1535-6108(20)30431-1. [Epub ahead of print]

A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer.

Han Chen, Han Liang.

  Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer transcription loci definition. Only a small proportion of human eRNA loci has been precisely identified, limiting investigations of enhancer-mediated oncogenic mechanisms. Here, we characterize super-enhancer regions using aggregated RNA sequencing (RNA-seq) data from large cohorts. Super-enhancers usually contain discrete loci featuring sharp eRNA expression peaks. We identify >300,000 eRNA loci in ∼377 Mb super-enhancer regions that are regulated by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer. The eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which super-enhancer activities can be quantified by RNA-seq and a user-friendly data portal, enabling a broad range of biomedical investigations.

Keywords:  GTEx; The Cancer Genome Atlas; immunotherapy; nucleosome binding; super enhancer

DOI:  https://doi.org/10.1016/j.ccell.2020.08.020
Nat Commun. 2020 Oct 02. 11(1): 4956

Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation.

Jie Lan, Nicholas Rajan, Martin Bizet, Audrey Penning, Nitesh K Singh, Diana Guallar, Emilie Calonne, Andrea Li Greci, Elise Bonvin, Rachel Deplus, Phillip J Hsu, Sigrid Nachtergaele, Chengjie Ma, Renhua Song, Alejandro Fuentes-Iglesias, Bouchra Hassabi, Pascale Putmans, Frédérique Mies, Gerben Menschaert, Justin J L Wong, Jianlong Wang, Miguel Fidalgo, Bifeng Yuan, François Fuks.

Tet-enzyme-mediated 5-hydroxymethylation of cytosines in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs reveals hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. During differentiation a large number of transcripts, including many encoding key pluripotency-related factors (such as Eed and Jarid2), show decreased cytosine hydroxymethylation. Using Tet-knockout ESCs, we find Tet enzymes to be partly responsible for deposition of 5hmC in mRNA. A transcriptome-wide search further reveals mRNA targets to which Tet1 and Tet2 bind, at sites showing a topology similar to that of 5hmC sites. Tet-mediated RNA hydroxymethylation is found to reduce the stability of crucial pluripotency-promoting transcripts. We propose that RNA cytosine 5-hydroxymethylation by Tets is a mark of transcriptome flexibility, inextricably linked to the balance between pluripotency and lineage commitment.

DOI: https://doi.org/10.1038/s41467-020-18729-6
Oncogene. 2020 Sep 28.

Histone demethylase JMJD2D activates HIF1 signaling pathway via multiple mechanisms to promote colorectal cancer glycolysis and progression.

Kesong Peng, Minghui Zhuo, Ming Li, Qiang Chen, Pingli Mo, Chundong Yu.

Hypoxia-inducible factor 1 (HIF1) signaling pathway plays a key role in cancer progression by enhancing glycolysis through activating the transcription of glycolytic genes. JMJD2D, a histone demethylase that specifically demethylates H3K9me2/3, can promote colorectal cancer (CRC) progression. However, it is unknown whether JMJD2D could promote CRC progression by enhancing glycolysis through activating HIF1 signaling pathway. In this study, we found that downregulation of JMJD2D inhibited the glycolysis in CRC cells through suppressing HIF1 signaling pathway to downregulate glycolytic gene expression. Restoring HIF1 signaling by enforced expression of HIF1α in JMJD2D-knockdown CRC cells partially recovered CRC cell glycolysis, proliferation, migration, invasion, xenograft growth, and metastasis, suggesting that JMJD2D promotes CRC progression by enhancing glycolysis through activating HIF1 signaling pathway. JMJD2D activated HIF1 signaling pathway through three different mechanisms: JMJD2D cooperated with the transcription factor SOX9 to enhance mTOR expression and then to promote HIF1α translation; JMJD2D cooperated with the transcription factor c-Fos to enhance HIF1β transcription; JMJD2D interacted and cooperated with HIF1α to enhance the expression of glycolytic gene. The demethylase-defective mutant of JMJD2D could not induce the expression of mTOR, HIF1α, HIF1β, and glycolytic genes, suggesting that the demethylase activity of JMJD2D is important for glycolysis through activating HIF1 signaling. Clinically, a highly positive correlation between the expression of JMJD2D and mTOR, HIF1β, and several glycolytic genes in human CRC specimens was identified. Collectively, our study reveals an important role of JMJD2D in CRC progression by enhancing glycolysis through activating HIF1 signaling pathway.

