Building Promoter Aware Transcriptional Regulatory Networks Using SiRNA Perturbation and DeepCAGE

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Aug 21

PMID 20724440

Citations 8

Authors

Morana Vitezic

Timo Lassmann

Alistair R R Forrest

Masanori Suzuki

Yasuhiro Tomaru

Jun Kawai

Piero Carninci

Harukazu Suzuki

Yoshihide Hayashizaki

Carsten O Daub

Affiliations

Soon will be listed here.

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.

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