bims-crepig 2022-10-16 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2022–10–16
eleven papers selected by
Connor Rogerson, University of Cambridge

CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos.
Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism.
scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data.
Epigenetic factor competition reshapes the EMT landscape.
CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research.
HiChIPdb: a comprehensive database of HiChIP regulatory interactions.
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.
A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish.
Activation of γ-globin expression by hypoxia-inducible factor 1α.
iEnhancer-MRBF: Identifying enhancers and their strength with a multiple Laplacian-regularized radial basis function network.
Sensitive image-based chromatin binding assays using inducible ERα to rapidly characterize estrogenic chemicals and mixtures.

EMBO J. 2022 Oct 10. e112012

CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos.

Meng Wang, Zhiyuan Chen, Yi Zhang.

  Epigenome reprogramming after fertilization enables transcriptionally quiescent maternal and paternal chromatin to acquire a permissive state for subsequent zygotic genome activation (ZGA). H3K27 acetylation (H3K27ac) is a well-established chromatin marker of active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos are not well-studied. By profiling the allelic landscape of H3K27ac during mouse MZT, we show that H3K27ac undergoes three waves of rapid global transitions between oocyte stage and 2-cell stage. Notably, germinal vesicle oocyte and zygote chromatin are globally hyperacetylated, with noncanonical, broad H3K27ac domains that correlate with broad H3K4 trimethylation (H3K4me3) and open chromatin. H3K27ac marks genomic regions primed for activation including ZGA genes, retrotransposons, and active alleles of imprinted genes. We show that CBP/p300 and HDAC activities play important roles in regulating H3K27ac dynamics and are essential for preimplantation development. Specifically, CBP/p300 acetyltransferase broadly deposits H3K27ac in zygotes to induce the opening of condensed chromatin at putative enhancers and ensure proper ZGA. On the contrary, HDACs revert broad H3K27ac domains to canonical domains and safeguard ZGA by preventing premature expression of developmental genes. In conclusion, coordinated activities of CBP/p300 and HDACs during mouse MZT are essential for ZGA and preimplantation development.

Keywords:  CBP/p300; H3K27ac; HDACs; MZT; ZGA

DOI:  https://doi.org/10.15252/embj.2022112012
Mol Cell. 2022 Oct 01. pii: S1097-2765(22)00905-4. [Epub ahead of print]

Yeast Mediator facilitates transcription initiation at most promoters via a Tail-independent mechanism.

Linda Warfield, Rafal Donczew, Lakshmi Mahendrawada, Steven Hahn.

  Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. In contrast, at most Tail-independent genes, we find MED primarily at promoters but not at the UASs. These results suggest that MED Tail and activator-mediated MED recruitment regulates only a small subset of genes. Furthermore, we define three classes of genes that differ in PIC assembly pathways and the requirements for MED Tail, SAGA, TFIID, and BET factors Bdf1/2. Our combined results have broad implications for the roles of MED, other coactivators, and mechanisms of transcriptional regulation at different gene classes.

Keywords:  BET factors; Mediator; SAGA; TFIID; coactivator; stress response; transcription; transcription activation; transcription factor; transcription initiation

DOI:  https://doi.org/10.1016/j.molcel.2022.09.016
Front Cell Dev Biol. 2022 ;10 981859

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data.

Kai Hu, Haibo Liu, Nathan D Lawson, Lihua Julie Zhu.

