bims-crepig 2022-04-24 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022‒04‒24
twenty-one papers selected by
Connor Rogerson
University of Cambridge, MRC Cancer Unit

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF.
A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.
Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers.
Tet1 Suppresses p21 to Ensure Proper Cell Cycle Progression in Embryonic Stem Cells.
Connecting high-resolution 3D chromatin organization with epigenomics.
HNF4A modulates glucocorticoid action in the liver.
In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation.
Continuous chromatin state feature annotation of the human epigenome.
Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase.
H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.
The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes.
Allosteric interactions prime androgen receptor dimerization and activation.
The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes.
Argonaute proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells.
CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart.
Chromatin remodeling complexes regulate genome architecture in Arabidopsis.
ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation.
Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity.
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.
PEGR: a flexible management platform for reproducible epigenomic and genomic research.
Functional elements of the cis-regulatory lincRNA-p21.

Nat Commun. 2022 Apr 19. 13(1): 2139

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF.

Abrar Aljahani, Peng Hua, Magdalena A Karpinska, Kimberly Quililan, James O J Davies, A Marieke Oudelaar.

Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date (20 bp resolution) and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

DOI: https://doi.org/10.1038/s41467-022-29696-5
Nat Commun. 2022 Apr 19. 13(1): 2042

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.

Gerard Llimos, Vincent Gardeux, Ute Koch, Judith F Kribelbauer, Antonina Hafner, Daniel Alpern, Joern Pezoldt, Maria Litovchenko, Julie Russeil, Riccardo Dainese, Riccardo Moia, Abdurraouf Mokhtar Mahmoud, Davide Rossi, Gianluca Gaidano, Christoph Plass, Pavlo Lutsik, Clarissa Gerhauser, Sebastian M Waszak, Alistair Boettiger, Freddy Radtke, Bart Deplancke.

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.

DOI: https://doi.org/10.1038/s41467-022-29625-6
Epigenetics Chromatin. 2022 Apr 19. 15(1): 13

Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers.

Roza Berhanu Lemma, Thomas Fleischer, Emily Martinsen, Marit Ledsaak, Vessela Kristensen, Ragnhild Eskeland, Odd Stokke Gabrielsen, Anthony Mathelier.

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.

DOI: https://doi.org/10.1186/s13072-022-00444-9
Cells. 2022 Apr 17. pii: 1366. [Epub ahead of print]11(8):

Tet1 Suppresses p21 to Ensure Proper Cell Cycle Progression in Embryonic Stem Cells.

Stephanie Chrysanthou, Julio C Flores, Meelad M Dawlaty.

  Ten eleven translocation 1 (Tet1) is a DNA dioxygenase that promotes DNA demethylation by oxidizing 5-methylcytosine. It can also partner with chromatin-activating and repressive complexes to regulate gene expressions independent of its enzymatic activity. Tet1 is highly expressed in embryonic stem cells (ESCs) and regulates pluripotency and differentiation. However, its roles in ESC cell cycle progression and proliferation have not been investigated. Using a series of Tet1 catalytic mutant (Tet1m/m), knockout (Tet1-/-) and wild type (Tet1+/+) mouse ESCs (mESCs), we identified a non-catalytic role of Tet1 in the proper cell cycle progression and proliferation of mESCs. Tet1-/-, but not Tet1m/m, mESCs exhibited a significant reduction in proliferation and delayed progression through G1. We found that the cyclin-dependent kinase inhibitor p21/Cdkn1a was uniquely upregulated in Tet1-/- mESCs and its knockdown corrected the slow proliferation and delayed G1 progression. Mechanistically, we found that p21 was a direct target of Tet1. Tet1 occupancy at the p21 promoter overlapped with the repressive histone mark H3K27me3 as well as with the H3K27 trimethyl transferase PRC2 component Ezh2. A loss of Tet1, but not loss of its catalytic activity, significantly reduced the enrichment of Ezh2 and H3K27 trimethylation at the p21 promoter without affecting the DNA methylation levels. We also found that the proliferation defects of Tet1-/- mESCs were independent of their differentiation defects. Together, these findings established a non-catalytic role for Tet1 in suppressing p21 in mESCs to ensure a rapid G1-to-S progression, which is a key hallmark of ESC proliferation. It also established Tet1 as an epigenetic regulator of ESC proliferation in addition to its previously defined roles in ESC pluripotency and differentiation.