DOI: https://doi.org/10.1038/s41388-020-01483-w
Nat Commun. 2020 09 28. 11(1): 4882

STAT5 promotes accessibility and is required for BATF-mediated plasticity at the Il9 locus.

Yongyao Fu, Jocelyn Wang, Gayathri Panangipalli, Benjamin J Ulrich, Byunghee Koh, Chengxian Xu, Rakshin Kharwadkar, Xiaona Chu, Yue Wang, Hongyu Gao, Wenting Wu, Jie Sun, Robert S Tepper, Baohua Zhou, Sarath Chandra Janga, Kai Yang, Mark H Kaplan.

T helper cell differentiation requires lineage-defining transcription factors and factors that have shared expression among multiple subsets. BATF is required for development of multiple Th subsets but functions in a lineage-specific manner. BATF is required for IL-9 production in Th9 cells but in contrast to its function as a pioneer factor in Th17 cells, BATF is neither sufficient nor required for accessibility at the Il9 locus. Here we show that STAT5 is the earliest factor binding and remodeling the Il9 locus to allow BATF binding in both mouse and human Th9 cultures. The ability of STAT5 to mediate accessibility for BATF is observed in other Th lineages and allows acquisition of the IL-9-secreting phenotype. STAT5 and BATF convert Th17 cells into cells that mediate IL-9-dependent effects in allergic airway inflammation and anti-tumor immunity. Thus, BATF requires the STAT5 signal to mediate plasticity at the Il9 locus.

DOI: https://doi.org/10.1038/s41467-020-18648-6
Cell Rep. 2020 Sep 29. pii: S2211-1247(20)31189-X. [Epub ahead of print]32(13): 108200

Activation of CpG-Rich Promoters Mediated by MLL Drives MOZ-Rearranged Leukemia.

Ryo Miyamoto, Hiroshi Okuda, Akinori Kanai, Satoshi Takahashi, Takeshi Kawamura, Hirotaka Matsui, Toshio Kitamura, Issay Kitabayashi, Toshiya Inaba, Akihiko Yokoyama.

  Uncontrolled self-renewal of hematopoietic progenitors induces leukemia. To self-renew, leukemia cells must continuously activate genes that were previously active in their mother cells. Here, we describe the circuitry of a transactivation system responsible for oncogenic self-renewal. MLL recruits RNA polymerase II (RNAP2) to unmethylated CpG-rich promoters by its CXXC domain and activates transcription by transcriptional regulators, including the AF4 family/ENL family/P-TEFb complex, DOT1L, and p300/CBP histone acetyl transferases. MOZ also targets a broad range of CpG-rich promoters through association with RNAP2 and MLL. Leukemic fusion proteins such as MOZ-TIF2 and MLL-AFX constitutively activate CpG-rich promoters by aberrantly recruiting p300/CBP. Pharmacological inhibition of MLL or DOT1L induces differentiation of MOZ-TIF2-transformed cells. These results reveal that activation of unmethylated CpG-rich promoters mediated by MLL is the central mechanism of oncogenic self-renewal in MOZ-rearranged leukemia and indicate that the molecularly targeted therapies intended for MLL-rearranged leukemia can be applied for MOZ-rearranged leukemia.

Keywords:  CXXC domain; ENL; MLL; MOZ; RNA polymerase II; histone acetyl transferase; leukemia; self-renewal; transcription; unmethylated CpG

DOI:  https://doi.org/10.1016/j.celrep.2020.108200
Epigenetics Chromatin. 2020 Oct 02. 13(1): 39

Characterization of universal features of partially methylated domains across tissues and species.

