News & Views |
Featured
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Article
| Open Access
Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice
LiMCA offers a tool for co-profiling 3D genome structure and gene expression at the single-cell level, enabling researchers to elucidate the olfactory receptor gene selection process.
- Honggui Wu
- , Jiankun Zhang
- & X. Sunney Xie
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Method to Watch |
Spatially resolved multiomics
Spatially resolved multimodal omics offers a collective way to capture molecular information in complex tissues.
- Lei Tang
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Article
| Open Access
Combinatorial single-cell profiling of major chromatin types with MAbID
MAbID offers a multiplexing approach to uncover the genomic distributions of various epigenetic markers, enabling the study of how these markers jointly direct gene expression.
- Silke J. A. Lochs
- , Robin H. van der Weide
- & Jop Kind
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Technology Feature |
A tough ask: high-efficiency, large-cargo prime editing
Researchers like the gene-editing method called prime editing for its precision and versatility. As they ask the method to do more, many factors shape what happens next.
- Vivien Marx
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Article
| Open Access
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
Multiplex-genome architecture mapping (multiplex-GAM) enables rapid, unbiased, ligation-free mapping of genome-wide chromatin interactions.
- Robert A. Beagrie
- , Christoph J. Thieme
- & Ana Pombo
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Research Highlight |
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
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Research Briefing |
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.
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Article
| Open Access
Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation
This work presents RT&Tag, which captures RNA molecules in proximity to a protein of interest in intact nuclei.
- Nadiya Khyzha
- , Steven Henikoff
- & Kami Ahmad
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Research Briefing |
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.
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Article |
ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells
ISSAAC-seq offers a sensitive and modular tool for joint profiling gene expression and chromatin accessibility in single cells.
- Wei Xu
- , Weilong Yang
- & Xi Chen
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Research Highlight |
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
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Research Highlight |
Epigenetic clock of cell dynamics
Clonal evolution of stem cells unveiled by modeling DNA methylation fluctuation.
- Lin Tang
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Research Highlight |
Sketching open and closed chromatin
Single-cell GET-seq (scGET-seq) enables the probing of compacted as well as accessible chromatin in single cells, covering a greater portion of the genome, which provides insights into genomic and epigenetic dynamics.
- Lei Tang
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Research Highlight |
Arsenal of single-cell multi-omics methods expanded
Chromatin accessibility, proteins levels and other features measured from the same cells.
- Lin Tang
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Research Highlight |
Walking through chromatin modifications
The Cell-TALKING technique probes DNA modifications around a histone modification in fixed cells.
- Lei Tang
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Article |
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia
This work reports a dual transposase–peroxidase fusion to survey the accessible chromatin regions and the proximal proteome in one assay, providing a tool to capture both the genomic and proteomic contents of open chromatin.
- Jonathan D. Lee
- , Joao A. Paulo
- & Pier Paolo Pandolfi
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Article |
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
Using nanopore sequencing as readout, nanoNOMe–seq enables chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility on human cells, in which the chromatin accessibility is profiled through exogenous GpC methylation introduced by a GpC methyltransferase.
- Isac Lee
- , Roham Razaghi
- & Winston Timp
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Brief Communication |
CRISPR-assisted detection of RNA–protein interactions in living cells
CARPID uses CRISPR technology to navigate biotin ligase to specific lncRNAs, which allows proximal labeling and thus the querying of RNA–protein interactions in living cells.
- Wenkai Yi
- , Jingyu Li
- & Jian Yan
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Article |
Long-range single-molecule mapping of chromatin accessibility in eukaryotes
SMAC-seq combines long-read sequencing with open chromatin methylation by DNA methyltransferases to enable mapping of nucleosome position and chromatin accessibility.
- Zohar Shipony
- , Georgi K. Marinov
- & William J. Greenleaf
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Research Highlight |
HACs with non-repetitive centromeres
Engineering human centromeres will allow versatile applications.
- Nicole Rusk
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Article |
Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA
Robust m1A mapping of the human transcriptome is enabled by directed evolution of an HIV-1 reverse transcriptase with efficient read-through and high mutation rates at m1A sites along with development of new tools for data analysis.