Keywords:  ESC; Tet1; cell cycle; p21; proliferation

DOI:  https://doi.org/10.3390/cells11081366
Nat Commun. 2022 Apr 19. 13(1): 2054

Connecting high-resolution 3D chromatin organization with epigenomics.

Fan Feng, Yuan Yao, Xue Qing David Wang, Xiaotian Zhang, Jie Liu.

The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization is related to epigenomic states in human cells. Using publicly available Micro-C datasets, we develop a deep learning model, CAESAR, to learn a mapping function from epigenomic features to 3D chromatin organization. The model accurately predicts fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C fails to detect. With existing epigenomic datasets from ENCODE and Roadmap Epigenomics Project, we successfully impute high-resolution 3D chromatin contact maps for 91 human tissues and cell lines. In the imputed high-resolution contact maps, we identify the spatial interactions between genes and their experimentally validated regulatory elements, demonstrating CAESAR's potential in coupling transcriptional regulation with 3D chromatin organization at high resolution.

DOI: https://doi.org/10.1038/s41467-022-29695-6
Cell Rep. 2022 Apr 19. pii: S2211-1247(22)00455-7. [Epub ahead of print]39(3): 110697

HNF4A modulates glucocorticoid action in the liver.

A Louise Hunter, Toryn M Poolman, Donghwan Kim, Frank J Gonzalez, David A Bechtold, Andrew S I Loudon, Mudassar Iqbal, David W Ray.

  The glucocorticoid receptor (GR) is a nuclear receptor critical to the regulation of energy metabolism and inflammation. The actions of GR are dependent on cell type and context. Here, we demonstrate the role of liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver specificity of GR action. In mouse liver, the HNF4A motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodeled, with loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites associates with loss of GR binding at weak GRE motifs. GR binding and chromatin accessibility are gained at sites characterized by strong GRE motifs, which show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is indicated by an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.

Keywords:  CP: Molecular biology; ChIP; HNF4A; chromatin; cistrome; glucocorticoid receptor; liver; mouse; nuclear receptor; tissue specificity

DOI:  https://doi.org/10.1016/j.celrep.2022.110697
Genes Dev. 2022 Apr 21.

In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation.

Glòria Mas, Fabio Santoro, Enrique Blanco, Gianni Paolo Gamarra Figueroa, François Le Dily, Gianmaria Frigè, Enrique Vidal, Francesca Mugianesi, Cecilia Ballaré, Arantxa Gutierrez, Aleksandra Sparavier, Marc A Marti-Renom, Saverio Minucci, Luciano Di Croce.

  Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.

Keywords:  chromatin; chromatin topology; gene regulation; leukemia

DOI:  https://doi.org/10.1101/gad.349115.121
Bioinformatics. 2022 Apr 22. pii: btac283. [Epub ahead of print]

Continuous chromatin state feature annotation of the human epigenome.

Habib Daneshpajouh, Bowen Chen, Neda Shokraneh, Shohre Masoumi, Kay C Wiese, Maxwell W Libbrecht.

MOTIVATION: Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These methods take as input a set of sequencing-based assays of epigenomic activity, such as ChIP-seq measurements of histone modification and transcription factor binding. They output an annotation of the genome that assigns a chromatin state label to each genomic position. Existing SAGA methods have several limitations caused by the discrete annotation framework: such annotations cannot easily represent varying strengths of genomic elements, and they cannot easily represent combinatorial elements that simultaneously exhibit multiple types of activity. To remedy these limitations, we propose an annotation strategy that instead outputs a vector of chromatin state features at each position rather than a single discrete label. Continuous modeling is common in other fields, such as in topic modeling of text documents. We propose a method, epigenome-ssm-nonneg, that uses a non-negative state space model to efficiently annotate the genome with chromatin state features. We also propose several measures of the quality of a chromatin state feature annotation and we compare the performance of several alternative methods according to these quality measures.RESULTS: We show that chromatin state features from epigenome-ssm-nonneg are more useful for several downstream applications than both continuous and discrete alternatives, including their ability to identify expressed genes and enhancers. Therefore, we expect that these continuous chromatin state features will be valuable reference annotations to be used in visualization and downstream analysis.
AVAILABILITY: Source code for epigenome-ssm is available at https://github.com/habibdanesh/epigenome-ssm.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac283
Nucleic Acids Res. 2022 Apr 22. pii: gkac259. [Epub ahead of print]

Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase.

