dELL is an essential RNA polymerase II elongation factor with a general role in development

Chromatin marks and machines, the missing nucleosome is a theme: gene regulation up and downstream

A remarkable insight to emerge from chromatin immunoprecipitation studies is that the steps leading to chromatin remodeling and preinitiation complex (PIC) assembly differ significantly, depending upon the gene and its biological context (Cosma, 2002). However, when multiple systems are compared, the differences illuminate checkpoints and generalities that provide insights into the most salient features of mechanism. This concept dominated presentations at the 2004 Chromatin and Transcription by RNA Polymerase II meeting held at the Lake Tahoe Granlibakken Conference Center.

Elongation by RNA polymerase II: the short and long of it

Appreciable advances into the process of transcript elongation by RNA polymerase II (RNAP II) have identified this stage as a dynamic and highly regulated step of the transcription cycle. Here, we discuss the many factors that regulate the elongation stage of transcription. Our discussion includes the classical elongation factors that modulate the activity of RNAP II, and the more recently identified factors that facilitate elongation on chromatin templates. Additionally, we discuss the factors that associate with RNAP II, but do not modulate its catalytic activity. Elongation is highlighted as a central process that coordinates multiple stages in mRNA biogenesis and maturation.

In vivo requirement of the RNA polymerase II elongation factor elongin A for proper gene expression and development

A number of transcription factors that increase the catalytic rate of mRNA synthesis by RNA polymerase II (Pol II) have been purified from higher eukaryotes. Among these are the ELL family, DSIF, and the heterotrimeric elongin complex. Elongin A, the largest subunit of the elongin complex, is the transcriptionally active subunit, while the smaller elongin B and C subunits appear to act as regulatory subunits. While much is known about the in vitro properties of elongin A and other members of this class of elongation factors, the physiological role(s) of these proteins remain largely unclear. To elucidate in vivo functions of elongin A, we have characterized its Drosophila homologue (dEloA). dEloA associates with transcriptionally active puff sites within Drosophila polytene chromosomes and exhibits many of the expected biochemical and cytological properties consistent with a Pol II-associated elongation factor. RNA interference-mediated depletion of dEloA demonstrated that elongin A is an essential factor that is required for proper metamorphosis. Consistent with this observation, dEloA expression peaks during the larval stages of development, suggesting that this factor may be important for proper regulation of developmental events during these stages. The discovery of the role of elongin A in an in vivo model system defines the novel contribution played by RNA polymerase II elongation machinery in regulation of gene expression that is required for proper development.

Inhibition of the canonical Wnt signaling pathway in cytoplasm: a novel property of the carboxyl terminal domains of two Xenopus ELL genes

The Wnt signaling pathways are important in many developmental events. The canonical Wnt pathway is one of the three major Wnt-mediated intracellular signaling pathways and is thought to activate Dvl followed by the stabilization of beta-catenin. In Xenopus, this pathway is involved in dorsal determination, anterior-posterior patterning during gastrulation, and neural induction. Here we describe a role for the Xenopus ELL (Eleven-nineteen Lysine-rich Leukemia) gene product in canonical Wnt signaling. Translocation of ELL has been associated with acute myeloid leukemia and the protein possesses three functional domains. We identified rELL-C from a rat brain cDNA library as a binding factor for Dishevelled (Dvl); it represents a partial sequence of rat ELL lacking the pol II elongation domain and has been shown to suppress canonical Wnt signaling. Next, we isolated two Xenopus homologs of ELL, xELL1 and xELL2. No obvious phenotypes were observed with microinjection of full-length xELL1 or xELL2 mRNA, however, microinjection with their occludin homology domain inhibited Wnt signaling at the level of Dvl and upstream of beta-catenin. Intracellular localization of microinjected xELL1- and xELL2-GFP mRNAs showed localization of the full-length products in the nucleus and the occludin-homology domain products in cytoplasm. These results raise the possibility that ELL, which is thought to function as a transcription factor in nuclei, can serve other, novel roles to suppress canonical Wnt signaling in the cytoplasm.

