Identification of the Promoter and a Transcriptional Enhancer of The
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Molecular Basis of the Function of Transcriptional Enhancers
cells Review Molecular Basis of the Function of Transcriptional Enhancers 1,2, 1, 1,3, Airat N. Ibragimov y, Oleg V. Bylino y and Yulii V. Shidlovskii * 1 Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; [email protected] (A.N.I.); [email protected] (O.V.B.) 2 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia 3 I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia * Correspondence: [email protected]; Tel.: +7-4991354096 These authors contributed equally to this study. y Received: 30 May 2020; Accepted: 3 July 2020; Published: 5 July 2020 Abstract: Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription. Keywords: enhancer; promoter; chromatin; transcriptional bursting; transcription factories; enhancer RNA; epigenetic marks 1. Introduction Gene transcription is precisely organized in time and space. The process requires the participation of hundreds of molecules, which form an extensive interaction network. Substantial progress was achieved recently in our understanding of the molecular processes that take place in the cell nucleus (e.g., see [1–9]). -
Medium Reiteration Frequency Repetitive Sequences in the Human Genome
k.-_:) 1991 Oxford University Press Nucleic Acids Research, Vol. 19, No. 17 4731-4738 Medium reiteration frequency repetitive sequences in the human genome David J.Kaplan, Jerzy Jurka1, Joseph F.Solus and Craig H.Duncan* Center for Molecular Biology, Wayne State University, Detroit, Ml and 'Linus Pauling Institute of Science and Medicine, 440 Page Mill Road, Palo Alto, CA 94306, USA Received April 24, 1991; Revised and Accepted August 7, 1991 EMBL accession nos X59017-X59026 (incl.) ABSTRACT Fourteen novel medium reiteration frequency (MER) Isolation of novel MER families from sequence libraries families were found, in the human genome, by using The Alu fragment library. Human genomic DNA (250 isg) was two different methods. Repetition frequencies per digested to completion with the restriction enzyme AluI. The haploid human genome were estimated for each of resulting fragments were fractionated on a 6% polyacrylamide these families as well as for six previously described gel and fragments in the 500-1000 bp region were isolated. MER DNA families. By these measurements, the 50 ng of this size fractionated DNA was ligated to 500 ng of families were found to contain variable numbers of SnaI cleaved Ml3mpl9 RF DNA (5). The vector was elements, ranging from 200 to 10,000 copies per phosphatased before use. The ligated DNA was mixed with haploid human genome. competent JM 109 bacteria (Stratagene Inc.) and 20,000 resulting transformants were plated at a density of 1,650 plaques per 10 cm INTRODUCTION petri dish. Duplicate filter replicates were prepared and were incubated separately with either of two radioactive oligonucleotide The human genome, like those of other higher eukaryotes, probes. -
Promoter Architecture and Sex-Specific Gene Expression In
| INVESTIGATION Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex R. Taylor Raborn,*,†,1 Ken Spitze,* Volker P. Brendel,*,†,2 and Michael Lynch*,2 *Department of Biology and †School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405 ORCID IDs: 0000-0001-6249-8033 (R.T.R.); 0000-0003-4289-6637 (K.S.); 0000-0002-8055-7508 (V.P.B.) ABSTRACT Large-scale transcription start site (TSS) profiling produces a high-resolution, quantitative picture of transcription initiation and core promoter locations within a genome. However, application of TSS profiling to date has largely been restricted to a small set of prominent model systems. We sought to characterize the cis-regulatory landscape of the water flea Daphnia pulex, an emerging model arthropod that reproduces both asexually (via parthenogenesis) and sexually (via meiosis). We performed Cap Analysis of Gene Expression (CAGE) with RNA isolated from D. pulex within three developmental states: sexual females, asexual females, and males. Identified TSSs were utilized to generate a “Daphnia Promoter Atlas,” i.e., a catalog of active promoters across the surveyed states. Analysis of the distribution of promoters revealed