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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Vitezic M,Lassmann T,Forrest AR,Suzuki M,Tomaru Y,Kawai J,Carninci P,Suzuki H,Hayashizaki Y,Daub CO

doi

10.1093/nar/gkq729

subject

Has Abstract

pub_date

2010-12-01 00:00:00

pages

8141-8

issue

22

eissn

0305-1048

issn

1362-4962

pii

gkq729

journal_volume

38

pub_type

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