"Comprehensive search for HNF-1ß-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi".

Taku Tanaka ^{1, 2}, Yasuhiro Tomaru ^{2, 3}, Yuki Nomura ^{1, 2}, Hisashi Miura ^{1, 2}, Masanori Suzuki ^{1, 2,} *, and Yoshihide Hayashizaki ^{1, 2,  3}

¹ Division of Genomics, Science of Biological Supramolecular Systems, Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tusurumi-Ku, Yokohama, Kanagawa 230-0045, Japan,
² Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan,  and
³ Institute of Basic Medical Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki
305-8577, Japan

*To whom correspondence should be addressed. Tel: +81 045 508 7241; Fax: +81 045 508 7370;
Email:   msuzuki@gsc.riken.go.jp

The identification of genes targeted by a specific transcription regulatory factor (TRF) is essential to our understanding of the regulatory mechanism of gene expression. We constructed a system for the comprehensive identification of genes directly regulated by a TRF. It includes a combination of perturbation of gene expression by RNA interference (RNAi) of the TRF, cDNA microarray analysis, computer searches for the putative TRF recognition sequences, and in vivo and in vitro TRF–DNA binding assays. Endogenous hepatocyte nuclear factor-1ß (HNF-1ß) mRNA was efficiently degraded by transfection of mouse hepatoma cells with short interfering RNAs. Expression profile analysis with 20 K mouse cDNA microarrays detected 243 genes whose expression levels were decreased by >50% upon RNAi of HNF-1ß. The upstream regions of the top 26 downregulated genes were searched for the HNF-1ß consensus recognition sequences leading to the
extraction of 13 candidate genes. Finally, TRF–DNA binding assays identified five novel as well as three known
HNF-1ß-regulated genes. In combination with quantitative real-time RT–PCR, the present system revealed the existence of a more expanded regulatory network among seven HNF family members, demonstrating its practicability to identify the TRF network as well as genes directly regulated by a specific TRF. 

1. Persengiev SP, Zhu X, and Green MR, "Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs)".

2. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG, and Sen GC, "A Comprehensive View of Regulation of Gene Expression by Double-Stranded RNA-Mediated Cell Signaling".

Further Topics in:  Euchromatin,  active DNA, and  RNA  ribo-regulators:

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

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