27 Result(s)

Article

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, Jason A. Caldwell, Joshua McKeever… in Nature Immunology (2024)

Article

Systematic benchmarking of single-cell ATAC-sequencing protocols

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of syst...

Florian V. De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila… in Nature Biotechnology (2024)

Article

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome

In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystall...

Georgi K. Marinov, **nyi Chen, Matthew P. Swaffer, Tingting **ang… in Genome Biology (2024)

Article

Multicenter integrated analysis of noncoding CRISPRi screens

The ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to ...

David Yao, Josh Tycko, ** Woo Oh, Lexi R. Bounds, Sager J. Gosai… in Nature Methods (2024)

Article

The chromatin landscape of the euryarchaeon Haloferax volcanii

Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations fir...

Georgi K. Marinov, S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje… in Genome Biology (2023)

Article

Global map** of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions

Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs a...

Charles Limouse, Owen K. Smith, David Jukam, Kelsey A. Fryer… in Nature Communications (2023)

Article

Integration of spatial and single-cell data across modalities with weakly linked features

Although single-cell and spatial sequencing methods enable simultaneous measurement of more than one biological modality, no technology can capture all modalities within the same cell. For current data integra...

Shuxiao Chen, Bokai Zhu, Sijia Huang, John W. Hickey, Kevin Z. Lin… in Nature Biotechnology (2023)

Article

Organization of the human intestine at single-cell resolution

The intestine is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota and affects overall health¹. The intes...

John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron Horning… in Nature (2023)

Article

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA map**

Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity...

Georgi K. Marinov, Samuel H. Kim, S. Tansu Bagdatli, Soon Il Higashino… in Genome Biology (2023)

Article

Aging-associated HELIOS deficiency in naive CD4⁺ T cells alters chromatin remodeling and promotes effector cell responses

Immune aging combines cellular defects in adaptive immunity with the activation of pathways causing a low-inflammatory state. Here we examined the influence of age on the kinetic changes in the epigenomic and ...

Huimin Zhang, Rohit R. Jadhav, Wenqiang Cao, Isabel N. Goronzy… in Nature Immunology (2023)

Article

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agaros...

King L. Hung, Jens Luebeck, Siavash R. Dehkordi, Caterina I. Colón… in Nature Genetics (2022)

Article

A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4

Genomic methods have been valuable for identifying RNA-binding proteins (RBPs) and the genes, pathways, and processes they regulate. Nevertheless, standard motif descriptions cannot be used to predict all RNA ...

Christoph Sadée, Lauren D. Hagler, Winston R. Becker… in Nature Communications (2022)

Article

Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility prof...

Winston R. Becker, Stephanie A. Nevins, Derek C. Chen, Roxanne Chiu… in Nature Genetics (2022)

Article

Author Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

A Correction to this paper has been published: https://doi.org/10.1038/s41588-021-00850-x.

Jeffrey M. Granja, M. Ryan Corces, Sarah E. Pierce, S. Tansu Bagdatli… in Nature Genetics (2021)

Article

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

Chromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. H...

Sarah E. Pierce, Jeffrey M. Granja, William J. Greenleaf in Nature Communications (2021)

Article

Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum

Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem ...

Georgi K. Marinov, Alexandro E. Trevino, Tingting **ang, Anshul Kundaje… in Nature Genetics (2021)

Article

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological mea...

Jeffrey M. Granja, M. Ryan Corces, Sarah E. Pierce, S. Tansu Bagdatli… in Nature Genetics (2021)

Article

Comprehensive sequence-to-function map** of cofactor-dependent RNA catalysis in the glmS ribozyme

Massively parallel, quantitative measurements of biomolecular activity across sequence space can greatly expand our understanding of RNA sequence-function relationships. We report the development of an RNA-arr...

Johan O. L. Andreasson, Andrew Savinov, Steven M. Block… in Nature Communications (2020)

Article

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

Pooled CRISPR-Cas9 screens are a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated...

Josh Tycko, Michael Wainberg, Georgi K. Marinov, Oana Ursu… in Nature Communications (2019)

Article

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

The Satb1 genome organizer regulates multiple cellular and developmental processes. It is not yet clear how Satb1 selects different sets of targets throughout the genome. Here we have used live-cell single mol...

Rajarshi P. Ghosh, Quanming Shi, Linfeng Yang, Michael P. Reddick… in Nature Communications (2019)