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

Yuefeng Li; Kiran Nakka; Thomas Olender; Philippe Gingras-Gelinas; Matthew Man-Kin Wong; Daniel C L Robinson; Hina Bandukwala; Carmen G Palii; Odile Neyret; Marjorie Brand; Alexandre Blais; F Jeffrey Dilworth

doi:10.1016/j.xpro.2021.100751

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

STAR Protoc. 2021 Aug 19;2(3):100751. doi: 10.1016/j.xpro.2021.100751. eCollection 2021 Sep 17.

Authors

Yuefeng Li^{1

2}, Kiran Nakka^{1

2}, Thomas Olender^{1

2}, Philippe Gingras-Gelinas³, Matthew Man-Kin Wong^{1

2}, Daniel C L Robinson^{1

2}, Hina Bandukwala¹, Carmen G Palii¹, Odile Neyret³, Marjorie Brand^{1

2

4}, Alexandre Blais^{5

6

7}, F Jeffrey Dilworth^{1

2

4

5}

Affiliations

¹ Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada.
² Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
³ Molecular Biology Platform, Institut de Recherche Clinique de Montreal, Montreal, QC, Canada.
⁴ LIFE Research Institute, University of Ottawa, Ottawa, ON, Canada.
⁵ Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, ON, Canada.
⁶ Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.
⁷ CI3, University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, ON, Canada.

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).

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cardiotoxins / administration & dosage
Chromatin / genetics*
Chromatin / metabolism
Hematopoietic Stem Cells / cytology
Hematopoietic Stem Cells / physiology
Histones / immunology
Humans
Mice
Mice, Transgenic
Molecular Biology / instrumentation
Molecular Biology / methods*
Muscle, Skeletal / cytology
Muscle, Skeletal / drug effects
Polymerase Chain Reaction
Stem Cells / cytology
Stem Cells / physiology*
Transcription Factors / genetics
Transcription Factors / metabolism*

Substances

Cardiotoxins
Chromatin
Histones
Transcription Factors

Abstract

Publication types

MeSH terms

Substances

Grants and funding