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

Abstract

Cell cycle proteins are important regulators of diverse cell fate decisions, and in this capacity have pivotal roles in neurogenesis and brain development. The mechanisms by which cell cycle regulation is integrated with cell fate control in the brain and other tissues are poorly understood, and an outstanding question is whether the cell cycle machinery regulates fate decisions directly or instead as a secondary consequence of proliferative control. Identification of the genes targeted by E2 promoter binding factor (E2f) transcription factors, effectors of the pRb/E2f cell cycle pathway, will provide essential insights into these mechanisms. We identified the promoter regions bound by three neurogenic E2f factors in neural precursor cells in a genome-wide manner. Through bioinformatic analyses and integration of published genomic data sets we uncovered hundreds of transcriptionally active E2f-bound promoters corresponding to genes that control cell fate processes, including key transcriptional regulators and members of the Notch, fibroblast growth factor, Wnt and Tgf-β signaling pathways. We also demonstrate a striking enrichment of the CCCTC binding factor transcription factor (Ctcf) at E2f3-bound nervous system-related genes, suggesting a potential regulatory co-factor for E2f3 in controlling differentiation. Finally, we provide the first demonstration of extensive tissue specificity among E2f target genes in mammalian cells, whereby E2f3 promoter binding is well conserved between neural and muscle precursors at genes associated with cell cycle processes, but is tissue-specific at differentiation-associated genes. Our findings implicate the cell cycle pathway as a widespread regulator of cell fate genes, and suggest that E2f3 proteins control cell typespecific differentiation programs by regulating unique sets of target genes. This work significantly enhances our understanding of how the cell cycle machinery impacts cell fate and differentiation, and will importantly drive further discovery regarding the mechanisms of cell fate control and transcriptional regulation in the brain, as well as in other tissues.

RB controls growth, survival, and neuronal migration in human cerebral organoids

“…This increase in cell proliferation is in agreement with results described in primary tumors, such as human glioblastoma, and in mouse cells, such as retinal progenitor cells, and in different regions of the nervous system, including the central and peripheral nervous system and lens (Classon and Harlow, 2002;McClellan and Slack, 2006;Julian et al, 2016;MacPherson et al, 2003;Naser et al, 2016;Cen et al, 2012;Zhang et al, 2004). Although we did not find any differences in the percentage of Ki67 + cells in wild-type compared with RB1-KO organoids, the cell cycle analysis and BrdU-incorporation assay revealed an increase in S-phase entry of DCX + cells in RB1-KO organoids at 28 DIV.…”

“…Since the discovery of the tumor suppressor gene RB1, many studies have demonstrated its role in regulating the G1-to-S transition in various cell types (Classon and Harlow, 2002;McClellan and Slack, 2006;Julian et al, 2016;MacPherson et al, 2003;Naser et al, 2016). Moreover, KO mouse models have revealed the role of RB during neuronal differentiation and migration, as well as in the regulation of cell death in the embryo and adult brain (Andrusiak et al, 2011;Ghanem et al, 2012;McClellan et al, 2007;Christie et al, 2014;Ferguson et al, 2005;Macleod et al, 1996;Vandenbosch et al, 2016;Yu et al, 2012).…”

“…Later, mutations in the RB1 gene were found in a wide variety of human tumors (Giacinti and Giordano, 2006). Initially, RB was described as regulating the G1/S transition of the cell cycle through E2F-mediated transcriptional regulation in many tissues, including the nervous system (Classon and Harlow, 2002;McClellan and Slack, 2006;Julian et al, 2016;MacPherson et al, 2003;Naser et al, 2016). Recently, studies of brain-specific Rb1-KO mice revealed other roles of the Rb1 gene that extend beyond cell cycle control, such as regulation of neuronal differentiation and migration (Andrusiak et al, 2011;Ghanem et al, 2012;McClellan et al, 2007;Christie et al, 2014;Ferguson et al, 2005).…”

Formula G1: Cell cycle in the driver's seat of stem cell fate determination

“…In addition to the broad epigenetic mechanisms that we now know regulate stem cell fate, earlier studies have also implicated lineage‐specific and cell cycle related transcription factor activity in the control of stem cell differentiation and self‐renewal. E2F transcription factors, which are direct effectors of the core cell cycle machinery, have been implicated in the transcriptional regulation of extensive networks of cell fate‐related genes in multiple stem and progenitor cell types (reviewed in ). Additionally, recent findings have demonstrated that alterations in the activity of the SMAD2/3 transcription factors controls the balance between self‐renewal and differentiation in PSCs , and similarly Cyclin D‐dependent modulation of target gene binding of SMAD2/3 throughout G1 directs lineage choice in PSCs (Fig.…”

A tumor suppressor Retinoblastoma1 is essential for embryonic development in the sea urchin

“…Free E2F then drives transcription of various cell cycle regulators and oncogenes, promoting cell proliferation and tumorigenesis. Other targets of Rb1/E2F pathway include cell fate determinants, of which include: key transcriptional regulators and members of the Notch, fibroblasts growth factor, Wnt, and TGF‐beta signaling pathways . Overexpression of those factors under Rb1‐inactivation has been proposed to contribute to plasticity of stem cells or cancer cells .…”