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Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors

May, Gillian ; Soneji, Shamit ; Tipping, Alex J. ; Teles, José LU ; McGowan, Simon J. ; Wu, Mengchu ; Guo, Yanping ; Fugazza, Cristina ; Brown, John and Karlsson, Göran LU , et al. (2013) In Cell Stem Cell 13(6). p.754-768
Abstract
We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (1) differential complexity of sequence motifs bound by GATA1, GATA2, and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression trajectories based on global associations between TF-binding data and target... (More)
We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (1) differential complexity of sequence motifs bound by GATA1, GATA2, and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression; and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. This rubric exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis. (Less)
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published
subject
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Cell Stem Cell
volume
13
issue
6
pages
754 - 768
publisher
Cell Press
external identifiers
  • wos:000329571700017
  • scopus:84890129231
  • pmid:24120743
ISSN
1934-5909
DOI
10.1016/j.stem.2013.09.003
language
English
LU publication?
yes
id
09996566-910e-4825-b857-5f7a113293a6 (old id 4320072)
date added to LUP
2016-04-01 09:56:26
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2020-08-12 01:11:24
@article{09996566-910e-4825-b857-5f7a113293a6,
  abstract     = {We used the paradigmatic GATA-PU.1 axis to explore, at the systems level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIP-seq of GATA1, GATA2, and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (1) differential complexity of sequence motifs bound by GATA1, GATA2, and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression; and (4) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. This rubric exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis.},
  author       = {May, Gillian and Soneji, Shamit and Tipping, Alex J. and Teles, José and McGowan, Simon J. and Wu, Mengchu and Guo, Yanping and Fugazza, Cristina and Brown, John and Karlsson, Göran and Pina, Cristina and Olariu, Victor and Taylor, Stephen and Tenen, Daniel G. and Peterson, Carsten and Enver, Tariq},
  issn         = {1934-5909},
  language     = {eng},
  number       = {6},
  pages        = {754--768},
  publisher    = {Cell Press},
  series       = {Cell Stem Cell},
  title        = {Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors},
  url          = {http://dx.doi.org/10.1016/j.stem.2013.09.003},
  doi          = {10.1016/j.stem.2013.09.003},
  volume       = {13},
  year         = {2013},
}