Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF

Nucleic Acids Res. 2012 Jun;40(11):4754-64. doi: 10.1093/nar/gks139. Epub 2012 Feb 16.

Abstract

Recently, much attention has been given to elucidate how long-range gene regulation comes into play and how histone modifications and distal transcription factor binding contribute toward this mechanism. Androgen receptor (AR), a key regulator of prostate cancer, has been shown to regulate its target genes via distal enhancers, leading to the hypothesis of global long-range gene regulation. However, despite numerous flows of newly generated data, the precise mechanism with respect to AR-mediated long-range gene regulation is still largely unknown. In this study, we carried out an integrated analysis combining several types of high-throughput data, including genome-wide distribution data of H3K4 di-methylation (H3K4me2), CCCTC binding factor (CTCF), AR and FoxA1 cistrome data as well as androgen-regulated gene expression data. We found that a subset of androgen-responsive genes was significantly enriched near AR/H3K4me2 overlapping regions and FoxA1 binding sites within the same CTCF block. Importantly, genes in this class were enriched in cancer-related pathways and were downregulated in clinical metastatic versus localized prostate cancer. Our results suggest a relatively short combinatorial long-range regulation mechanism facilitated by CTCF blocking. Under such a mechanism, H3K4me2, AR and FoxA1 within the same CTCF block combinatorially regulate a subset of distally located androgen-responsive genes involved in prostate carcinogenesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Androgens / pharmacology
  • Binding Sites
  • CCCTC-Binding Factor
  • Cell Line, Tumor
  • Gene Expression Regulation, Neoplastic*
  • Genome, Human
  • HeLa Cells
  • Hepatocyte Nuclear Factor 3-alpha / metabolism
  • Histones / metabolism
  • Humans
  • Jurkat Cells
  • Male
  • Neoplasm Metastasis
  • Prostate / metabolism
  • Prostatic Neoplasms / genetics*
  • Prostatic Neoplasms / metabolism
  • Prostatic Neoplasms / pathology
  • Receptors, Androgen / metabolism*
  • Repressor Proteins / metabolism*

Substances

  • Androgens
  • CCCTC-Binding Factor
  • CTCF protein, human
  • FOXA1 protein, human
  • Hepatocyte Nuclear Factor 3-alpha
  • Histones
  • Receptors, Androgen
  • Repressor Proteins