Embryonic stem cell-based mapping of developmental transcriptional programs

Esteban O. Mazzoni; Shaun Mahony; Michelina Iacovino; Carolyn A. Morrison; George Mountoufaris; Michael Closser; Warren A. Whyte; Richard A. Young; Michael Kyba; David K. Gifford; Hynek Wichterle

doi:10.1038/nmeth.1775

Embryonic stem cell-based mapping of developmental transcriptional programs

Esteban O. Mazzoni
, Shaun Mahony
, Michelina Iacovino
, Carolyn A. Morrison
, George Mountoufaris
, Michael Closser
, Warren A. Whyte
, Richard A. Young
, Michael Kyba
, David K. Gifford
, Hynek Wichterle

Research output: Contribution to journal › Article › peer-review

63 Scopus citations

Abstract

The study of developmentally regulated transcription factors by chromatin immunoprecipitation and deep sequencing (ChIP-seq) faces two major obstacles: availability of ChIP-grade antibodies and access to sufficient number of cells. We describe versatile genome-wide analysis of transcription-factor binding sites by combining directed differentiation of embryonic stem cells and inducible expression of tagged proteins. We demonstrate its utility by mapping DNA-binding sites of transcription factors involved in motor neuron specification.

Original language	English (US)
Pages (from-to)	1056-1060
Number of pages	5
Journal	Nature methods
Volume	8
Issue number	12
DOIs	https://doi.org/10.1038/nmeth.1775
State	Published - Dec 2011

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.1775

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title = "Embryonic stem cell-based mapping of developmental transcriptional programs",

abstract = "The study of developmentally regulated transcription factors by chromatin immunoprecipitation and deep sequencing (ChIP-seq) faces two major obstacles: availability of ChIP-grade antibodies and access to sufficient number of cells. We describe versatile genome-wide analysis of transcription-factor binding sites by combining directed differentiation of embryonic stem cells and inducible expression of tagged proteins. We demonstrate its utility by mapping DNA-binding sites of transcription factors involved in motor neuron specification.",

author = "Mazzoni, \{Esteban O.\} and Shaun Mahony and Michelina Iacovino and Morrison, \{Carolyn A.\} and George Mountoufaris and Michael Closser and Whyte, \{Warren A.\} and Young, \{Richard A.\} and Michael Kyba and Gifford, \{David K.\} and Hynek Wichterle",

note = "Funding Information: E.O.M. is funded as the David and Sylvia Lieb Fellow of the Damon Runyon Cancer Research Foundation (DRG-1937-07). We thank R. Sherwood (Harvard University) for sharing unpublished observations and T Jessell (Columbia University) for anti-Hoxc4 antibody. Personnel and work were supported by US National Institutes of Health grant P01 NS055923 (D.K.G., R.A.Y. and H.W.), R01 NS058502 (H.W.), R01HL081186 (M.K.) and Helmsley Stem Cell Starter grant (H.W.).",

year = "2011",

month = dec,

doi = "10.1038/nmeth.1775",

language = "English (US)",

volume = "8",

pages = "1056--1060",

journal = "Nature methods",

issn = "1548-7091",

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T1 - Embryonic stem cell-based mapping of developmental transcriptional programs

AU - Mazzoni, Esteban O.

AU - Mahony, Shaun

AU - Iacovino, Michelina

AU - Morrison, Carolyn A.

AU - Mountoufaris, George

AU - Closser, Michael

AU - Whyte, Warren A.

AU - Young, Richard A.

AU - Kyba, Michael

AU - Gifford, David K.

AU - Wichterle, Hynek

N1 - Funding Information: E.O.M. is funded as the David and Sylvia Lieb Fellow of the Damon Runyon Cancer Research Foundation (DRG-1937-07). We thank R. Sherwood (Harvard University) for sharing unpublished observations and T Jessell (Columbia University) for anti-Hoxc4 antibody. Personnel and work were supported by US National Institutes of Health grant P01 NS055923 (D.K.G., R.A.Y. and H.W.), R01 NS058502 (H.W.), R01HL081186 (M.K.) and Helmsley Stem Cell Starter grant (H.W.).

PY - 2011/12

Y1 - 2011/12

N2 - The study of developmentally regulated transcription factors by chromatin immunoprecipitation and deep sequencing (ChIP-seq) faces two major obstacles: availability of ChIP-grade antibodies and access to sufficient number of cells. We describe versatile genome-wide analysis of transcription-factor binding sites by combining directed differentiation of embryonic stem cells and inducible expression of tagged proteins. We demonstrate its utility by mapping DNA-binding sites of transcription factors involved in motor neuron specification.

AB - The study of developmentally regulated transcription factors by chromatin immunoprecipitation and deep sequencing (ChIP-seq) faces two major obstacles: availability of ChIP-grade antibodies and access to sufficient number of cells. We describe versatile genome-wide analysis of transcription-factor binding sites by combining directed differentiation of embryonic stem cells and inducible expression of tagged proteins. We demonstrate its utility by mapping DNA-binding sites of transcription factors involved in motor neuron specification.

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DO - 10.1038/nmeth.1775

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JO - Nature methods

JF - Nature methods

IS - 12

ER -

Embryonic stem cell-based mapping of developmental transcriptional programs

Abstract

All Science Journal Classification (ASJC) codes

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