Benjamin E Decato, Jianghan Qu, Xiaojing Ji, Elvin Wagenblast, Simon R V Knott, Gregory J Hannon, Andrew D Smith.

  BACKGROUND: Partially methylated domains (PMDs) are a hallmark of epigenomes in reproducible and specific biological contexts, including cancer cells, the placenta, and cultured cell lines. Existing methods for deciding whether PMDs exist in a sample, as well as their identification, are few, often tailored to specific biological questions, and require high coverage samples for accurate identification.RESULTS: In this study, we outline a set of axioms that take a step towards a functional definition for PMDs, describe an improved method for comparable PMD detection across samples with substantially differing sequencing depths, and refine the decision criteria for whether a sample contains PMDs using a data-driven approach. Applying our method to 267 methylomes from 7 species, we corroborated recent results regarding the general association between replication timing and PMD state, and report identification of several reproducibly "escapee" genes within late-replicating domains that escape the reduced expression and hypomethylation of their immediate genomic neighborhood. We also explored the discordant PMD state of orthologous genes between human and mouse, and observed a directional association of PMD state with gene expression and local gene density.
CONCLUSIONS: Our improved method makes low sequencing depth, population-level studies of PMD variation possible and our results further refine the model of PMD formation as one where sequence context and regional epigenomic features both play a role in gradual genome-wide hypomethylation.

Keywords:  Cancer; DNA methylation; Hidden Markov models; Partially methylated domains

DOI:  https://doi.org/10.1186/s13072-020-00363-7
Nat Commun. 2020 Oct 02. 11(1): 4627

PQM-1 controls hypoxic survival via regulation of lipid metabolism.

Thomas Heimbucher, Julian Hog, Piyush Gupta, Coleen T Murphy.

Animals have evolved responses to low oxygen conditions to ensure their survival. Here, we have identified the C. elegans zinc finger transcription factor PQM-1 as a regulator of the hypoxic stress response. PQM-1 is required for the longevity of insulin signaling mutants, but surprisingly, loss of PQM-1 increases survival under hypoxic conditions. PQM-1 functions as a metabolic regulator by controlling oxygen consumption rates, suppressing hypoxic glycogen levels, and inhibiting the expression of the sorbitol dehydrogenase-1 SODH-1, a crucial sugar metabolism enzyme. PQM-1 promotes hypoxic fat metabolism by maintaining the expression of the stearoyl-CoA desaturase FAT-7, an oxygen consuming, rate-limiting enzyme in fatty acid biosynthesis. PQM-1 activity positively regulates fat transport to developing oocytes through vitellogenins under hypoxic conditions, thereby increasing survival rates of arrested progeny during hypoxia. Thus, while pqm-1 mutants increase survival of mothers, ultimately this loss is detrimental to progeny survival. Our data support a model in which PQM-1 controls a trade-off between lipid metabolic activity in the mother and her progeny to promote the survival of the species under hypoxic conditions.

DOI: https://doi.org/10.1038/s41467-020-18369-w
Elife. 2020 Oct 02. pii: e56450. [Epub ahead of print]9

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks.

Kelsey H Elliott, Xiaoting Chen, Joseph Salomone, Praneet Chaturvedi, Preston A Schultz, Sai K Balchand, Jeffrey D Servetas, Aimée Zuniga, Rolf Zeller, Brian Gebelein, Matthew T Weirauch, Kevin A Peterson, Samantha A Brugmann.

  Despite a common understanding that Gli TFs are utilized to reiterate a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli binding motifs (<strong>d</strong>GBMs). Functional validation revealed these <strong>d</strong>GBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.

Keywords:  developmental biology; mouse

DOI:  https://doi.org/10.7554/eLife.56450
Nat Cell Biol. 2020 Oct;22(10): 1223-1238

Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinases.

