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Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.


ABSTRACT: Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the human monocyte leukemia THP-1 cell line and profiled the genome-wide transcriptional response of individual transcription starting sites using deep sequencing based Cap Analysis of Gene Expression. From the proximal promoter regions of the responding transcription starting sites, we derived de novo binding-site motifs, characterized their biological function and constructed a network. We found a previously described composite motif for PU.1 and IRF8 that explains the overlapping set of transcriptional responses upon knockdown of either factor.

SUBMITTER: Vitezic M 

PROVIDER: S-EPMC3001087 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

Vitezic Morana M   Lassmann Timo T   Forrest Alistair R R AR   Suzuki Masanori M   Tomaru Yasuhiro Y   Kawai Jun J   Carninci Piero P   Suzuki Harukazu H   Hayashizaki Yoshihide Y   Daub Carsten O CO  

Nucleic acids research 20100819 22


Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the human monocyte leukemia THP-1 cell line and profiled the genome-wide transcriptional response of individual transcription starting sites using deep sequencing based Cap Analysis of Gene  ...[more]

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