2. Relationship between different epigenomic marks: DNA accessibility and methylation, histone marks, and RNA

AbstractThe ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

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Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition

Nature Communications ◽

10.1038/s41467-021-20979-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

E. Agirre ◽

A. J. Oldfield ◽

N. Bellora ◽

A. Segelle ◽

R. F. Luco

Keyword(s):

Alternative Splicing ◽

Rna Binding ◽

Embryonic Stem ◽

Chromatin Modifications ◽

Histone Marks ◽

Splicing Regulators ◽

Machine Learning Approach ◽

Alternatively Spliced ◽

Rna Motif ◽

Regulation Changes

AbstractAlternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary.

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Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression

Journal of Developmental Biology ◽

10.3390/jdb9010006 ◽

2021 ◽

Vol 9 (1) ◽

pp. 6

Author(s):

Narendra Pratap Singh ◽

Bony De Kumar ◽

Ariel Paulson ◽

Mark E. Parrish ◽

Carrie Scott ◽

...

Keyword(s):

Dna Binding ◽

Target Genes ◽

Embryonic Stem ◽

Binding Motif ◽

Binding Assays ◽

Histone Marks ◽

Genome Wide ◽

Hox Cofactors

Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.

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Fast detection of differential chromatin domains with SCIDDO

Bioinformatics ◽

10.1093/bioinformatics/btaa960 ◽

2020 ◽

Author(s):

Peter Ebert ◽

Marcel H Schulz

Keyword(s):

Differentially Expressed Genes ◽

Differentially Expressed ◽

Chromatin State ◽

Supplementary Information ◽

Differential Analysis ◽

Chromatin Domains ◽

Chromatin Dynamics ◽

Histone Marks ◽

Chromatin Immunoprecipitation Sequencing ◽

Downstream Analysis

Abstract Motivation The generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing (ChIP-seq) is a standard approach to dissect the complexity of the epigenome. Interpretation and differential analysis of histone datasets remains challenging due to regulatory meaningful co-occurrences of histone marks and their difference in genomic spread. To ease interpretation, chromatin state segmentation maps are a commonly employed abstraction combining individual histone marks. We developed the tool SCIDDO as a fast, flexible, and statistically sound method for the differential analysis of chromatin state segmentation maps. Results We demonstrate the utility of SCIDDO in a comparative analysis that identifies differential chromatin domains (DCD) in various regulatory contexts and with only moderate computational resources. We show that the identified DCDs correlate well with observed changes in gene expression and can recover a substantial number of differentially expressed genes. We showcase SCIDDO’s ability to directly interrogate chromatin dynamics such as enhancer switches in downstream analysis, which simplifies exploring specific questions about regulatory changes in chromatin. By comparing SCIDDO to competing methods, we provide evidence that SCIDDO’s performance in identifying differentially expressed genes (DEG) via differential chromatin marking is more stable across a range of cell-type comparisons and parameter cut-offs. Availability The SCIDDO source code is openly available under github.com/ptrebert/sciddo Supplementary information Supplementary data are available at Bioinformatics online.

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Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays

Scientific Reports ◽

10.1038/srep34808 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 13

Author(s):

Laxmi N. Mishra ◽

Sharon Pepenella ◽

Ryan Rogge ◽

Jeffrey C. Hansen ◽

Jeffrey J. Hayes

Keyword(s):

Dna Accessibility ◽

Nucleosome Arrays

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Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

AJP Lung Cellular and Molecular Physiology ◽

10.1152/ajplung.00253.2016 ◽

2016 ◽

Vol 311 (6) ◽

pp. L1245-L1258 ◽

Cited By ~ 19

Author(s):

Isaac K. Sundar ◽

Irfan Rahman

Keyword(s):

Gene Expression ◽

Lung Cancer ◽

Dna Methylation ◽

Cigarette Smoke ◽

Histone Modifications ◽

Expression Patterns ◽

Chromatin Modification ◽

Gene Expression Patterns ◽

Validation Data ◽

Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

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