101
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Fernandez-Valverde SL, Degnan BM. Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. Sci Rep 2016; 6:22496. [PMID: 26931148 PMCID: PMC4773876 DOI: 10.1038/srep22496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/15/2016] [Indexed: 12/13/2022] Open
Abstract
The regulatory systems underlying animal development must have evolved prior to the emergence of eumetazoans (cnidarians and bilaterians). Although representatives of earlier-branching animals - sponges ctenophores and placozoans - possess most of the developmental transcription factor families present in eumetazoans, the DNA regulatory elements that these transcription factors target remain uncharted. Here we characterise the core promoter sequences, U1 snRNP-binding sites (5' splice sites; 5'SSs) and polyadenylation sites (PASs) in the sponge Amphimedon queenslandica. Similar to unicellular opisthokonts, Amphimedon's genes are tightly packed in the genome and have small introns. In contrast, its genes possess metazoan-like core promoters populated with binding motifs previously deemed to be specific to vertebrates, including Nrf-1 and Krüppel-like elements. Also as in vertebrates, Amphimedon's PASs and 5'SSs are depleted downstream and upstream of transcription start sites, respectively, consistent with non-elongating transcripts being short-lived; PASs and 5'SSs are more evenly distributed in bidirectional promoters in Amphimedon. The presence of bilaterian-like regulatory DNAs in sponges is consistent with these being early and essential innovations of the metazoan gene regulatory repertoire.
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Affiliation(s)
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
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102
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Elling R, Chan J, Fitzgerald KA. Emerging role of long noncoding RNAs as regulators of innate immune cell development and inflammatory gene expression. Eur J Immunol 2016; 46:504-12. [PMID: 26820238 DOI: 10.1002/eji.201444558] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/17/2015] [Accepted: 01/21/2016] [Indexed: 12/22/2022]
Abstract
The innate immune system represents the first line of defense during infection and is initiated by the detection of conserved microbial products by germline-encoded pattern recognition receptors (PRRs). Sensing through PRRs induces broad transcriptional changes that elicit powerful inflammatory responses. Tight regulation of these processes depends on multiple regulatory checkpoints, including noncoding RNA species such as microRNAs. In addition, long noncoding RNAs (lncRNAs) have recently gained attention as important regulators of gene expression acting through versatile interactions with DNA, RNA, or proteins. As such, these RNAs have a multitude of mechanisms to modulate gene expression. Here, we summarize recent advances in this rapidly moving and evolving field. We highlight the contribution of lncRNAs to both the development and activation of innate immune cells, whether it is in the nucleus, where lncRNAs alter the transcription of target genes through interaction with transcription factors, chromatin-modifying complexes or heterogeneous ribonucleoprotein complexes, or in the cytosol where they can control the stability of target mRNAs. In addition, we discuss experimental approaches required to comprehensively investigate the function of a candidate noncoding RNA locus, including loss-of-function approaches encompassing genomic deletions, RNA interference, locked nucleic acids, and various adaptions of the CRISPR/Cas9 technology.