- Huiqing Zhou
- , Simone Rauch
- & Bryan C. Dickinson
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Brief Communication |
Joint profiling of DNA methylation and chromatin architecture in single cells
Methyl-HiC combines the elucidation of chromatin architecture with the reading of DNA methylomes in pools and single cells. Regions that are distant on the linear-genome but close in three-dimensional space show coordinated DNA methylation.
- Guoqiang Li
- , Yaping Liu
- & Bing Ren
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Research Highlight |
Variability in genome structure
Comparisons of genome organization in many individual cells with high-throughput FISH show extensive variation.
- Nicole Rusk
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Analysis |
A reassessment of DNA-immunoprecipitation-based genomic profiling
Reanalysis of DNA-immunoprecipitation-based data shows that modification-specific antibodies bind unmodified short tandem repeats, and IgG controls are needed to avoid false positives.
- Antonio Lentini
- , Cathrine Lagerwall
- & Colm E. Nestor
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Correspondence |
ATAC Primer Tool for targeted analysis of accessible chromatin
- Kathryn E Yost
- , Ava C Carter
- & Howard Y Chang
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Methods in Brief |
Single-cell hat trick
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Tools in Brief |
Off-targets in epigenome editing
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Methods in Brief |
Chromosome accessibility and methylation status in one
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Brief Communication |
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.
- M Ryan Corces
- , Alexandro E Trevino
- & Howard Y Chang
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Research Highlights |
Native chromosome conformation
Isolation of nuclei in an isotonic buffer retains chromosome loops and allows the probing of intrinsic loop conformation.
- Nicole Rusk
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Review Article |
How best to identify chromosomal interactions: a comparison of approaches
In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use.
- James O J Davies
- , A Marieke Oudelaar
- & Jim R Hughes
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Brief Communication |
Massively multiplex single-cell Hi-C
Single-cell combinatorial indexed Hi-C (sciHi-C) is a streamlined protocol for generating thousands of high-quality single-cell chromosome conformation data sets that resemble bulk Hi-C data in aggregate.
- Vijay Ramani
- , Xinxian Deng
- & Jay Shendure
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Brief Communication |
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.
- Maxwell R Mumbach
- , Adam J Rubin
- & Howard Y Chang
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Methods in Brief |
Are super-enhancers really super?
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Research Highlights |
Tracing cell lineage with 5hmC
Single-cell 5hmC sequencing uncovers cell-to-cell differences in the two DNA strands of a given chromosome.
- Irene Jarchum
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Brief Communication |
Single-cell multimodal profiling reveals cellular epigenetic heterogeneity
sc-GEM enables the dissection of cellular heterogeneity by simultaneously assaying the status of DNA mutations, gene expression and DNA methylation at multiple targeted loci in individual cells.
- Lih Feng Cheow
- , Elise T Courtois
- & William F Burkholder
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News & Views |
A glance at N6-methyladenosine in transcript isoforms
A sequencing approach, m6A-LAIC-seq, globally quantifies the proportion of m6A-modified transcripts of a specific gene and the differential m6A modification levels among its isoforms.
- Hailing Shi
- & Chuan He
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Article |
m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome
m6A-LAIC-seq quantifies the levels of N6-methyladenosine in isoforms of the same gene in a cell-type-specific manner.
- Benoit Molinie
- , Jinkai Wang
- & Cosmas C Giallourakis
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Research Highlights |
Reprogrammed cells leave their past lives behind
Genetic background trumps tissue of origin as a source of variability between induced pluripotent stem cell lines, diminishing the role of somatic memory in reprogrammed cells.
- Tal Nawy
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Brief Communication |
epiGBS: reference-free reduced representation bisulfite sequencing
EpiGBS (epi-genotyping by sequencing) constructs de novo references using reduced representation bisulfite sequencing followed by variant calling and methylation detection.
- Thomas P van Gurp
- , Niels C A M Wagemaker
- & Koen J F Verhoeven
LiMCA: Hi-C gets an RNA twist
Resolving epigenetic base ambiguity
Diving deeper in the 3D genome