evidence for widespread alternative promoter usage in D. pulex, in addition to a prominent fraction of compactly-arranged promoters in divergent orientations. We carried out de novo motif discovery using CAGE- defined TSSs and identified eight candidate core promoter motifs; this collection includes canonical promoter elements (e.g., TATA and Initiator) in addition to others lacking obvious orthologs. A comparison of promoter activities found evidence for considerable state- specific differential gene expression between states. Our work represents the first global definition of transcription initiation and promoter architecture in crustaceans. -
Escherichia Coli (Gene Fusion/Attenuator/Terminator/RNA Polymerase/Ribosomal Proteins) GERARD BARRY, CATHERINE L
Proc. Natl. Acad. Sci. USA Vol. 76, No. 10, pp. 4922-4926, October 1979 Biochemistry Control features within the rplJL-rpoBC transcription unit of Escherichia coli (gene fusion/attenuator/terminator/RNA polymerase/ribosomal proteins) GERARD BARRY, CATHERINE L. SQUIRES, AND CRAIG SQUIRES Department of Biological Sciences, Columbia University, New York, New York 10027 Communicated by Cyrus Levinthal, July 2, 1979 ABSTRACT Gene fusions constructed in vitro have been regulation could occur (4-7). Yet under certain conditions, used to examine transcription regulatory signals from the operon coordinate of the RNA which encodes ribosomal proteins L10 and L7/12 and the RNA expression polymerase subunits and polymerase P and #I subunits (the rplJL-rpoBC operon). Por- ribosomal proteins is not observed. This is especially true of the tions of this operon, which were obtained by in vitro deletions, rplJL-rpoBC transcription unit which encodes the ribosomal have been placed between the ara promoter and the lacZgene proteins L10 and L7/12 and the RNA polymerase subunits 13 in the gene-fusion plasmid pMC81 developed by M. Casadaban and 13'. For example, only the ribosomal proteins are modulated and S. Cohen. The effect of the inserted DNA segment on the by the stringent regulation system (8, 9) whereas a transient expression of the IacZ gene (in the presence and absence of arabinose) permits the localization of regulatory signals to dis- stimulatory effect of rifampicin is specific for the RNA poly- crete regions of the rpIJL-rpoBC operon. An element that re- merase subunits (10, 11). In addition, different amounts of duces the level of distal gene expression to one-sixth is located mRNA hybridize to the rpl and rpo regions of the rplJL-rpoBC on a fragment which spans the rplL-rpoB intercistronic region. -
Promoter RNA Sequencing
www.nature.com/scientificreports OPEN Promoter RNA sequencing (PRSeq) for the massive and quantitative promoter analysis in vitro Received: 7 August 2018 Shoji Ohuchi1,3, Thorsten Mascher 1 & Beatrix Suess2 Accepted: 1 February 2019 Analysis of promoter strength and specifcity is important for understanding and engineering gene Published: xx xx xxxx regulation. Here, we report an in vitro promoter analysis method that can achieve both massiveness and quantitativeness. In this approach, a pool of single-stranded DNA with a partially randomized promoter sequence to be analyzed is chemically synthesized. Through enzymatic reactions, the randomized sequence will be copied to the downstream region, resulting in a template DNA pool that carries its own promoter information on its transcribed region. After in vitro transcription of the DNA pool with an RNA polymerase of interest, the sequences of the resulting transcripts will be analyzed. Since the promoter strength linearly correlates to the copy number of transcript, the strength of each promoter sequence can be evaluated. A model experiment of T7 promoter variants demonstrated the quantitativeness of the method, and the method was applied for the analysis of the promoter of cyanophage Syn5 RNA polymerase. This method provides a powerful approach for analyzing the complexity of promoter specifcity and discrimination for highly abundant and often redundant alternative sigma factors such as the extracellular function (ECF) sigma factors. Transcription initiation is the key step for controlling gene expression especially in bacterial and archaeal cells. Tus, analysis of promoter strength and specifcity is important for understanding gene regulation. Traditionally, promoter analysis is performed employing in vivo reporter gene fusions [reviewed in1]. -
