A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

Abstract

Using ChIP-chip assays (employing ENCODE arrays and core promoter arrays), we examined the binding patterns of three members of the E2F family in five cell types. We determined that most E2F1, E2F4, and E2F6 binding sites are located within 2 kb of a transcription start site, in both normal and tumor cells. In fact, the majority of promoters that are active (as defined by TAF1 or POLR2A binding) in GM06990 B lymphocytes and Ntera2 carcinoma cells were also bound by an E2F. This very close relationship between E2F binding sites and binding sites for general transcription factors in both normal and tumor cells suggests that a chromatin-bound E2F may be a signpost for active transcription initiation complexes. In general, we found that several E2Fs bind to a given promoter and that there is only modest cell type specificity of the E2F family. Thus, it is difficult to assess the role of any particular E2F in transcriptional regulation, due to extreme redundancy of target promoters. However, Ntera2 carcinoma cells were exceptional in that a large set of promoters were bound by E2F6, but not by E2F1 or E2F4. It has been proposed that E2F6 contributes to gene silencing by recruiting enzymes involved in methylating histone H3. To test this hypothesis, we created Ntera2 cell lines harboring shRNAs to E2F6. We found that reduction of E2F6 only induced minimal alteration of the transcriptome of Ntera2 transcriptome. Our results support the concept of functional redundancy in the E2F family and suggest that E2F6 is not critical for histone methylation.

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

“…YY1 and E2F4 are associated with apoptosis and proliferation in tumor cells, and can act as transcriptional regulators, either directly or indirectly, via cofactor recruitment [48–51]. In our study, the expression of YY1 and E2F4 was not affected by JQ1.…”

Tissue-specific targeting of cell fate regulatory genes by E2f factors

“…We determined the genomic binding sites of E2f3 and E2f4 in NPCs derived from telencephalic tissue at embryonic day 14.5 (E14.5), a peak stage of cortical neurogenesis. As E2f binding sites are typically found within close proximity of a transcriptional start site (TSS) 8,17,20,24,26 we focused our analysis on promoter regions by coupling chromatin immunoprecipitation (ChIP) using antibodies towards E2f3 and E2f4 (Figure 1a and b) with proximal promoter DNA microarrays (details in Supplementary Text S1). We have validated the specificity of these antibodies previously 8 and here (Supplementary Figure S1 and S2).…”

“…10 Together, these findings demonstrate a direct role for pRb/E2f at cell fate-associated genes, but the extent of this interaction is unknown. Many of these studies focused on single pRb or E2f factor knock-out models, and because E2fs exhibit extensive redundancy in their biological functions and genomic binding patterns, 20,21 it is likely that more E2f target genes relevant to cell fate exist than those that have been reported. Understanding the full regulatory potential of the cell cycle machinery in the brain therefore necessitates an appreciation of the repertoire of E2f target genes in NPCs.…”

“…Understanding the full regulatory potential of the cell cycle machinery in the brain therefore necessitates an appreciation of the repertoire of E2f target genes in NPCs. Genome-wide targets have been reported for E2f4 (and E2f1) in a number of immortalized and transformed cell lines, 20,22,23 and for E2f3 in immortal mouse myoblasts, myotubes and embryonic fibroblasts. 24,25 E2f targets have, however, not been identified on a genome-wide level in any neural cells, nor in any primary cell types.…”

Biological reprogramming in acquired resistance to endocrine therapy of breast cancer

“…Transcriptional reprogramming was further evaluated using data on chromatin immunoprecipitation assays (that is, genomic response elements) and expression profiles linked to cell proliferation and canonical ERa transcriptional function (Balciunaite et al, 2005;Carroll et al, 2006;Xu et al, 2007). In agreement with TFBSs predictions and breast cancer profiles, the underexpressed set showed infra-representation of E2F1-AP2 …”