Maheshi Udugama, Benjamin Vinod, F Lyn Chan, Linda Hii, Andrew Garvie, Philippe Collas, Paul Kalitsis, David Steer, Partha P Das, Pratibha Tripathi, Jeffrey R Mann, Hsiao P J Voon, Lee H Wong.

Histone H3.3 is an H3 variant which differs from the canonical H3.1/2 at four residues, including a serine residue at position 31 which is evolutionarily conserved. The H3.3 S31 residue is phosphorylated (H3.3 S31Ph) at heterochromatin regions including telomeres and pericentric repeats. However, the role of H3.3 S31Ph in these regions remains unknown. In this study, we find that H3.3 S31Ph regulates heterochromatin accessibility at telomeres during replication through regulation of H3K9/K36 histone demethylase KDM4B. In mouse embryonic stem (ES) cells, substitution of S31 with an alanine residue (H3.3 A31 -phosphorylation null mutant) results in increased KDM4B activity that removes H3K9me3 from telomeres. In contrast, substitution with a glutamic acid (H3.3 E31, mimics S31 phosphorylation) inhibits KDM4B, leading to increased H3K9me3 and DNA damage at telomeres. H3.3 E31 expression also increases damage at other heterochromatin regions including the pericentric heterochromatin and Y chromosome-specific satellite DNA repeats. We propose that H3.3 S31Ph regulation of KDM4B is required to control heterochromatin accessibility of repetitive DNA and preserve chromatin integrity.

DOI: https://doi.org/10.1093/nar/gkac259
Oncogene. 2022 Apr 19.

H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.

Runsheng He, Besa Xhabija, Lijin K Gopi, Jiji T Kurup, Zhishan Xu, Zhe Liu, Benjamin L Kidder.

The H3K4 demethylase KDM5B is overexpressed in multiple cancer types, and elevated expression levels of KDM5B is associated with decreased survival. However, the underlying mechanistic contribution of dysregulated expression of KDM5B and H3K4 demethylation in cancer is poorly understood. Our results show that loss of KDM5B in multiple types of cancer cells leads to increased proliferation and elevated expression of cancer stem cell markers. In addition, we observed enhanced tumor formation following KDM5B depletion in a subset of representative cancer cell lines. Our findings also support a role for KDM5B in regulating epigenetic plasticity, where loss of KDM5B in cancer cells with elevated KDM5B expression leads to alterations in activity of chromatin states, which facilitate activation or repression of alternative transcriptional programs. In addition, we define KDM5B-centric epigenetic and transcriptional patterns that support cancer cell plasticity, where KDM5B depleted cancer cells exhibit altered epigenetic and transcriptional profiles resembling a more primitive cellular state. This study also provides a resource for evaluating associations between alterations in epigenetic patterning upon depletion of KDM5B and gene expression in a diverse set of cancer cells.

DOI: https://doi.org/10.1038/s41388-022-02311-z
Nucleic Acids Res. 2022 Apr 19. pii: gkac258. [Epub ahead of print]

The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes.

Arnulf Hertweck, Maria Vila de Mucha, Paul R Barber, Robert Dagil, Hayley Porter, Andres Ramos, Graham M Lord, Richard G Jenner.

Lineage-determining transcription factors (LD-TFs) drive the differentiation of progenitor cells into a specific lineage. In CD4+ T cells, T-bet dictates differentiation of the TH1 lineage, whereas GATA3 drives differentiation of the alternative TH2 lineage. However, LD-TFs, including T-bet and GATA3, are frequently co-expressed but how this affects LD-TF function is not known. By expressing T-bet and GATA3 separately or together in mouse T cells, we show that T-bet sequesters GATA3 at its target sites, thereby removing GATA3 from TH2 genes. This redistribution of GATA3 is independent of GATA3 DNA binding activity and is instead mediated by the T-bet DNA binding domain, which interacts with the GATA3 DNA binding domain and changes GATA3's sequence binding preference. This mechanism allows T-bet to drive the TH1 gene expression program in the presence of GATA3. We propose that redistribution of one LD-TF by another may be a common mechanism that could explain how specific cell fate choices can be made even in the presence of other transcription factors driving alternative differentiation pathways.

DOI: https://doi.org/10.1093/nar/gkac258
Mol Cell. 2022 Apr 15. pii: S1097-2765(22)00291-X. [Epub ahead of print]

Allosteric interactions prime androgen receptor dimerization and activation.