Cian J Lynch, Raquel Bernad, Ana Martínez-Val, Marta N Shahbazi, Sandrina Nóbrega-Pereira, Isabel Calvo, Carmen Blanco-Aparicio, Carolina Tarantino, Elena Garreta, Laia Richart-Ginés, Noelia Alcazar, Osvaldo Graña-Castro, Gonzalo Gómez-Lopez, Irene Aksoy, Maribel Muñoz-Martín, Sonia Martinez, Sagrario Ortega, Susana Prieto, Elisabeth Simboeck, Alain Camasses, Camille Stephan-Otto Attolini, Agustin F Fernandez, Marta I Sierra, Mario F Fraga, Joaquin Pastor, Daniel Fisher, Nuria Montserrat, Pierre Savatier, Javier Muñoz, Magdalena Zernicka-Goetz, Manuel Serrano.

Pluripotent stem cells (PSCs) transition between cell states in vitro, reflecting developmental changes in the early embryo. PSCs can be stabilized in the naive state by blocking extracellular differentiation stimuli, particularly FGF-MEK signalling. Here, we report that multiple features of the naive state in human and mouse PSCs can be recapitulated without affecting FGF-MEK signalling or global DNA methylation. Mechanistically, chemical inhibition of CDK8 and CDK19 (hereafter CDK8/19) kinases removes their ability to repress the Mediator complex at enhancers. CDK8/19 inhibition therefore increases Mediator-driven recruitment of RNA polymerase II (RNA Pol II) to promoters and enhancers. This efficiently stabilizes the naive transcriptional program and confers resistance to enhancer perturbation by BRD4 inhibition. Moreover, naive pluripotency during embryonic development coincides with a reduction in CDK8/19. We conclude that global hyperactivation of enhancers drives naive pluripotency, and this can be achieved in vitro by inhibiting CDK8/19 kinase activity. These principles may apply to other contexts of cellular plasticity.

DOI: https://doi.org/10.1038/s41556-020-0573-1
Nat Commun. 2020 10 01. 11(1): 4928

Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation.

Jingxue Xin, Hui Zhang, Yaoxi He, Zhana Duren, Caijuan Bai, Lang Chen, Xin Luo, Dong-Sheng Yan, Chaoyu Zhang, Xiang Zhu, Qiuyue Yuan, Zhanying Feng, Chaoying Cui, Xuebin Qi, Ouzhuluobu, Wing Hung Wong, Yong Wang, Bing Su.

High-altitude adaptation of Tibetans represents a remarkable case of natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting a pressing need to understand the functional role of non-coding regulatory elements (REs). Here, we generate time courses of paired ATAC-seq and RNA-seq data on cultured HUVECs under hypoxic and normoxic conditions. We further develop a variant interpretation methodology (vPECA) to identify active selected REs (ASREs) and associated regulatory network. We discover three causal SNPs of EPAS1, the key adaptive gene for Tibetans. These SNPs decrease the accessibility of ASREs with weakened binding strength of relevant TFs, and cooperatively down-regulate EPAS1 expression. We further construct the downstream network of EPAS1, elucidating its roles in hypoxic response and angiogenesis. Collectively, we provide a systematic approach to interpret phenotype-associated noncoding variants in proper cell types and relevant dynamic conditions, to model their impact on gene regulation.

DOI: https://doi.org/10.1038/s41467-020-18638-8
PeerJ. 2020 ;8 e9950

TET1 may contribute to hypoxia-induced epithelial to mesenchymal transition of endometrial epithelial cells in endometriosis.

Jingni Wu, Xidie Li, Hongyan Huang, Xiaomeng Xia, Mengmeng Zhang, Xiaoling Fang.