A family of genes clustered at the Triplo-lethal locus of Drosophila melanogaster has an unusual evolutionary history and significant synteny with Anopheles gambiae

Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

Expression of murine ELL-associated factor 2 (Eaf2) is developmentally regulated

Eaf2, ELL-associated factor 2, encodes a protein that is homologous to the human EAF1, which was shown to interact with the transcriptional elongation factor MEN/ELL. During mouse embryogenesis, Eaf2 is preferentially expressed in the central nervous system and in sensory and neuroendocrine organs, including the brain, spinal cord, cranial and spinal ganglia, developing otocyst, the retina, and the pituitary. Eaf2 transcripts were also found in sites where active epithelium-mesenchymal interactions are occurring. These included the invaginating tooth buds, mammary gland anlage, submandibular glands, the lung, the pancreas, and the kidney. Other sites of expression included bladder and intestine. In the developing lens, Eaf2 transcripts were absent in the proliferating anterior lens epithelial cells but were present in the terminally differentiated primary lens fiber cells and also in nonproliferating lens fiber cells in the equatorial zone where lens epithelial cells withdraw from cell cycle and terminally differentiate into secondary lens fiber cells. This spatially restricted pattern of Eaf2 expression in the developing lens suggests that Eaf2 may play an important role in regulating lens maturation.

Transcriptional elongation control by RNA polymerase II: a new frontier

The transcription elongation complex, once thought to be composed of merely the DNA template, RNA polymerase II and the nascent RNA transcript, is now burgeoning as a unit as multifaceted and complicated as the transcription initiation complex. Studies concentrated in defining the elongation stage of transcription during the past recent years have resulted in the discovery of a diverse collection of transcription elongation factors that are either directly involved in the regulation of the rate of the elongating RNA polymerase II or can modulate messenger RNA (mRNA) processing and transport. Such studies have demonstrated that the elongation stage of transcription is highly regulated and has opened a new era of studies defining the molecular role of such transcription elongation factors in cellular development, differentiation and disease progression. Recent studies on the role of RNA polymerase II elongation factors in regulating of the overall rate of transcription both in vitro and in vivo, histone modification by methylation and organismal development will be reviewed here.

The RNA polymerase II elongation complex

Synthesis of eukaryotic mRNA by RNA polymerase II is an elaborate biochemical process that requires the concerted action of a large set of transcription factors. RNA polymerase II transcription proceeds through multiple stages designated preinitiation, initiation, and elongation. Historically, studies of the elongation stage of eukaryotic mRNA synthesis have lagged behind studies of the preinitiation and initiation stages; however, in recent years, efforts to elucidate the mechanisms governing elongation have led to the discovery of a diverse collection of transcription factors that directly regulate the activity of elongating RNA polymerase II. Moreover, these studies have revealed unanticipated roles for the RNA polymerase II elongation complex in such processes as DNA repair and recombination and the proper processing and nucleocytoplasmic transport of mRNA. Below we describe these recent advances, which highlight the important role of the RNA polymerase II elongation complex in regulation of eukaryotic gene expression.

Transcriptional elongation by RNA polymerase II and histone methylation

mRNA synthesis in eukaryotic organisms is a key biological process that is regulated at multiple levels. From the covalent modifications of chromatin by a number of chromatin remodeling complexes during the initiation and activation steps of transcription to the processing of mRNA transcripts, a very large consortium of proteins and multiprotein complexes is critical for gene expression by RNA polymerase II. The list of proteins essential for the successful synthesis of mRNA continues to grow at a rapid pace. Recent advances in this area of research have been focused on transcription through chromatin. In this article, we will review the recent literature linking the key biochemical process of transcriptional elongation by RNA polymerase II to histone methylation by COMPASS, Dot1p, and Set2 methyltransferases.

The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation

Methylation of histone proteins is one of their many modifications that affect chromatin structure and regulate gene expression. Methylation of histone H3 on lysines 4 and 79, catalyzed by the Set1-containing complex COMPASS and Dot1p, respectively, is required for silencing of expression of genes located near chromosome telomeres in yeast. We report that the Paf1 protein complex, which is associated with the elongating RNA polymerase II, is required for methylation of lysines 4 and 79 of histone H3 and for silencing of expression of a telomere-associated gene. We show that the Paf1 complex is required for recruitment of the COMPASS methyltransferase to RNA polymerase II and that the subunits of these complexes interact physically and genetically. Collectively, our results suggest that the Paf1 complex is required for histone H3 methylation, therefore linking transcriptional elongation to chromatin methylation.