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Article
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Spatial profiling of chromatin accessibility in mouse and human tissues
Spatial-ATAC-seq—spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing—delineated tissue-region-specific epigenetic landscapes in mouse embryos and identified gene regulators involved in the development of the central nervous system and the lymphoid tissue.
- Yanxiang Deng
- , Marek Bartosovic
- & Rong Fan
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Article |
Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency
Inverted-repeat Alu elements are the main source of drug-induced immunogenic double-stranded RNAs, which are destabilized by the RNA deaminase ADAR1, thereby limiting activation of the immune response.
- Parinaz Mehdipour
- , Sajid A. Marhon
- & Daniel D. De Carvalho
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Letter |
The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape
H3K36me2 targets DNMT3A to intergenic regions and this process, together with H3K36me3-mediated recruitment of DNMT3B, has a key role in establishing and maintaining genomic DNA methylation landscapes.
- Daniel N. Weinberg
- , Simon Papillon-Cavanagh
- & Chao Lu
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Letter |
Sensitive tumour detection and classification using plasma cell-free DNA methylomes
An immunoprecipitation-based protocol is developed to analyse DNA methylation in small quantities of circulating cell-free DNA, and can detect and classify cancers in plasma samples from several tumour types.
- Shu Yi Shen
- , Rajat Singhania
- & Daniel D. De Carvalho
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Letter |
Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing
Single-cell micrococcal nuclease sequencing simultaneously measures chromatin accessibility and genome-wide nucleosome positioning in single cells to reveal principles of nucleosome organization.
- Binbin Lai
- , Weiwu Gao
- & Keji Zhao
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Letter |
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Using a single-nucleus Hi-C protocol, the authors find that spatial organization of chromatin during oocyte-to-zygote transition differs between paternal and maternal nuclei within a single-cell zygote.
- Ilya M. Flyamer
- , Johanna Gassler
- & Kikuë Tachibana-Konwalski
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Letter
| Open Access
Comparative analysis of metazoan chromatin organization
A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin.
- Joshua W. K. Ho
- , Youngsook L. Jung
- & Peter J. Park
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Outlook |
Epigenetics: Reversible tags
Enzymes that modify gene expression without changing the DNA sequence are now viewed as central to the development of leukaemia — and may lead to new drugs.
- Jessica Wright
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Technology Feature |
Reading the second genomic code
Transient changes to the genome make its code more complex to interpret but they still put a gleam in the eye of drug and technology developers.
- Vivien Marx
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Letter |
Topological domains in mammalian genomes identified by analysis of chromatin interactions
The three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types is investigated, revealing that large, megabase-sized chromatin interaction domains are a pervasive and conserved structural feature of genome organization.
- Jesse R. Dixon
- , Siddarth Selvaraj
- & Bing Ren
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Article |
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study presents a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. Nine prevalent chromatin states are described. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. The work provides a resource of unprecedented scale for future experimental investigations.
- Peter V. Kharchenko
- , Artyom A. Alekseyenko
- & Peter J. Park
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics