Literature DB >> 34467227

Chromatin and transcription factor profiling in rare stem cell populations using CUT&Tag.

Yuefeng Li1,2, Kiran Nakka1,2, Thomas Olender1,2, Philippe Gingras-Gelinas3, Matthew Man-Kin Wong1,2, Daniel C L Robinson1,2, Hina Bandukwala1, Carmen G Palii1, Odile Neyret3, Marjorie Brand1,2,4, Alexandre Blais5,6,7, F Jeffrey Dilworth1,2,4,5.   

Abstract

Muscle stem cells (MuSCs) are a rare stem cell population that provides myofibers with a remarkable capacity to regenerate after tissue injury. Here, we have adapted the Cleavage Under Target and Tagmentation technology to the mapping of the chromatin landscape and transcription factor binding in 50,000 activated MuSCs isolated from injured mouse hindlimb muscles. We have applied this same approach to human CD34+ hematopoietic stem and progenitor cells. This protocol could be adapted to any rare stem cell population. For complete details on the use and execution of this protocol, please refer to Robinson et al. (2021).
© 2021 The Author(s).

Entities:  

Keywords:  ChIPseq; cell biology; cell isolation; chromatin immunoprecipitation (ChIP); flow cytometry/mass cytometry; molecular biology; sequence analysis; sequencing; stem cells

Mesh:

Substances:

Year:  2021        PMID: 34467227      PMCID: PMC8384913          DOI: 10.1016/j.xpro.2021.100751

Source DB:  PubMed          Journal:  STAR Protoc        ISSN: 2666-1667


  22 in total

1.  Polycomb protein Ezh1 promotes RNA polymerase II elongation.

Authors:  Kambiz Mousavi; Hossein Zare; A Hongjun Wang; Vittorio Sartorelli
Journal:  Mol Cell       Date:  2011-12-22       Impact factor: 17.970

2.  Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential.

Authors:  Robert N Judson; Marco Quarta; Menno J Oudhoff; Hesham Soliman; Lin Yi; Chih Kai Chang; Gloria Loi; Ryan Vander Werff; Alissa Cait; Mark Hamer; Justin Blonigan; Patrick Paine; Linda T N Doan; Elena Groppa; WenJun He; Le Su; Regan H Zhang; Peter Xu; Christine Eisner; Marcela Low; Ingrid Barta; Coral-Ann B Lewis; Colby Zaph; Mohammad M Karimi; Thomas A Rando; Fabio M Rossi
Journal:  Cell Stem Cell       Date:  2018-01-25       Impact factor: 24.633

3.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

4.  UTX demethylase activity is required for satellite cell-mediated muscle regeneration.

Authors:  Hervé Faralli; Chaochen Wang; Kiran Nakka; Aissa Benyoucef; Soji Sebastian; Lenan Zhuang; Alphonse Chu; Carmen G Palii; Chengyu Liu; Brendan Camellato; Marjorie Brand; Kai Ge; F Jeffrey Dilworth
Journal:  J Clin Invest       Date:  2016-03-21       Impact factor: 14.808

5.  Impaired Notch Signaling Leads to a Decrease in p53 Activity and Mitotic Catastrophe in Aged Muscle Stem Cells.

Authors:  Ling Liu; Gregory W Charville; Tom H Cheung; Bryan Yoo; Pauline J Santos; Matthew Schroeder; Thomas A Rando
Journal:  Cell Stem Cell       Date:  2018-09-20       Impact factor: 24.633

6.  Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications.

Authors:  Adrian T Grzybowski; Rohan N Shah; William F Richter; Alexander J Ruthenburg
Journal:  Nat Protoc       Date:  2019-11-13       Impact factor: 13.491

7.  MultiQC: summarize analysis results for multiple tools and samples in a single report.

Authors:  Philip Ewels; Måns Magnusson; Sverker Lundin; Max Käller
Journal:  Bioinformatics       Date:  2016-06-16       Impact factor: 6.937

8.  The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Authors:  Haley M Amemiya; Anshul Kundaje; Alan P Boyle
Journal:  Sci Rep       Date:  2019-06-27       Impact factor: 4.379

9.  Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling.

Authors:  Michael P Meers; Dan Tenenbaum; Steven Henikoff
Journal:  Epigenetics Chromatin       Date:  2019-07-12       Impact factor: 4.954

10.  deepTools2: a next generation web server for deep-sequencing data analysis.

Authors:  Fidel Ramírez; Devon P Ryan; Björn Grüning; Vivek Bhardwaj; Fabian Kilpert; Andreas S Richter; Steffen Heyne; Friederike Dündar; Thomas Manke
Journal:  Nucleic Acids Res       Date:  2016-04-13       Impact factor: 16.971

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  1 in total

1.  Multi-CUT&Tag to simultaneously profile multiple chromatin factors.

Authors:  Sneha Gopalan; Thomas G Fazzio
Journal:  STAR Protoc       Date:  2022-01-20
  1 in total

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