Epigenomics

Epigenomics is the systematic analysis of the global state of gene expression not attributable to mutational changes in the underlying DNA genome. An organism has multiple, cell type-specific, epigenomes comprising epigenetic marks such as DNA methylation, histone modification and specifically positioned nucleosomes.

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News & Views | 06 June 2022

Histone gene editing probes functions of H3K27 modifications in mammals
- Alessandro Scacchetti
- & Roberto Bonasio
Nature Genetics 54, 746-747

Latest Research and Reviews

Research
28 June 2022 | Open Access

Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation

Despite the availability of chromatin conformation capture experiments, discerning the relationship between the 1D genome and 3D conformation remains a challenge. Here, the authors propose a method that produces low-dimensional latent representations that summarize intra-chromosomal Hi-C contacts.
- Kevin B. Dsouza
- , Alexandra Maslova
- & Maxwell W. Libbrecht
Nature Communications 13, 3704
Research
16 June 2022 | Open Access

Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Anchor-Based Bisulfite Sequencing (ABBS) is a sequencing based method that enables analysis of DNA methylation states, based on specific hybridization of bisulfite-refractory methylcytosines with 8-aza-7-deaza-2-deoxyguanosine, incorporated in a primer at the end of 5 random nucleotides.
- Nathaniel Chapin
- , Joseph Fernandez
- & Benjamin Delatte
Communications Biology 5, 596
Research | 16 June 2022

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

Genome-wide analyses identify hundreds of loci associated with kidney function. Integrated analyses of expression, methylation and single-cell open chromatin and expression data derived from human kidney samples prioritize genes and mechanisms underlying renal disease.
- Hongbo Liu
- , Tomohito Doke
- & Katalin Susztak
Nature Genetics, 1-13
Research | 16 June 2022

Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops

Here, authors use targeted degradation and Hi-C in eukaryotic cells to show that acetylation of the cohesin subunit Smc3 stops loop extrusion during DNA replication by recruiting Pds5, also required for sister chromatid cohesion, and by preventing Scc2-dependent loop expansion.
- Nathalie Bastié
- , Christophe Chapard
- & Romain Koszul
Nature Structural & Molecular Biology 29, 575-585
Research | 13 June 2022

Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms

Allelic imbalance analysis applied to ATAC-Seq data from 23 cancer types identifies 7,262 allele-specific accessibility quantitative trait loci, which are enriched for cancer risk heritability and altered transcription factor binding motifs.
- Dennis Grishin
- & Alexander Gusev
Nature Genetics 54, 837-849
Research
09 June 2022 | Open Access

Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation

Cohesin complex is essential for transcriptional regulation and chromosome folding. Here the authors provide a large-scale multi-omics analysis suggesting that cohesin bound on gene bodies has a specific role in transcriptional regulation.
- Jiankang Wang
- , Masashige Bando
- & Ryuichiro Nakato
Nature Communications 13, 3218

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News and Comment

Comments & Opinion | 09 June 2022

The missing diversity in human epigenomic studies

Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic studies are lacking in diversity and propose several solutions to address this problem.
- Charles E. Breeze
- , Stephan Beck
- & Nora Franceschini
Nature Genetics 54, 737-739
News & Views | 06 June 2022

Histone gene editing probes functions of H3K27 modifications in mammals

A new study employs CRISPR–Cas9-based base editing for simultaneous mutagenesis of all copies of histone H3 genes in mammals, highlighting the functional importance of H3K27me3 for Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.
- Alessandro Scacchetti
- & Roberto Bonasio
Nature Genetics 54, 746-747
News & Views | 01 June 2022

Team architecture in 3D genomic interactions revealed through nanopore sequencing

Are major decisions in the cell made through pairs of interacting loci (enhancers and promoters) or larger teams of cooperating regulatory elements? A new genome-wide assay and algorithm answers this question and provides a scalable technology to link new dimensions of genome structure with cellular function.

Nature Biotechnology, 1-2
News & Views | 26 May 2022

Chromatin profiling of coronary artery illuminates genetic risk for heart disease

A large-scale single-nucleus chromatin accessibility profiling study in coronary artery samples from patients with coronary artery disease generated a landscape of the regulatory activity during the disease. These data highlight cell type-specific gene programs that can improve the interpretation of human genome-wide association studies findings for cardiovascular diseases.

Nature Genetics 54, 750-751
Research Highlights | 11 May 2022

Cell-free DNA cues for gene expression

Cell-free DNA ‘fragmentomics’ empowers cancer detection and classification.
- Lin Tang
Nature Methods 19, 519
News & Views | 09 May 2022

DNMT3A binds ubiquitinated histones to regulate bivalent genes

A new study demonstrates that the disordered N-terminal domain of DNMT3A1 binds PRC1-catalyzed H2AK119ub, targeting DNA methylation to bivalent promoters in mouse brain cortical cells. Methylation around bivalent genes is critical for mouse postnatal development, and could be equally important in other cell types and in disease.
- Aled J. Parry
- & Wolf Reik
Nature Genetics 54, 537-538

All News & Comment

Epigenomics

Featured

Histone gene editing probes functions of H3K27 modifications in mammals

Latest Research and Reviews

Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of conformation

Anchor-based bisulfite sequencing determines genome-wide DNA methylation

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops

Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms

Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation

News and Comment

The missing diversity in human epigenomic studies

Histone gene editing probes functions of H3K27 modifications in mammals

Team architecture in 3D genomic interactions revealed through nanopore sequencing

Chromatin profiling of coronary artery illuminates genetic risk for heart disease

Cell-free DNA cues for gene expression

DNMT3A binds ubiquitinated histones to regulate bivalent genes

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