Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263

Seth Frietze, Xun Lan, Victor X. Jin, Peggy J. Farnham

Research output: Contribution to journalArticle

58 Citations (Scopus)

Abstract

Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on in vitro studies, a zinc finger code has been developed that predicts a binding motif for a particular zinc finger factor (ZNF). However, very few studies have performed genome-wide analyses of ZNF binding patterns, and thus, it is not clear if the binding code developed in vitro will be useful for identifying target genes of a particular ZNF. We performed genome-wide ChIP-seq for ZNF263, a C2H2 ZNF that contains 9 finger domains, a KRAB repression domain, and a SCAN domain and identified more than 5000 binding sites in K562 cells. Our results suggest that ZNF263 binds to a 24-nt site that differs from the motif predicted by the zinc finger code in several positions. Interestingly, many of the ZNF263 binding sites are located within the transcribed region of the target gene. Although ZNFs containing a KRAB domain are thought to function mainly as transcriptional repressors, many of the ZNF263 target genes are expressed at high levels. To address the biological role of ZNF263, we identified genes whose expression was altered by treatment of cells with ZNF263-specific small interfering RNAs. Our results suggest that ZNF263 can have both positive and negative effects on transcriptional regulation of its target genes.

Original languageEnglish (US)
Pages (from-to)1393-1403
Number of pages11
JournalJournal of Biological Chemistry
Volume285
Issue number2
DOIs
StatePublished - 2010

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Zinc Fingers
Zinc
Genes
Proteins
Binding Sites
Genome
Gene expression
K562 Cells
Small Interfering RNA
Fingers
Transcription Factors
Gene Expression
DNA
Cells
In Vitro Techniques
CYS2-HIS2 Zinc Fingers

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. / Frietze, Seth; Lan, Xun; Jin, Victor X.; Farnham, Peggy J.

In: Journal of Biological Chemistry, Vol. 285, No. 2, 2010, p. 1393-1403.

Research output: Contribution to journalArticle

Frietze, Seth ; Lan, Xun ; Jin, Victor X. ; Farnham, Peggy J. / Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. In: Journal of Biological Chemistry. 2010 ; Vol. 285, No. 2. pp. 1393-1403.
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