  Background: Endometriosis (EMs) is a non-malignant gynecological disease, whose pathogenesis remains to be clarified. Recent studies have found that hypoxia induces epithelial-mesenchymal transition (EMT) as well as epigenetic modification in EMs. However, the relationship between EMT and demethylation modification under hypoxia status in EMs remains unknown.Methods: The expression of N-cadherin, E-cadherin and TET1 in normal endometria, eutopic endometria and ovarian endometriomas was assessed by immunohistochemistry and immunofluorescence double staining. 5-hmC was detected by fluorescence-based ELISA kit using a specific 5-hmC antibody. Overexpression and inhibition of TET1 or hypoxia-inducible factor 2α (HIF-2α) were performed by plasmid and siRNA transfection. The expression of HIF-2α, TET1 and EMT markers in Ishikawa (ISK) cells (widely used as endometrial epithelial cells) was evaluated by western blotting. The interaction of HIF-2α and TET1 was analyzed by chromatin immunoprecipitation.
Results: Demethylation enzyme TET1 (ten-eleven translocation1) was elevated in glandular epithelium of ovarian endometrioma, along with the activation of EMT (increased expression of N-cadherin, and decreased expression of E-cadherin) and global increase of epigenetic modification marker 5-hmC(5-hydroxymethylcytosine). Besides, endometriosis lesions had more TET1 and N-cadherin co-localized cells. Further study showed that ISK cells exhibited enhanced EMT, and increased expression of TET1 and HIF-2α under hypoxic condition. Hypoxia-induced EMT was partly regulated by TET1 and HIF-2α. HIF-2α inhibition mitigated TET1 expression changes provoked by hypoxia.
Conclusions: Hypoxia induces the expression of TET1 regulated by HIF-2α, thus may promote EMT in endometriosis.

Keywords:  EMT; Endometriosis; HIF-2α; TET1

DOI:  https://doi.org/10.7717/peerj.9950
Bioinformatics. 2020 Sep 29. pii: btaa845. [Epub ahead of print]

NoPeak: k-mer based motif discovery in ChIP-Seq data without peak calling.

Michael Menzel, Sabine Hurka, Stefan Glasenhardt, Andreas Gogol-Döring.

MOTIVATION: The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise.RESULTS: Here we present a novel approach to reliably identify transcription factor binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines.
AVAILABILITY: NoPeak is published under the GNU General Public License and available as a standalone console based Java application at https://github.com/menzel/nopeak.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btaa845
Elife. 2020 Oct 01. pii: e57858. [Epub ahead of print]9

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen.

Hao Zhang, Yang Zhang, Xinyue Zhou, Shaela Wright, Judith Hyle, Lianzhong Zhao, Jie An, Xujie Zhao, Ying Shao, Beisi Xu, Hyeong-Min Lee, Taosheng Chen, Yang Zhou, Xiang Chen, Rui Lu, Chunliang Li.

  Aberrant HOXA9 expression is a hallmark of most aggressive acute leukemias, notably those with KMT2A (MLL) gene rearrangements. HOXA9 overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding of HOXA9 regulation in leukemia is limited, hindering development of therapeutic strategies. Here, we generated the HOXA9-mCherry knock-in reporter cell lines to dissect HOXA9 regulation. By utilizing the reporter and CRISPR/Cas9 screens, we identified transcription factors controlling HOXA9 expression, including a novel regulator, USF2, whose depletion significantly down-regulated HOXA9 expression and impaired MLLr leukemia cell proliferation. Ectopic expression of Hoxa9 rescued impaired leukemia cell proliferation upon USF2 loss. Cut&Run analysis revealed the direct occupancy of USF2 at HOXA9 promoter in MLLr leukemia cells. Collectively, the HOXA9 reporter facilitated the functional interrogation of the HOXA9 regulome and has advanced our understanding of the molecular regulation network in HOXA9-driven leukemia.

Keywords:  cancer biology; human

DOI:  https://doi.org/10.7554/eLife.57858
Cell Rep. 2020 Sep 29. pii: S2211-1247(20)31195-5. [Epub ahead of print]32(13): 108206

tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis.

Chao Zhang, Zihan Xu, Shangda Yang, Guohuan Sun, Lumeng Jia, Zhaofeng Zheng, Quan Gu, Wei Tao, Tao Cheng, Cheng Li, Hui Cheng.

