Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia.

Chromatin / metabolism DNA / genetics Gene Expression Regulation / genetics Gene Regulatory Networks Histones / metabolism Humans Leukemia, Promyelocytic, Acute / genetics Transcription Factors / metabolism

Journal

Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604

Informations de publication

Date de publication:
03 2021
Historique:
received: 04 03 2020
accepted: 20 01 2021
pubmed: 3 3 2021
medline: 27 4 2021
entrez: 2 3 2021
Statut: ppublish

Résumé

The architecture of chromatin regulates eukaryotic cell states by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase-peroxidase approach, integrative DNA and protein tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights. Our findings demonstrate the power of iDAPT as a platform for studying the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.

Identifiants

DOI: 10.1038/s41592-021-01077-8 PMID: 33649590 PMC: PMC8272231
pubmed: 33649590
doi: 10.1038/s41592-021-01077-8
pii: 10.1038/s41592-021-01077-8
pmc: PMC8272231
mid: NIHMS1665499
doi:

Substances chimiques

Chromatin 0
Histones 0
Transcription Factors 0
DNA 9007-49-2

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

293-302

Subventions

Organisme : NCI NIH HHS
ID : R35 CA197529
Pays : United States
Organisme : NHLBI NIH HHS
ID : P01 HL131477
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA197697
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA232105
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM067945
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM132129
Pays : United States

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Auteurs

Jonathan D Lee (JD)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. jdlee@post.harvard.edu.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. jdlee@post.harvard.edu.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. jdlee@post.harvard.edu.
Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. jdlee@post.harvard.edu.
ORCID: 0000-0002-1229-0098

Joao A Paulo (JA)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-4291-413X

Ryan R Posey (RR)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

Vera Mugoni (V)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

Nikki R Kong (NR)

Harvard Stem Cell Institute, Boston, MA, USA.

Giulia Cheloni (G)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.

Yu-Ru Lee (YR)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.

Frank J Slack (FJ)

HMS Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-8263-0409

Daniel G Tenen (DG)

Harvard Stem Cell Institute, Boston, MA, USA.
Cancer Science Institute of Singapore, Singapore, Singapore.

John G Clohessy (JG)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-5186-9775

Steven P Gygi (SP)

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-7626-0034

Pier Paolo Pandolfi (PP)

Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. pierpaolo.pandolfiderinaldis@renown.org.
Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. pierpaolo.pandolfiderinaldis@renown.org.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. pierpaolo.pandolfiderinaldis@renown.org.
MBC, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy. pierpaolo.pandolfiderinaldis@renown.org.
Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA. pierpaolo.pandolfiderinaldis@renown.org.
ORCID: 0000-0002-5352-5295

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Dual DNA and protein tagging of open chromatin...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Dual DNA and protein tagging of open chromatin...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Dual DNA and protein tagging of open chromatin...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Séquences d'acides nucléiques régulatrices › Réseaux de régulation génique › Dual DNA and protein tagging of open chromatin...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Histone › Dual DNA and protein tagging of open chromatin...
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questionsmedicales.fr › Tumeurs › Tumeurs par type histologique › Leucémies › Leucémie myéloïde › Leucémie aigüe myéloïde › Leucémie aiguë promyélocytaire › Dual DNA and protein tagging of open chromatin...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Dual DNA and protein tagging of open chromatin...