Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks

Abstract

Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest.

Ki-67 Contributes to Normal Cell Cycle Progression and Inactive X Heterochromatin in p21 Checkpoint-Proficient Human Cells

“…A strong candidate for such a factor is the DREAM complex, which represses G 1 /S-expressed cell cycle genes in a p21-dependent manner (26,54). We noticed frequent downregulation of DREAM complex targets in Ki-67-depleted cells, which led us to test whether sensitivity to Ki-67 depletion was also p21 dependent.…”

“…As a CDK inhibitor (32,33), p21 blocks CDK-mediated Rb phosphorylation, thereby inhibiting E2F-driven transcription (56). Likewise, it maintains the activity of the transcriptionally repressive DREAM complex, which contains Rb-related p107/p130 "pocket protein" subunits (26,27,54). p21 also directly interacts with PCNA and directly inhibits DNA synthesis (35).…”

“…One clue was provided by comparison of the si-Ki-67 RNA-seq data to a metadata analysis of binding by subunits of a transcription repressor complex termed DREAM (26). We observed that genes with the highest predicted probability of DREAM binding were very frequently downregulated upon Ki-67 depletion (Fig.…”

Ki67 is a Graded Rather than a Binary Marker of Proliferation versus Quiescence

“…Consistent with the reported role of Cdh1 in Ki67 degradation (Sobecki et al, 2016), we found that knockdown of Cdh1 (FZR1) via small interfering RNA (siRNA) resulted in the reduced degradation of Ki67 in G1 and overall elevated Ki67 levels (Figure 4C), supporting the notion that APC/C Cdh1 mediates degradation of Ki67 in G1. The Ki67 gene promoter harbors a CHR motif that binds the MMB (Myb-MuvB) complex (Sadasivam and DeCaprio, 2013), and the Ki67 promoter has been consistently pulled down in several chromatin immunoprecipitation sequencing (ChIP-seq) experiments by multiple components of the MMB complex (Fischer et al, 2016). Therefore, we knocked down two different transcription factors of the MMB complex, MYBL2 (B-Myb) and FOXM1 .…”

Essential role for centromeric factors following p53 loss and oncogenic transformation

“…2). A subset of DREAM targets is also bound by FOXM1, controlling expression of genes in G2/M (Fischer et al 2016). The identification of putative CDE/CHR motifs within the promoters of CENP-A and HJURP (Fig.…”