Epigenetics analysis

Epigenetics analysis is the study of heritable changes that are distinct from changes in DNA sequence. Epigenetic changes include covalent modifications to the DNA bases or histone proteins that make up chromatin; they can be influenced by the environment and transmitted through DNA replication.

Latest Research and Reviews

Research
03 February 2023 | Open Access

DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis
- Mikkel E. Dupont
- , Steffan N. Christiansen
- & Jeppe D. Andersen
Scientific Reports 13, 2004
Reviews | 18 January 2023

Navigating the pitfalls of mapping DNA and RNA modifications

The ability to map DNA and RNA modifications has improved our understanding of these marks, but in some cases inconsistent results have been problematic. Here, Kong et al. discuss how to recognize and resolve issues associated with commonly used sequencing-based approaches to minimize mapping errors.
- Yimeng Kong
- , Edward A. Mead
- & Gang Fang
Nature Reviews Genetics, 1-19
Research
17 January 2023 | Open Access

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

Here the authors present the low input capture Hi-C (liCHi-C) method, a cost-effective, flexible method to map and robustly compare promoter interactomes at high resolution. liCHi-C identifies new disease-associated genes and structural variants to ultimately illuminate their pathogenic effects.
- Laureano Tomás-Daza
- , Llorenç Rovirosa
- & Biola M. Javierre
Nature Communications 14, 268
Research
02 January 2023 | Open Access

scChIX-seq infers dynamic relationships between histone modifications in single cells

Analysis of two histone marks in single cells reveals interplay between modifications.
- Jake Yeung
- , Maria Florescu
- & Alexander van Oudenaarden
Nature Biotechnology, 1-11
Research
27 December 2022 | Open Access

High-precision mapping reveals rare N⁶-deoxyadenosine methylation in the mammalian genome
- Li-Qian Chen
- , Zhang Zhang
- & Guan-Zheng Luo
Cell Discovery 8, 138
Research
24 December 2022 | Open Access

Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing

The interplay between histone modifications and DNA methylation plays a crucial role in establishing and maintaining the epigenomic landscape. Here, the authors develop a nanopore sequencing based method for mapping histone modifications and DNA methylation from native, long, single DNA molecules.
- Xue Yue
- , Zhiyuan Xie
- & Yimeng Yin
Nature Communications 13, 7939

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News and Comment

Research Highlights | 02 December 2022

Spatially resolved epigenomics

An approach combining in situ tagmentation and transcription with MERFISH enables spatial profiling of the epigenome in tissues with single-cell resolution.
- Rita Strack
Nature Methods 19, 1516
News & Views | 07 November 2022

Profiling chromatin–protein crosstalk at locus resolution in single cells

Development is orchestrated in part by myriad chromatin-associated proteins that decorate the genome and physically coordinate in ways that are often unclear. An epigenomics technique called MulTI-Tag maps the genomic locations of different chromatin proteins in the same individual cells, helping to unveil their interactions.

Nature Biotechnology, 1-2
Correspondence
11 October 2022 | Open Access

scNanoATAC-seq: a long-read single-cell ATAC sequencing method to detect chromatin accessibility and genetic variants simultaneously within an individual cell
- Yuqiong Hu
- , Zhenhuan Jiang
- & Fuchou Tang
Cell Research 33, 83-86
News & Views | 03 October 2022

An in situ method for tagging chromatin-associated RNAs

RNA comprises a substantial fraction of eukaryotic chromatin, but techniques to identify and map RNAs are cumbersome. We adapted existing tagmentation-based profiling techniques to enable chromatin-associated RNAs to be profiled in a simple workflow, enhancing the capability to identify regulatory RNAs.

Nature Methods 19, 1351-1352
News & Views | 15 September 2022

Sensitive, flexible and modular single-cell multi-omics profiling with ISSAAC-seq

Joint profiling of multiple modalities in the same cell is challenging. We developed a method with a modular design to enable the simultaneous detection of chromatin accessibility and the transcriptome within single cells with flexible throughput.

Nature Methods 19, 1183-1184
Research Highlights | 11 March 2022

Reassessing 6mA in eukaryotes

A metagenomic approach to identifying the sources of N⁶-methyldeoxyadenine (6mA) in eukaryotic DNA found no evidence of high 6mA abundances in sampled eukaryotes.
- Lei Tang
Nature Methods 19, 270

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Epigenetics analysis

Latest Research and Reviews

DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis

Navigating the pitfalls of mapping DNA and RNA modifications

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

scChIX-seq infers dynamic relationships between histone modifications in single cells

High-precision mapping reveals rare N⁶-deoxyadenosine methylation in the mammalian genome

Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing

News and Comment

Spatially resolved epigenomics

Profiling chromatin–protein crosstalk at locus resolution in single cells

scNanoATAC-seq: a long-read single-cell ATAC sequencing method to detect chromatin accessibility and genetic variants simultaneously within an individual cell

An in situ method for tagging chromatin-associated RNAs

Sensitive, flexible and modular single-cell multi-omics profiling with ISSAAC-seq

Reassessing 6mA in eukaryotes

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Epigenetics analysis

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