  Single cell ATAC-seq (scATAC-seq) has become the most widely used method for profiling open chromatin landscape of heterogeneous cell populations at a single-cell resolution. Although numerous software tools and pipelines have been developed, an easy-to-use, scalable, reproducible, and comprehensive pipeline for scATAC-seq data analyses is still lacking. To fill this gap, we developed scATACpipe, a Nextflow pipeline, for performing comprehensive analyses of scATAC-seq data including extensive quality assessment, preprocessing, dimension reduction, clustering, peak calling, differential accessibility inference, integration with scRNA-seq data, transcription factor activity and footprinting analysis, co-accessibility inference, and cell trajectory prediction. scATACpipe enables users to perform the end-to-end analysis of scATAC-seq data with three sub-workflow options for preprocessing that leverage 10x Genomics Cell Ranger ATAC software, the ultra-fast Chromap procedures, and a set of custom scripts implementing current best practices for scATAC-seq data preprocessing. The pipeline extends the R package ArchR for downstream analysis with added support to any eukaryotic species with an annotated reference genome. Importantly, scATACpipe generates an all-in-one HTML report for the entire analysis and outputs cluster-specific BAM, BED, and BigWig files for visualization in a genome browser. scATACpipe eliminates the need for users to chain different tools together and facilitates reproducible and comprehensive analyses of scATAC-seq data from raw reads to various biological insights with minimal changes of configuration settings for different computing environments or species. By applying it to public datasets, we illustrated the utility, flexibility, versatility, and reliability of our pipeline, and demonstrated that our scATACpipe outperforms other workflows.

Keywords:  chromatin accessibility; integration of scATAC-seq and scRNA-seq; nextflow; pipeline; scATAC-seq; single cell; trajectory inference; transcription factor activity and footprinting analysis

DOI:  https://doi.org/10.3389/fcell.2022.981859
Proc Natl Acad Sci U S A. 2022 Oct 18. 119(42): e2210844119

Epigenetic factor competition reshapes the EMT landscape.

M Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D Sontag, Herbert Levine.

  The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene-regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as gene-regulatory networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators, in addition to local transcription factors, and show the counterintuitive consequences of such interactions. We apply our approach to recent experimental findings on the epithelial-mesenchymal transition (EMT). We show that it can explain the puzzling experimental data, as well as provide verifiable predictions.

Keywords:  EMT; epigenetic; gene network

DOI:  https://doi.org/10.1073/pnas.2210844119
Genome Med. 2022 Oct 13. 14(1): 118

CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research.

Haizhou Liu, Mengqin Yuan, Ramkrishna Mitra, Xu Zhou, Min Long, Wanyue Lei, Shunheng Zhou, Yu-E Huang, Fei Hou, Christine M Eischen, Wei Jiang.

   BACKGROUND: Pathway enrichment analysis (PEA) is a common method for exploring functions of hundreds of genes and identifying disease-risk pathways. Moreover, different pathways exert their functions through crosstalk. However, existing PEA methods do not sufficiently integrate essential pathway features, including pathway crosstalk, molecular interactions, and network topologies, resulting in many risk pathways that remain uninvestigated.
METHODS: To overcome these limitations, we develop a new crosstalk-based PEA method, CTpathway, based on a global pathway crosstalk map (GPCM) with >440,000 edges by combing pathways from eight resources, transcription factor-gene regulations, and large-scale protein-protein interactions. Integrating gene differential expression and crosstalk effects in GPCM, we assign a risk score to genes in the GPCM and identify risk pathways enriched with the risk genes.
RESULTS: Analysis of >8300 expression profiles covering ten cancer tissues and blood samples indicates that CTpathway outperforms the current state-of-the-art methods in identifying risk pathways with higher accuracy, reproducibility, and speed. CTpathway recapitulates known risk pathways and exclusively identifies several previously unreported critical pathways for individual cancer types. CTpathway also outperforms other methods in identifying risk pathways across all cancer stages, including early-stage cancer with a small number of differentially expressed genes. Moreover, the robust design of CTpathway enables researchers to analyze both bulk and single-cell RNA-seq profiles to predict both cancer tissue and cell type-specific risk pathways with higher accuracy.
CONCLUSIONS: Collectively, CTpathway is a fast, accurate, and stable pathway enrichment analysis method for cancer research that can be used to identify cancer risk pathways. The CTpathway interactive web server can be accessed here http://www.jianglab.cn/CTpathway/ . The stand-alone program can be accessed here https://github.com/Bioccjw/CTpathway .