CG-3'-Rich Region in the Promoter of the Transcriptionally Frequently Silenced RET Protooncogene Lacks Methylated Cytidine Residues
Oncogene (1998) 17, 2573 ± 2583 ã 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc A5'-CG-3'-rich region in the promoter of the transcriptionally frequently silenced RET protooncogene lacks methylated cytidine residues Marc Munnes1, Giovanna Patrone2, Birgit Schmitz1, Giovanni Romeo2 and Walter Doer¯er1 1Institut fuÈr Genetik, UniversitaÈtzuKoÈln, D-50931 KoÈln, Germany; and 2UniversitaÁ di Genova, FacoltaÁ di Medicina e Laboratorio di Genetica Molecolare, Istituto G. Gaslini, I-16148 Genova, Italy In a large proportion of familial and sporadic cases of Keywords: HSCR patients; RET protooncogene Hirschsprung disease (HSCR) mutations in the RET promoter; 5'-CG-3'-rich region in the RET promoter (rearranged during transfection) protooncogene have been described. We have investigated the structure of the RET gene promoter and have analysed a region of approximately 1000 nucleotides in its promoter and 5'- Introduction upstream segments for the occurrence of 5-methyldeoxy- cytidine (5-mC) residues by using the bisul®te protocol of The human RET protooncogene is controlled by a the genomic sequencing method. With an estimated promoter harboring several transcription factor sensitivity of about 93% of this technique, not a single binding sites (Itoh et al., 1992), such as four 5-mC residue could be detected in the control region of a tandemly repeated GC-boxes (Dynan and Tjian, gene that seems to be silenced or exhibit low activity in 1985), an ETF binding site (Kageyama et al., 1989) many adult tissues. In these experiments, the DNAs of and Sp1 and AP-2 binding sites. Most of these sites peripheral white blood cells (PWBC) from four healthy are located within the 5'-CpG-3'-rich region in individuals, from seven patients with familial HSCR, as proximity to the transcriptional start site. -
Regulation of RNA Polymerase II Transcription
Regulation of RNA polymerase II transcription Ronny Drapkin, Alejandro Merino and Danny Reinberg Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, USA Transcription initiation plays a central role in the regulation of gene expression. Exciting developments in the last year have furthered our understanding of the interactions between general transcription factors and how these factors respond to modulators of transcription. Current Opinion in Cell Biology 1993, 5:469-476 Introduction TFIIJ. Formation of the DAB--polFEHJ complex, in the presence of each of four ribonucleoside triphosphates, Cellular growth and differentiation employ precise mech- enables RNAPII to clear the promoter region and initiate anisms to regulate the expression of various genes. One RNA synthesis from a specific start site [ 51. of the most rudimentary mechanisms for a cell to control The past year has seen intense activity aimed at elucidat- the functional levels of a protein is to modulate the lev- ing the molecular mechanisms underlying transcription els of mRNA encoding that polypeptide. It is therefore not initiation. In particular, the interactions that GTFs can surprising that most of the genetic programs that main- mediate, the GTF requirements for initiation, the role tain the cell in a constant state of flux mediate their effects of RNAPII phosphorylation, and the phenomenon of by impinging on mechanisms that control transcription antirepression in the process of activation have been initiation. the subject of many studies. These most recent develop- In contrast to prokaryotic RNA polymerase, eukaryotic ments are the focus of this review. enzymes require multiple accessory proteins to acquire promoter specificity. -
Super Short Operations on Both Gene Order and Intergenic Sizes Andre R