Elizabeth V Wasmuth, Arnaud Vanden Broeck, Justin R LaClair, Elizabeth A Hoover, Kayla E Lawrence, Navid Paknejad, Kyrie Pappas, Doreen Matthies, Biran Wang, Weiran Feng, Philip A Watson, John C Zinder, Wouter R Karthaus, M Jason de la Cruz, Richard K Hite, Katia Manova-Todorova, Zhiheng Yu, Susan T Weintraub, Sebastian Klinge, Charles L Sawyers.

  The androgen receptor (AR) is a nuclear receptor that governs gene expression programs required for prostate development and male phenotype maintenance. Advanced prostate cancers display AR hyperactivation and transcriptome expansion, in part, through AR amplification and interaction with oncoprotein cofactors. Despite its biological importance, how AR domains and cofactors cooperate to bind DNA has remained elusive. Using single-particle cryo-electron microscopy, we isolated three conformations of AR bound to DNA, showing that AR forms a non-obligate dimer, with the buried dimer interface utilized by ancestral steroid receptors repurposed to facilitate cooperative DNA binding. We identify novel allosteric surfaces which are compromised in androgen insensitivity syndrome and reinforced by AR's oncoprotein cofactor, ERG, and by DNA-binding motifs. Finally, we present evidence that this plastic dimer interface may have been adopted for transactivation at the expense of DNA binding. Our work highlights how fine-tuning AR's cooperative interactions translate to consequences in development and disease.

Keywords:  allostery; cooperativity; nuclear receptor; prostate cancer; transcription factors

DOI:  https://doi.org/10.1016/j.molcel.2022.03.035
Cell Stem Cell. 2022 Apr 13. pii: S1934-5909(22)00150-3. [Epub ahead of print]

The nuclear receptor THRB facilitates differentiation of human PSCs into more mature hepatocytes.

Haiting Ma, Esmée de Zwaan, Yang Eric Guo, Paloma Cejas, Prathapan Thiru, Martijn van de Bunt, Jacob F Jeppesen, Sudeepa Syamala, Alessandra Dall'Agnese, Brian J Abraham, Dongdong Fu, Carrie Garrett-Engele, Tong Ihn Lee, Henry W Long, Linda G Griffith, Richard A Young, Rudolf Jaenisch.

  To understand the mechanisms regulating the in vitro maturation of hPSC-derived hepatocytes, we developed a 3D differentiation system and compared gene regulatory elements in human primary hepatocytes with those in hPSC-hepatocytes that were differentiated in 2D or 3D conditions by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Regulome comparisons showed a reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and active enhancers without a reduced transcription of THRB. The addition of thyroid hormone T3 increased the binding of THRB to the CYP3A4 proximal enhancer, restored the super-enhancer status and gene expression of NFIC, and reduced the expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status, and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the hPSC-hepatocytes resulted in the engraftment of human hepatocytes into the mouse liver without disrupting normal liver histology. This work implicates the environmental factor-nuclear receptor axis in regulating the maturation of hPSC-hepatocytes.

Keywords:  3D culture; epigenetics; hepatocytes differentiation and maturation; human pluripotent stem cells; nuclear receptors; pBAF; transcriptional regulation

DOI:  https://doi.org/10.1016/j.stem.2022.03.015
Stem Cell Reports. 2022 Apr 06. pii: S2213-6711(22)00147-3. [Epub ahead of print]

Argonaute proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells.

Madlen Müller, Moritz Schaefer, Tara Fäh, Daniel Spies, Victoria Hermes, Richard Patryk Ngondo, Rodrigo Peña-Hernández, Raffaella Santoro, Constance Ciaudo.

  The Argonaute proteins (AGOs) are well known for their role in post-transcriptional gene silencing in the microRNA (miRNA) pathway. Here we show that in mouse embryonic stem cells, AGO1&2 serve additional functions that go beyond the miRNA pathway. Through the combined deletion of both Agos, we identified a specific set of genes that are uniquely regulated by AGOs but not by the other miRNA biogenesis factors. Deletion of Ago2&1 caused a global reduction of the repressive histone mark H3K27me3 due to downregulation at protein levels of Polycomb repressive complex 2 components. By integrating chromatin accessibility, prediction of transcription factor binding sites, and chromatin immunoprecipitation sequencing data, we identified the pluripotency factor KLF4 as a key modulator of AGO1&2-regulated genes. Our findings revealed a novel axis of gene regulation that is mediated by noncanonical functions of AGO proteins that affect chromatin states and gene expression using mechanisms outside the miRNA pathway.