Keywords:  Molecular interaction; Network analysis; Pathway crosstalk; Pathway enrichment analysis; Risk pathway

DOI:  https://doi.org/10.1186/s13073-022-01119-6
Nucleic Acids Res. 2022 Oct 10. pii: gkac859. [Epub ahead of print]

HiChIPdb: a comprehensive database of HiChIP regulatory interactions.

Wanwen Zeng, Qiao Liu, Qijin Yin, Rui Jiang, Wing Hung Wong.

Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains ∼262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.

DOI: https://doi.org/10.1093/nar/gkac859
Nat Struct Mol Biol. 2022 Oct;29(10): 1011-1023

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.

Maria Victoria Neguembor, Juan Pablo Arcon, Diana Buitrago, Rafael Lema, Jürgen Walther, Ximena Garate, Laura Martin, Pablo Romero, Jumana AlHaj Abed, Marta Gut, Julie Blanc, Melike Lakadamyali, Chao-Ting Wu, Isabelle Brun Heath, Modesto Orozco, Pablo D Dans, Maria Pia Cosma.

The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes physically fold in the three-dimensional nuclear space. Here we describe immuno-OligoSTORM, an imaging strategy that reveals the distribution of nucleosomes within specific genes in super-resolution, through the simultaneous visualization of DNA and histones. We combine immuno-OligoSTORM with restraint-based and coarse-grained modeling approaches to integrate super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. The resulting method, called Modeling immuno-OligoSTORM, allows quantitative modeling of genes with nucleosome resolution and provides information about chromatin accessibility for regulatory factors, such as RNA polymerase II. With Modeling immuno-OligoSTORM, we explore intercellular variability, transcriptional-dependent gene conformation, and folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells, thereby obtaining the highest degree of data integration achieved so far to our knowledge.

DOI: https://doi.org/10.1038/s41594-022-00839-y
Cell Genom. 2022 Sep 14. pii: 100170. [Epub ahead of print]2(9):

A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish.

Erin Jimenez, Claire C Slevin, Wei Song, Zelin Chen, Stephen C Frederickson, Derek Gildea, Weiwei Wu, Abdel G Elkahloun, Ivan Ovcharenko, Shawn M Burgess.

Using adult zebrafish inner ears as a model for sensorineural regeneration, we ablated the mechanosensory receptors and characterized the single-cell epigenome and transcriptome at consecutive time points during hair cell regeneration. We utilized deep learning on the regeneration-induced open chromatin sequences and identified cell-specific transcription factor (TF) motif patterns. Enhancer activity correlated with gene expression and identified potential gene regulatory networks. A pattern of overlapping Sox- and Six-family TF gene expression and binding motifs was detected, suggesting a combinatorial program of TFs driving regeneration and cell identity. Pseudotime analysis of single-cell transcriptomic data suggested that support cells within the sensory epithelium changed cell identity to a "progenitor" cell population that could differentiate into hair cells. We identified a 2.6 kb DNA enhancer upstream of the sox2 promoter that, when deleted, showed a dominant phenotype that resulted in a hair-cell-regeneration-specific deficit in both the lateral line and adult inner ear.

DOI: https://doi.org/10.1016/j.xgen.2022.100170
Nature. 2022 Oct 12.

Activation of γ-globin expression by hypoxia-inducible factor 1α.

Ruopeng Feng, Thiyagaraj Mayuranathan, Peng Huang, Phillip A Doerfler, Yichao Li, Yu Yao, Jingjing Zhang, Lance E Palmer, Kalin Mayberry, Georgios E Christakopoulos, Peng Xu, Chunliang Li, Yong Cheng, Gerd A Blobel, M Celeste Simon, Mitchell J Weiss.