  Spatiotemporal chromatin reorganization during hematopoietic differentiation has not been comprehensively characterized, mainly because of the large numbers of starting cells required for current chromatin conformation capture approaches. Here, we introduce a low-input tagmentation-based Hi-C (tagHi-C) method to capture the chromatin structures of hundreds of cells. Using tagHi-C, we are able to map the spatiotemporal dynamics of chromatin structure in ten primary hematopoietic stem, progenitor, and differentiated cell populations from mouse bone marrow. Our results reveal that changes in compartment dynamics and the Rabl configuration occur during hematopoietic cell differentiation. We identify gene-body-associating domains (GADs) as general structures for highly expressed genes. Moreover, we extend the body of knowledge regarding genes influenced by genome-wide association study (GWAS) loci through spatial chromatin looping. Our study provides the tagHi-C method for studying the three-dimensional (3D) genome of a small number of cells and maps the comprehensive 3D chromatin landscape of bone marrow hematopoietic cells.

Keywords:  GAD; Rabl configuration; chromatin structure; gene-body-associating domain; hematopoietic differentiation; loops; low input; tagHi-C; tagmentation-based Hi-C

DOI:  https://doi.org/10.1016/j.celrep.2020.108206
Oncogene. 2020 Sep 28.

Role of androgen receptor splice variant-7 (AR-V7) in prostate cancer resistance to 2nd-generation androgen receptor signaling inhibitors.

Yezi Zhu, Susan L Dalrymple, Ilsa Coleman, S Lilly Zheng, Jianfeng Xu, Jody E Hooper, Emmanuel S Antonarakis, Angelo M De Marzo, Alan K Meeker, Peter S Nelson, William B Isaacs, Samuel R Denmeade, Jun Luo, W Nathaniel Brennen, John T Isaacs.

The role of truncated androgen receptor splice variant-7 (AR-V7) in prostate cancer biology is an unresolved question. Is it simply a marker of resistance to 2nd-generation androgen receptor signaling inhibitors (ARSi) like abiraterone acetate (Abi) and enzalutamide (Enza) or a functional driver of lethal resistance via its ligand-independent transcriptional activity? To resolve this question, the correlation between resistance to ARSi and genetic chances and expression of full length AR (AR-FL) vs. AR-V7 were evaluated in a series of independent patient-derived xenografts (PDXs). While all PDXs lack PTEN expression, there is no consistent requirement for mutation in TP53, RB1, BRCA2, PIK3CA, or MSH2, or expression of SOX2 or ERG and ARSi resistance. Elevated expression of AR-FL alone is sufficient for Abi but not Enza resistance, even if AR-FL is gain-of-function (GOF) mutated. Enza resistance is consistently correlated with enhanced AR-V7 expression. In vitro and in vivo growth responses of Abi-/Enza-resistant LNCaP-95 cells in which CRISPR-Cas9 was used to knockout AR-FL or AR-V7 alone or in combination were evaluated. Combining these growth responses with RNAseq analysis demonstrates that both AR-FL- and AR-V7-dependent transcriptional complementation are needed for Abi/Enza resistance.

DOI: https://doi.org/10.1038/s41388-020-01479-6
Mol Cell. 2020 Sep 19. pii: S1097-2765(20)30613-4. [Epub ahead of print]

High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.

Pranitha Vangala, Rachel Murphy, Sofia A Quinodoz, Kyle Gellatly, Patrick McDonel, Mitchell Guttman, Manuel Garber.

  Eukaryotic gene expression regulation involves thousands of distal regulatory elements. Understanding the quantitative contribution of individual enhancers to gene expression is critical for assessing the role of disease-associated genetic risk variants. Yet, we lack the ability to accurately link genes with their distal regulatory elements. To address this, we used 3D enhancer-promoter (E-P) associations identified using split-pool recognition of interactions by tag extension (SPRITE) to build a predictive model of gene expression. Our model dramatically outperforms models using genomic proximity and can be used to determine the quantitative impact of enhancer loss on gene expression in different genetic backgrounds. We show that genes that form stable E-P hubs have less cell-to-cell variability in gene expression. Finally, we identified transcription factors that regulate stimulation-dependent E-P interactions. Together, our results provide a framework for understanding quantitative contributions of E-P interactions and associated genetic variants to gene expression.

