CUT&Tag for efficient epigenomic profiling of small samples and single cells
Hatice S. Kaya-Okur,Steven J. Wu,Steven J. Wu,Christine A. Codomo,Erica S. Pledger,Terri D. Bryson,Jorja G. Henikoff,Kami Ahmad,Steven Henikoff +8 more
TLDR
Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components, is described.Abstract:
Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells.read more
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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.
Jaime A. Castro-Mondragon,Rafael Riudavets-Puig,Ieva Rauluseviciute,Roza Berhanu Lemma,Laura Turchi,Romain Blanc-Mathieu,Jérémy Lucas,Paul Boddie,Aziz Khan,Nicolás Manosalva Pérez,Oriol Fornes,Tiffany Y. Leung,Alejandro Aguirre,Fayrouz Hammal,Daniel Schmelter,Damir Baranasic,Benoit Ballester,Albin Sandelin,Boris Lenhard,Klaas Vandepoele,Wyeth W. Wasserman,François Parcy,Anthony Mathelier,Anthony Mathelier +23 more
TL;DR: JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups as mentioned in this paper.
Journal ArticleDOI
Single-cell chromatin state analysis with Signac.
TL;DR: Signac as mentioned in this paper is a comprehensive toolkit for the analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with singlecell gene expression datasets, DNA motif analysis and interactive visualization.
Journal ArticleDOI
Improved CUT&RUN chromatin profiling tools.
Michael P. Meers,Terri D Bryson,Terri D Bryson,Jorja G. Henikoff,Steven Henikoff,Steven Henikoff +5 more
TL;DR: Three enhancements to CUT&RUN are introduced: A hybrid protein A-Protein G-MNase construct that expands antibody compatibility and simplifies purification, a modified digestion protocol that inhibits premature release of the nuclease-bound complex, and a calibration strategy based on carry-over of E. coli DNA introduced with the fusion protein.
Journal ArticleDOI
Single-cell multimodal omics: the power of many.
TL;DR: Development of single-cell multimodal omics tools is another major step toward understanding the inner workings of biological systems.
Journal ArticleDOI
Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
TL;DR: Sarse Enrichment Analysis for CUT&RUN (SEACR) is an analysis strategy that uses the global distribution of background signal to calibrate a simple threshold for peak calling and is a highly selective peak caller that definitively validates the accuracy of CUT &RUN for datasets with known true negatives.
References
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Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
TL;DR: The feasibility of analyzing an individual's epigenome on a timescale compatible with clinical decision-making is demonstrated and classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with nucleosomes are discovered.
Journal ArticleDOI
Massively parallel digital transcriptional profiling of single cells
Grace X.Y. Zheng,Jessica M. Terry,Phillip Belgrader,Paul Ryvkin,Zachary Bent,Ryan Wilson,Solongo B. Ziraldo,Tobias Daniel Wheeler,Geoffrey P. McDermott,Junjie Zhu,Mark T. Gregory,Joe Shuga,Luz Montesclaros,Jason G. Underwood,Donald A. Masquelier,Stefanie Y. Nishimura,Michael Schnall-Levin,Paul Wyatt,Christopher Hindson,Rajiv Bharadwaj,Alexander Wong,Kevin D. Ness,Lan Beppu,H. Joachim Deeg,Christopher McFarland,Keith R. Loeb,Keith R. Loeb,William J. Valente,William J. Valente,Nolan G. Ericson,Emily A. Stevens,Jerald P. Radich,Tarjei S. Mikkelsen,Benjamin J. Hindson,Jason H. Bielas +34 more
TL;DR: A droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample is described and sequence variation in the transcriptome data is used to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.
Journal ArticleDOI
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Stephen G. Landt,Georgi K. Marinov,Anshul Kundaje,Pouya Kheradpour,Florencia Pauli,Serafim Batzoglou,Bradley E. Bernstein,Peter J. Bickel,James B. Brown,Philip Cayting,Yiwen Chen,Gilberto DeSalvo,Charles B. Epstein,Katherine I. Fisher-Aylor,Ghia Euskirchen,Mark Gerstein,Jason Gertz,Alexander J. Hartemink,Michael M. Hoffman,Vishwanath R. Iyer,Youngsook L. Jung,Subhradip Karmakar,Manolis Kellis,Peter V. Kharchenko,Qiang Li,Tao Liu,X. Shirley Liu,Lijia Ma,Aleksandar Milosavljevic,Richard M. Myers,Peter J. Park,Michael J. Pazin,Marc D. Perry,Debasish Raha,Timothy E. Reddy,Joel Rozowsky,Noam Shoresh,Arend Sidow,Matthew Slattery,John A. Stamatoyannopoulos,Michael Y. Tolstorukov,Kevin P. White,Simon Xi,Peggy J. Farnham,Jason D. Lieb,Barbara J. Wold,Michael Snyder +46 more
TL;DR: This work discusses how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data and develops a set of working standards and guidelines for ChIP experiments that are updated routinely.