Around birth, globin expression in human red blood cells (RBCs) shifts from γ-globin to β-globin, which results in fetal haemoglobin (HbF, α2γ2) being gradually replaced by adult haemoglobin (HbA, α2β2)1. This process has motivated the development of innovative approaches to treat sickle cell disease and β-thalassaemia by increasing HbF levels in postnatal RBCs2. Here we provide therapeutically relevant insights into globin gene switching obtained through a CRISPR-Cas9 screen for ubiquitin-proteasome components that regulate HbF expression. In RBC precursors, depletion of the von Hippel-Lindau (VHL) E3 ubiquitin ligase stabilized its ubiquitination target, hypoxia-inducible factor 1α (HIF1α)3,4, to induce γ-globin gene transcription. Mechanistically, HIF1α-HIF1β heterodimers bound cognate DNA elements in BGLT3, a long noncoding RNA gene located 2.7 kb downstream of the tandem γ-globin genes HBG1 and HBG2. This was followed by the recruitment of transcriptional activators, chromatin opening and increased long-range interactions between the γ-globin genes and their upstream enhancer. Similar induction of HbF occurred with hypoxia or with inhibition of prolyl hydroxylase domain enzymes that target HIF1α for ubiquitination by the VHL E3 ubiquitin ligase. Our findings link globin gene regulation with canonical hypoxia adaptation, provide a mechanism for HbF induction during stress erythropoiesis and suggest a new therapeutic approach for β-haemoglobinopathies.

DOI: https://doi.org/10.1038/s41586-022-05312-w
Methods. 2022 Oct 08. pii: S1046-2023(22)00218-3. [Epub ahead of print]

iEnhancer-MRBF: Identifying enhancers and their strength with a multiple Laplacian-regularized radial basis function network.

Zhichao Xiao, Lizhuang Wang, Yijie Ding, Liang Yu.

  An enhancer is a short DNA sequence containing many binding sites of transcription factors that plays a crucial role in the gene expression of major eukaryotes. It is difficult to avoid the time consumption and high cost of experimental methods. Therefore, with the continuous development of genomics, it is an urgent task to identify enhancers and their intensities by computational methods. In this paper, we propose a two-layer model called iEnhancer-MRBF, wherein the first layer is used to identify enhancers, and the identified enhancers are divided into strong enhancers and weak enhancers according to their strength in the second layer. In iEnhancer-MRBF, a new classifier multiple Laplacian-regularized radial basis function network (MLR-RBFN) is proposed, and three feature extraction methods, namely, kmer, nucleotide binary profiles (NBP) and ac-cumulated nucleotide frequency (ANF), as well as feature selection, are used to process DNA sequences. The experimental results reveal that this model is obviously better than previous predictors, and the accuracy rates on the independent dataset test for the first layer and second layer are 79.75% and 83.50%, respectively.

Keywords:  DNA sequence; Enhancers; Laplacian-regularized; Machine learning; Radial basis function network

DOI:  https://doi.org/10.1016/j.ymeth.2022.10.001
iScience. 2022 Oct 21. 25(10): 105200

Sensitive image-based chromatin binding assays using inducible ERα to rapidly characterize estrogenic chemicals and mixtures.

Adam T Szafran, Maureen G Mancini, Fabio Stossi, Michael A Mancini.

  The United States Environmental Protection Agency (EPA) has been pursuing new high throughput in vitro assays to characterize endocrine disrupting chemicals (EDCs) that interact with estrogen receptor signaling. We characterize two new PRL-HeLa cell models expressing either inducible C-terminal (iGFP-ER) or N-terminal (iER-GFP) tagged estrogen receptor-α (ERα) that allows direct visualization of chromatin binding. These models are an order of magnitude more sensitive, detecting 87 - 93% of very weak estrogens tested compared to only 27% by a previous PRL-HeLa variant and compares favorably to the 73% detected by an EPA-developed computational model using in vitro data. Importantly, the chromatin binding assays distinguished agonist- and antagonist-like phenotypes without activity specific assays. Finally, analysis of complex environmentally relevant chemical mixtures demonstrated how chromatin binding data can be used in risk assessment models to predict activity. These new assays should be a useful in vitro tool to screen for estrogenic activity.

Keywords:  Biological sciences research methodologies; Endocrinology

DOI:  https://doi.org/10.1016/j.isci.2022.105200