Keywords:  chromosome conformation; cis-regulatory elements; dendritic cells; enhancers; genetic variation; innate immunity; machine learning; multiway promoter interactions; single cell; single molecule

DOI:  https://doi.org/10.1016/j.molcel.2020.09.005
Dev Cell. 2020 Sep 24. pii: S1534-5807(20)30713-9. [Epub ahead of print]

Pancreatic Cancer Cells Require the Transcription Factor MYRF to Maintain ER Homeostasis.

Marta Milan, Chiara Balestrieri, Gabriele Alfarano, Sara Polletti, Elena Prosperini, Paola Nicoli, Paola Spaggiari, Alessandro Zerbi, Vincenzo Cirulli, Giuseppe R Diaferia, Gioacchino Natoli.

  Many tumors of endodermal origin are composed of highly secretory cancer cells that must adapt endoplasmic reticulum (ER) activity to enable proper folding of secreted proteins and prevent ER stress. We found that pancreatic ductal adenocarcinomas (PDACs) overexpress the myelin regulatory factor (MYRF), an ER membrane-associated transcription factor (TF) released by self-cleavage. MYRF was expressed in the well-differentiated secretory cancer cells, but not in the poorly differentiated quasi-mesenchymal cells that coexist in the same tumor. MYRF expression was controlled by the epithelial identity TF HNF1B, and it acted to fine-tune the expression of genes encoding highly glycosylated, cysteine-rich secretory proteins, thus preventing ER overload. MYRF-deficient PDAC cells showed signs of ER stress, impaired proliferation, and an inability to form spheroids in vitro, while in vivo they generated highly secretory but poorly proliferating and hypocellular tumors. These data indicate a role of MYRF in the control of ER homeostasis in highly secretory PDAC cells.

Keywords:  ER stress; MYRF; differentiation; pancreatic cancer; stress response; transcription; tumor heterogeneity; unfolded protein response

DOI:  https://doi.org/10.1016/j.devcel.2020.09.011
Commun Biol. 2020 Oct 01. 3(1): 546

BRAF status modulates Interelukin-8 expression through a CHOP-dependent mechanism in colorectal cancer.

Fabiana Conciatori, Chiara Bazzichetto, Carla Azzurra Amoreo, Isabella Sperduti, Sara Donzelli, Maria Grazia Diodoro, Simonetta Buglioni, Italia Falcone, Senji Shirasawa, Giovanni Blandino, Gianluigi Ferretti, Francesco Cognetti, Michele Milella, Ludovica Ciuffreda.

Inflammation might substantially contribute to the limited therapeutic success of current systemic therapies in colorectal cancer (CRC). Amongst cytokines involved in CRC biology, the proinflammatory chemokine IL-8 has recently emerged as a potential prognostic/predictive biomarker. Here, we show that BRAF mutations and PTEN-loss are associated with high IL-8 levels in CRC models in vitro and that BRAF/MEK/ERK, but not PI3K/mTOR, targeting controls its production in different genetic contexts. In particular, we identified a BRAF/ERK2/CHOP axis affecting IL-8 transcription, through regulation of CHOP subcellular localization, and response to targeted inhibitors. Moreover, RNA Pol II and an open chromatin status in the CHOP-binding region of the IL-8 gene promoter cooperate towards increased IL-8 expression, after a selective BRAF inhibition. Overall, our data show that IL-8 production is finely and differentially regulated depending on the tumor genetic context and might be targeted for therapeutic purposes in molecularly defined subgroups of CRC patients.

DOI: https://doi.org/10.1038/s42003-020-01263-y