DRM complex

Abstract: The pocket protein family controls several cellular functions such as cell cycle, differentiation, and apoptosis, among others. However, its role in stress has been poorly explored. The roundworm Caenorhabditis elegans is a simple model organism whose genes are highly conserved during evolution. C. elegans has only one pocket protein, LIN-35; a retinoblastoma protein (pRB)-related protein similar to p130. To control the expression of some of its targets, LIN-35 interacts with E2F-DP (E2 transcription factor/dimerization partner complex) transcription factors and LIN-52, a member of SynMUV (Synthetic Muv) complex. Together, these proteins form the DRM complex, which is also known as the DREAM complex in mammals. In this review, we will focus on the role of LIN-35 and its partners in the stress response. It has been shown that LIN-35 is required to control starvation in L1 and L4 larval stages, and to induce starvation-induced germ apoptosis. Remarkably, during L1 starvation, insulin/IGF-1 receptor signaling (IIS), as well as the pathogenic, toxin, and oxidative stress-responsive genes, are repressed by LIN-35. The lack of lin-35 also triggers a downregulation of oxidative stress genes. Recent works showed that lin-35 and hpl-2 mutant animals showed enhanced resistance to UPRER. Additionally, hpl-2 mutant animals also exhibited upregulation of autophagic genes, suggesting that SynMuv/DRM proteins participate in this process. Finally, lin-35(n745) mutant animals overexpressed hsp-6, a chaperone that participated in the UPRmt. All of these data demonstrate that LIN-35 and its partners play an important role during the stress response.

Abstract: DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in the cell cycle and cancer. Recent work has unveiled a new aspect of DRM function in regulating genes involved in development and differentiation. These studies, however, were performed with cultured cells and a genome-wide study involving intact organisms undergoing active proliferation and differentiation was lacking. Our goal was to extend the knowledge of the role of DRM in gene regulation through development and in multiple tissues. To accomplish this, we employed genomic approaches to determine genome-wide targets of DRM using the nematode Caenorhabditis elegans as a model system. In this dissertation, I focus on the DRM component LIN-54 since it was proposed to exhibit DNA-binding activity. First, we confirmed the DNA-binding activity of C.elegans LIN-54 in vivo, and showed it is essential to recruit the DRM complex to its target genes. Next, chromatin immunoprecipitation and gene expression profiling revealed that LIN-54 controls transcription of genes implicated in cell division, development and reproduction. This work identified an interesting contrast in DRM function in soma vs. germline: DRM promotes transcription of germline-specific genes in the germline, but prevents their ectopic expression in the soma. Furthermore, we discovered a novel characteristic of DRM, sex chromosome-biased binding and function. We demonstrated that C. elegans DRM preferentially binds autosomes, yet regulates X-chromosome silencing by counteracting the H3K36 histone methyltransferase MES-4. By using genomics, cytology, and genetics, we defined DRM as an important player in the regulation of germline X-chromosome gene expression, and addressed molecular mechanisms vii behind the antagonistic interactions between DRM and MES-4. I present a model to explain the interplay of DRM and MES-4, and propose a novel function of DRM and MES-4 in maintaining proper chromosome gene expression dosage. This work extends our knowledge of the conserved roles of DRM in development, and provides a new view of differing DRM functions in soma versus germline. Furthermore, we defined a novel chromosome-specific aspect of DRM-mediated regulation.

Abstract: DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54. We show that LIN-54 DNA-binding activity recruits DRM to promoters enriched for adjacent putative E2F/DP and LIN-54 binding sites, suggesting that these two DNA–binding moieties together direct DRM to its target genes. Chromatin immunoprecipitation and gene expression profiling reveals conserved roles for DRM in regulating genes involved in cell division, development, and reproduction. We find that LIN-54 promotes expression of reproduction genes in the germline, but prevents ectopic activation of germline-specific genes in embryonic soma. Strikingly, C. elegans DRM does not act uniformly throughout the genome: the DRM recruitment motif, DRM binding, and DRM-regulated embryonic genes are all under-represented on the X chromosome. However, germline genes down-regulated in lin-54 mutants are over-represented on the X chromosome. We discuss models for how loss of autosome-bound DRM may enhance germline X chromosome silencing. We propose that autosome-enriched binding of DRM arose in C. elegans as a consequence of germline X chromosome silencing and the evolutionary redistribution of germline-expressed and essential target genes to autosomes. Sex chromosome gene regulation may thus have profound evolutionary effects on genome organization and transcriptional regulatory networks.