Nature Search

High-throughput chromatin accessibility profiling at single-cell resolution

Single-cell chromatin accessibility is a promising means to identify regulatory programs in mixtures of cells. Here the authors describe µ-ATAC-seq, a low-cost method that can generate thousands of accessibility profiles per day.

Anja Mezger
Sandy Klemm
William Greenleaf
ResearchOpen Access07 Sept 2018
Nature Communications

Volume: 9, P: 1-6
Thymic epithelial cells amplify epigenetic noise to promote immune tolerance

The activity of the tumour-suppressor protein p53 is repressed in the thymus to augment fluctuations in background chromatin accessibility as a means of mediating ectopic gene expression and immune tolerance.

Noah Gamble
Jason A. Caldwell
Andrew S. Koh
ResearchOpen Access20 Aug 2025
Nature

Volume: 646, P: 724-733
Publisher Correction: PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape

Noah Gamble
Alexandra Bradu
Andrew S. Koh
Amendments and Corrections16 May 2024
Nature Immunology

Volume: 25, P: 1123
Transcriptional profiling of cells sorted by RNA abundance

Methods are described for preparing unbiased libraries for transcriptome profiling of cells sorted according to the abundance of a transcript of interest.

Sandy Klemm
Stefan Semrau
Alexander van Oudenaarden
Research30 Mar 2014
Nature Methods

Volume: 11, P: 549-551
PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape

Koh et al. show that loci active in differentiated effector T cells are poised in early T precursors before the expression of T cell antigen receptors in a manner dependent on the chromatin remodeling complex mammalian SWItch/Sucrose Non-Fermentable and the PU.1–RUNX1 and BCL11B–RUNX1 complexes.

Noah Gamble
Alexandra Bradu
Andrew S. Koh
Research17 Apr 2024
Nature Immunology

Volume: 25, P: 860-872
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

A primer database covering the mouse and human genomes allows easy and flexible generation of FISH probes covering any desired locus.

Magda Bienko
Nicola Crosetto
Alexander van Oudenaarden
Research23 Dec 2012
Nature Methods

Volume: 10, P: 122-124
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Analyzing DNA accessibility, transcriptome and protein expression in single cells uncovers cancer-regulatory programs.

Jeffrey M. Granja
Sandy Klemm
William J. Greenleaf
Research02 Dec 2019
Nature Biotechnology

Volume: 37, P: 1458-1465
Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons

Blum et al. performed single-nucleus RNA sequencing of the adult mouse spinal cord. This analysis revealed heterogeneity in the autonomic and skeletal motor systems and provides a resource to study motor neurons in health and disease.

Jacob A. Blum
Sandy Klemm
Aaron D. Gitler
Research15 Feb 2021
Nature Neuroscience

Volume: 24, P: 572-583
Chromatin accessibility and the regulatory epigenome

Chromatin accessibility comprises the positions, compaction and dynamics of nucleosomes, as well as the occupancy of DNA by other proteins such as transcription factors. In this Review, the authors discuss diverse methods for characterizing chromatin accessibility, how accessibility is determined and remodelled in cells and the regulatory roles of accessibility in gene expression and development.

Sandy L. Klemm
Zohar Shipony
William J. Greenleaf
Reviews23 Jan 2019
Nature Reviews Genetics

Volume: 20, P: 207-220
Deciphering the impact of genomic variation on function

The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

Jesse M. Engreitz
Heather A. Lawson
Ella K. Samer
Reviews04 Sept 2024
Nature

Volume: 633, P: 47-57

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