Skip to main content

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Publication ,  Journal Article
Lee, B-K; Bhinge, AA; Battenhouse, A; McDaniell, RM; Liu, Z; Song, L; Ni, Y; Birney, E; Lieb, JD; Furey, TS; Crawford, GE; Iyer, VR
Published in: Genome Res
January 2012

Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII), and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, while MYC showed the greatest cell-type specificity. MYC and RNAPII co-localized at many of their binding sites and putative target genes. Cell-type specific binding sites, in particular for MYC and RNAPII, were associated with cell-type specific functions. Patterns of binding in relation to gene features were generally conserved across different cell types. RNAPII occupancy was higher over exons than adjacent introns, likely reflecting a link between transcriptional elongation and splicing. TF binding was positively correlated with the expression levels of their putative target genes, but combinatorial binding, in particular of MYC and RNAPII, was even more strongly associated with higher gene expression. These data illuminate how combinatorial binding of transcription factors in diverse cell types is associated with gene expression and cell-type specific biology.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

January 2012

Volume

22

Issue

1

Start / End Page

9 / 24

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Response Elements
  • RNA Splicing
  • RNA Polymerase II
  • Organ Specificity
  • K562 Cells
  • Humans
  • Hep G2 Cells
  • Hela Cells
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Lee, B. K., Bhinge, A. A., Battenhouse, A., McDaniell, R. M., Liu, Z., Song, L., … Iyer, V. R. (2012). Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Research, 22(1), 9–24. https://doi.org/10.1101/gr.127597.111
Lee, B. K., A. A. Bhinge, A. Battenhouse, R. M. McDaniell, Z. Liu, L. Song, Y. Ni, et al. “Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.Genome Research 22, no. 1 (January 2012): 9–24. https://doi.org/10.1101/gr.127597.111.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome research. 2012 Jan;22(1):9–24.
Lee, B. K., et al. “Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.Genome Research, vol. 22, no. 1, Jan. 2012, pp. 9–24. Manual, doi:10.1101/gr.127597.111.
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome research. 2012 Jan;22(1):9–24.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

January 2012

Volume

22

Issue

1

Start / End Page

9 / 24

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Response Elements
  • RNA Splicing
  • RNA Polymerase II
  • Organ Specificity
  • K562 Cells
  • Humans
  • Hep G2 Cells
  • Hela Cells