Oliveira et al. Algorithms Mol Biol (2019) 14:21 https://doi.org/10.1186/s13015-019-0156-5 Algorithms for Molecular Biology RESEARCH Open Access Super short operations on both gene order and intergenic sizes Andre R. Oliveira1* , Géraldine Jean2 , Guillaume Fertin2 , Ulisses Dias3 and Zanoni Dias1 Abstract Background: The evolutionary distance between two genomes can be estimated by computing a minimum length sequence of operations, called genome rearrangements, that transform one genome into another. Usually, a genome is modeled as an ordered sequence of genes, and most of the studies in the genome rearrangement literature consist in shaping biological scenarios into mathematical models. For instance, allowing diferent genome rearrangements operations at the same time, adding constraints to these rearrangements (e.g., each rearrangement can afect at most a given number of genes), considering that a rearrangement implies a cost depending on its length rather than a unit cost, etc. Most of the works, however, have overlooked some important features inside genomes, such as the pres- ence of sequences of nucleotides between genes, called intergenic regions. Results and conclusions: In this work, we investigate the problem of computing the distance between two genomes, taking into account both gene order and intergenic sizes. The genome rearrangement operations we consider here are constrained types of reversals and transpositions, called super short reversals (SSRs) and super short transpositions (SSTs), which afect up to two (consecutive) genes. We denote by super short operations (SSOs) any SSR or SST. We show 3-approximation algorithms when the orientation of the genes is not considered when we allow SSRs, SSTs, or SSOs, and 5-approximation algorithms when considering the orientation for either SSRs or SSOs. -
Genome-Wide Analysis of the Intergenic Regions in Arabidopsis Thaliana Suggests the Existence of Bidirectional Promoters and Genetic Insulators Xiaohan Yang, Cara M
Current Topics in Plant Biology Vol. 12, 2011 Genome-wide analysis of the intergenic regions in Arabidopsis thaliana suggests the existence of bidirectional promoters and genetic insulators Xiaohan Yang, Cara M. Winter, Xiuying Xia, and Susheng Gan* Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, New York 14853-5904, USA ABSTRACT Our analysis suggests that specific intergenic The short regions flanked by divergent genes regions contain potential bidirectional promoters or genetic insulators, offering guidance for future provide a good opportunity for exploring experimental efforts to isolate those regulatory mechanisms of transcriptional regulation because of the confined nature of the upstream regulatory elements. elements of both genes. We performed a genome- wide analysis of coexpression levels of divergent KEYWORDS: Arabidopsis, bidirectional promoter, gene regulation, genetic insulator, intergenic gene pairs in Arabidopsis thaliana, along with convergent and parallel gene pairs as controls for region, rice comparison, and found that for adjacent genes INTRODUCTION ≤0.4 kb apart, there was a significantly higher portion of gene pairs showing coexpression The availability of complete genome sequence in divergent configuration than in parallel and gene annotation information and increasingly or convergent configuration. We divided the robust expression data sets for some model higher different expression patterns in adjacent divergent eukaryotes has made it possible to perform large- Arabidopsis gene pairs -
Saccharomyces Cerevisiae Promoter Engineering Before and During the Synthetic Biology Era
biology Review Saccharomyces cerevisiae Promoter Engineering before and during the Synthetic Biology Era Xiaofan Feng and Mario Andrea Marchisio * School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300072, China; [email protected] * Correspondence: [email protected] or [email protected] Simple Summary: Promoters are DNA sequences where the process of transcription starts. They can work constitutively or be controlled by environmental signals of different types. The quantity of proteins and RNA present in yeast genetic circuits highly depends on promoter strength. Hence, they have been deeply studied and modified over, at least, the last forty years, especially since the year 2000 when Synthetic Biology was born. Here, we present how promoter engineering changed over these four decades and discuss its possible future directions due to novel computational methods and technology. Abstract: Synthetic gene circuits are made of DNA sequences, referred to as transcription units, that communicate by exchanging proteins or RNA