Keywords:  Argonautes; CTCF; H3K27me3; KLF4; PRC2; integrative analysis

DOI:  https://doi.org/10.1016/j.stemcr.2022.03.014
Genes Dev. 2022 Apr 21.

CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart.

Zachary L Robbe, Wei Shi, Lauren K Wasson, Angel P Scialdone, Caralynn M Wilczewski, Xinlei Sheng, Austin J Hepperla, Brynn N Akerberg, William T Pu, Ileana M Cristea, Ian J Davis, Frank L Conlon.

  The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.

Keywords:  CHD4; NuRD; cardiac; chromatin remodeling; recruitment

DOI:  https://doi.org/10.1101/gad.349154.121
Plant Cell. 2022 Apr 21. pii: koac117. [Epub ahead of print]

Chromatin remodeling complexes regulate genome architecture in Arabidopsis.

Tingting Yang, Dingyue Wang, Guangmei Tian, Linhua Sun, Minqi Yang, Xiaochang Yin, Jun Xiao, Yu Sheng, Danmeng Zhu, Hang He, Yue Zhou.

In eukaryotes, three-dimensional (3D) chromatin architecture maintains genome stability and is important in regulating gene transcription. However, little is known about the mechanisms by which diverse ATP-dependent chromatin remodeling complexes regulate the 3D chromatin structure in plants. We examined the 3D chromatin structure within the ATPase subunit of the SWI/SNF, ISWI, INO80 and CHD remodeling complexes in wild-type (WT) and mutant Arabidopsis thaliana plants by combining high throughput sequencing with in situ Hi-C, the enrichment of histone marks, nucleosome density and gene expression. We found that compartment regions switched, and compartmental strength was significantly weakened in all four enzyme mutants. Chromatin remodeling complexes differentially regulated the nucleosome distribution pattern and density within the switching compartments. Alterations of nucleosome distribution pattern and density were associated with a reduction in H3K27me3 levels in the chromatin remodeling enzyme mutants and led to compartment switching. Our data show that chromatin remodeling complexes regulate the linear nucleosome distribution pattern and density to promote H3K27me3 deposition, which in turn regulates 3D chromatin structure.

DOI: https://doi.org/10.1093/plcell/koac117
Nat Commun. 2022 Apr 19. 13(1): 2011

ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation.

Zheqi Li, Olivia McGinn, Yang Wu, Amir Bahreini, Nolan M Priedigkeit, Kai Ding, Sayali Onkar, Caleb Lampenfeld, Carol A Sartorius, Lori Miller, Margaret Rosenzweig, Ofir Cohen, Nikhil Wagle, Jennifer K Richer, William J Muller, Laki Buluwela, Simak Ali, Tullia C Bruno, Dario A A Vignali, Yusi Fang, Li Zhu, George C Tseng, Jason Gertz, Jennifer M Atkinson, Adrian V Lee, Steffi Oesterreich.

Estrogen receptor alpha (ER/ESR1) is frequently mutated in endocrine resistant ER-positive (ER+) breast cancer and linked to ligand-independent growth and metastasis. Despite the distinct clinical features of ESR1 mutations, their role in intrinsic subtype switching remains largely unknown. Here we find that ESR1 mutant cells and clinical samples show a significant enrichment of basal subtype markers, and six basal cytokeratins (BCKs) are the most enriched genes. Induction of BCKs is independent of ER binding and instead associated with chromatin reprogramming centered around a progesterone receptor-orchestrated insulated neighborhood. BCK-high ER+ primary breast tumors exhibit a number of enriched immune pathways, shared with ESR1 mutant tumors. S100A8 and S100A9 are among the most induced immune mediators and involve in tumor-stroma paracrine crosstalk inferred by single-cell RNA-seq from metastatic tumors. Collectively, these observations demonstrate that ESR1 mutant tumors gain basal features associated with increased immune activation, encouraging additional studies of immune therapeutic vulnerabilities.

DOI: https://doi.org/10.1038/s41467-022-29498-9
Nat Commun. 2022 Apr 21. 13(1): 2169

Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity.

Xiaohan Shi, Yunguang Li, Qiuyue Yuan, Shijie Tang, Shiwei Guo, Yehan Zhang, Juan He, Xiaoyu Zhang, Ming Han, Zhuang Liu, Yiqin Zhu, Suizhi Gao, Huan Wang, Xiongfei Xu, Kailian Zheng, Wei Jing, Luonan Chen, Yong Wang, Gang Jin, Dong Gao.

Chromatin accessibility plays an essential role in controlling cellular identity and the therapeutic response of human cancers. However, the chromatin accessibility landscape and gene regulatory network of pancreatic cancer are largely uncharacterized. Here, we integrate the chromatin accessibility profiles of 84 pancreatic cancer organoid lines with whole-genome sequencing data, transcriptomic sequencing data and the results of drug sensitivity analysis of 283 epigenetic-related chemicals and 5 chemotherapeutic drugs. We identify distinct transcription factors that distinguish molecular subtypes of pancreatic cancer, predict numerous chromatin accessibility peaks associated with gene regulatory networks, discover regulatory noncoding mutations with potential as cancer drivers, and reveal the chromatin accessibility signatures associated with drug sensitivity. These results not only provide the chromatin accessibility atlas of pancreatic cancer but also suggest a systematic approach to comprehensively understand the gene regulatory network of pancreatic cancer in order to advance diagnosis and potential personalized medicine applications.

DOI: https://doi.org/10.1038/s41467-022-29857-6
Nucleic Acids Res. 2022 Apr 21. pii: gkac262. [Epub ahead of print]

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.

Alexandr Boytsov, Sergey Abramov, Ariuna Z Aiusheeva, Alexandra M Kasianova, Eugene Baulin, Ivan A Kuznetsov, Yurii S Aulchenko, Semyon Kolmykov, Ivan Yevshin, Fedor Kolpakov, Ilya E Vorontsov, Vsevolod J Makeev, Ivan V Kulakovskiy.

We present ANANASTRA, https://ananastra.autosome.org, a web server for the identification and annotation of regulatory single-nucleotide polymorphisms (SNPs) with allele-specific binding events. ANANASTRA accepts a list of dbSNP IDs or a VCF file and reports allele-specific binding (ASB) sites of particular transcription factors or in specific cell types, highlighting those with ASBs significantly enriched at SNPs in the query list. ANANASTRA is built on top of a systematic analysis of allelic imbalance in ChIP-Seq experiments and performs the ASB enrichment test against background sets of SNPs found in the same source experiments as ASB sites but not displaying significant allelic imbalance. We illustrate ANANASTRA usage with selected case studies and expect that ANANASTRA will help to conduct the follow-up of GWAS in terms of establishing functional hypotheses and designing experimental verification.

DOI: https://doi.org/10.1093/nar/gkac262
Genome Biol. 2022 Apr 19. 23(1): 99

PEGR: a flexible management platform for reproducible epigenomic and genomic research.

Danying Shao, Gretta D Kellogg, Ali Nematbakhsh, Prashant K Kuntala, Shaun Mahony, B Franklin Pugh, William K M Lai.

  Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform.

Keywords:  Data management system; Galaxy; Genomics; High-throughput sequencing; Reproducibility; Science gateway

DOI:  https://doi.org/10.1186/s13059-022-02671-5
Cell Rep. 2022 Apr 19. pii: S2211-1247(22)00445-4. [Epub ahead of print]39(3): 110687

Functional elements of the cis-regulatory lincRNA-p21.

Lauren Winkler, Maria Jimenez, Joshua T Zimmer, Adam Williams, Matthew D Simon, Nadya Dimitrova.

  The p53-induced long noncoding RNA (lncRNA) lincRNA-p21 is proposed to act in cis to promote p53-dependent expression of the neighboring cell cycle gene, Cdkn1a/p21. The molecular mechanism through which the transcribed lincRNA-p21 regulatory locus activates p21 expression remains poorly understood. To elucidate the functional elements of cis-regulation, we generate a series of genetic models that disrupt DNA regulatory elements, the transcription of lincRNA-p21, or the accumulation of mature lincRNA-p21. Unexpectedly, we determine that full-length transcription, splicing, and accumulation of lincRNA-p21 are dispensable for the chromatin organization of the locus and for cis-regulation. Instead, we find that production of lincRNA-p21 through conserved regions in exon 1 of lincRNA-p21 promotes cis-activation. These findings demonstrate that the activation of nascent transcription from this lncRNA locus, but not the generation or accumulation of a mature lncRNA transcript, is necessary to enact local gene expression control.

Keywords:  CP: Molecular biology; cis-regulation; genetic models; lincRNA-p21; long noncoding RNA; transcription

DOI:  https://doi.org/10.1016/j.celrep.2022.110687