molecules. Proteins are, mostly, transcription factors that bind promoter sequences to modulate the expression of other molecules. Promoters are, therefore, key components in genetic circuits. In this review, we focus our attention on the construction of artificial promoters for the yeast S. cerevisiae, a popular chassis for gene circuits. We describe the initial techniques and achievements in promoter engineering that predated the start of the Synthetic Biology epoch of about 20 years. We present the main applications of synthetic Citation: Feng, X.; Marchisio, M.A. promoters built via different methods and discuss the latest innovations in the wet-lab engineering Saccharomyces cerevisiae Promoter of novel promoter sequences. -
Biol. Pharm. Bull. 43(4): 742-746 (2020)
742 Biol. Pharm. Bull. 43, 742–746 (2020) Vol. 43, No. 4 Note PRC2 Components Maintain DNA Hypermethylation of the Upstream Promoter and Regulate Robo4 Expression in Endothelial Cells Kohei Izawa,# Keisuke Shirakura,# Koji Kakiuchi, Nobuaki Funahashi, Naoki Maekawa, Nobumasa Hino, Toru Tanaka, Takefumi Doi, and Yoshiaki Okada* Graduate School of Pharmaceutical Sciences, Osaka University; 1–6 Yamadaoka, Suita, Osaka 565–0871, Japan. Received November 15, 2019; accepted January 24, 2020 Roundabout4 (Robo4) is an endothelial cell-specific protein that stabilizes the vasculature in pathologi- cal angiogenesis and inflammation. We previously determined a 3-kb Robo4 promoter and demonstrated the importance of the upstream region for nuclear factor-kappaB (NF-κB)-mediated promoter activation in- duced by tumor necrosis factor α (TNFα). This region contains unique genomic features, including promoter region-specific DNA hypermethylation and chromatin condensation; however, the function of the region re- mains poorly understood. In this study, we analyzed the DNA sequences of the region and identified a motif for polycomb repressive complex 2 (PRC2). Chromatin immunoprecipitation assay indicates the binding of the PRC2 component, SUZ12, to the motif. A mutation in the motif decreased DNA methylation in embryonic stem cells and increased Robo4 promoter activity in endothelial cells. An inhibitor for the PRC2 component, EZH2, induced the promoter activity and expression of Robo4 in endothelial cells treated with or without TNFα. Taken together, these -
A Model-Based Approach for Identifying Functional Intergenic Transcribed Regions and Noncoding Rnas John P
A Model-Based Approach for Identifying Functional Intergenic Transcribed Regions and Noncoding RNAs John P. Lloyd,†,1 Zing Tsung-Yeh Tsai,2 Rosalie P. Sowers,3 Nicholas L. Panchy,‡,4 and Shin-Han Shiu*,1,4,5 1Department of Plant Biology, Michigan State University, East Lansing, MI 2Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 3Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 4Genetics Program, Michigan State University, East Lansing, MI 5Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI †Present address: Departments of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, MI ‡National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN *Corresponding author: E-mail: [email protected]. Associate editor: Jun Gojobori Abstract With advances in transcript profiling, the presence of transcriptional activities in intergenic regions has been well established. However, whether intergenic expression reflects transcriptional noise or activity of novel genes remains unclear. We identified intergenic transcribed regions (ITRs) in 15 diverse flowering plant species and found that the amount of intergenic expression correlates with genome size, a pattern that could be expected if intergenic expression is largely nonfunctional. To further assess the functionality of ITRs, we first built machine learning models using Arabidopsis thaliana as a model that accurately distinguish functional sequences (benchmark protein-coding and RNA genes) and likely nonfunctional ones (pseudogenes and unexpressed intergenic regions) by integrating 93 biochemical, evolutionary, and sequence-structure features. Next, by applying the models genome-wide, we found that 4,427 ITRs (38%) and 796 annotated ncRNAs (44%) had features significantly similar to benchmark protein-coding or RNA genes and thus were likely parts of functional genes.