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Affiliation(s)
- Roland Elling
- Program in Innate Immunity, Division of Infectious Diseases, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennie Chan
- Program in Innate Immunity, Division of Infectious Diseases, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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103
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Neme R, Tautz D. Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence. eLife 2016; 5:e09977. [PMID: 26836309 PMCID: PMC4829534 DOI: 10.7554/elife.09977] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 02/01/2016] [Indexed: 01/17/2023] Open
Abstract
Deep sequencing analyses have shown that a large fraction of genomes is transcribed, but the significance of this transcription is much debated. Here, we characterize the phylogenetic turnover of poly-adenylated transcripts in a comprehensive sampling of taxa of the mouse (genus Mus), spanning a phylogenetic distance of 10 Myr. Using deep RNA sequencing we find that at a given sequencing depth transcriptome coverage becomes saturated within a taxon, but keeps extending when compared between taxa, even at this very shallow phylogenetic level. Our data show a high turnover of transcriptional states between taxa and that no major transcript-free islands exist across evolutionary time. This suggests that the entire genome can be transcribed into poly-adenylated RNA when viewed at an evolutionary time scale. We conclude that any part of the non-coding genome can potentially become subject to evolutionary functionalization via de novo gene evolution within relatively short evolutionary time spans. DOI:http://dx.doi.org/10.7554/eLife.09977.001 Traditionally, the genome – the sum total of DNA within a cell – was thought to be divided into genes and ‘non-coding’ regions. Genes are copied, or “transcribed”, into molecules called RNA that perform essential tasks in the cell. The roles of the non-coding regions were often less clear, although it has since become apparent that some are also transcribed and generate low levels of RNA molecules. However, many debate how significant this transcription is to living organisms. Neme and Tautz have now used a technique called deep RNA sequencing to study the RNA molecules produced in several different species and types of mice whose last common ancestor lived 10 million years ago. Different species produced RNA molecules from different portions – both genes and non-coding regions – of their genomes. Comparing these RNA sequences suggests that changes to the regions that are transcribed occur relatively quickly for a large portion of the genome. Furthermore, there have been no significant areas of the common ancestor’s genome that have not been transcribed at some point in at least one of its descendent species. This therefore suggests that over a relatively short evolutionary period, any part of the genome can acquire the ability to be transcribed and potentially form a new gene. The next challenge is to find out how often these transcribed non-coding parts of the genome show important biochemical activities, and how they find their way into becoming new genes. DOI:http://dx.doi.org/10.7554/eLife.09977.002
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Affiliation(s)
- Rafik Neme
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
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104
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Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol 2016; 14:6. [PMID: 26801249 PMCID: PMC4724118 DOI: 10.1186/s12915-016-0229-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3’ untranslated regions (3’UTRs) in testes. Results By deep sequencing of the 3’ end region of poly(A) + transcripts, we report widespread shortening of 3’UTR through APA during the first wave of spermatogenesis in mouse, with 3’UTR size being the shortest in spermatids. Using genes without APA as a control, we show that shortening of 3’UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear highly potent during spermatogenesis. We additionally found widespread regulation of APA events in introns and exons that can affect the coding sequence of transcripts and global activation of antisense transcripts upstream of the transcription start site, suggesting modulation of splicing and initiation of transcription during spermatogenesis. Importantly, genes that display significant 3’UTR shortening tend to have functions critical for further sperm maturation, and testis-specific genes display greater 3’UTR shortening than ubiquitously expressed ones, indicating functional relevance of APA to spermatogenesis. Interestingly, genes with shortened 3’UTRs tend to have higher RNA polymerase II and H3K4me3 levels in spermatids as compared to spermatocytes, features previously known to be associated with open chromatin state. Conclusions Our data suggest that open chromatin may create a favorable cis environment for 3’ end processing, leading to global shortening of 3’UTR during spermatogenesis. mRNAs with shortened 3’UTRs are relatively stable thanks to evasion of powerful mRNA degradation mechanisms acting on 3’UTR elements. Stable mRNAs generated in spermatids may be important for protein production at later stages of sperm maturation, when transcription is globally halted. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wencheng Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ghassan Yehia
- Transgenic Core Facility, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA. .,Rutgers Cancer Institute of New Jersey, Newark, NJ, USA.
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105
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Ruiz-Orera J, Hernandez-Rodriguez J, Chiva C, Sabidó E, Kondova I, Bontrop R, Marqués-Bonet T, Albà M. Origins of De Novo Genes in Human and Chimpanzee. PLoS Genet 2015; 11:e1005721. [PMID: 26720152 PMCID: PMC4697840 DOI: 10.1371/journal.pgen.1005721] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.
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Affiliation(s)
- Jorge Ruiz-Orera
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | | | - Cristina Chiva
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Tomàs Marqués-Bonet
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M.Mar Albà
- Evolutionary Genomics Group, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- * E-mail:
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106
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Bogu GK, Vizán P, Stanton LW, Beato M, Di Croce L, Marti-Renom MA. Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse. Mol Cell Biol 2015; 36:809-19. [PMID: 26711262 PMCID: PMC4760218 DOI: 10.1128/mcb.00955-15] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/03/2015] [Accepted: 12/17/2015] [Indexed: 11/20/2022] Open
Abstract
Discovering and classifying long noncoding RNAs (lncRNAs) across all mammalian tissues and cell lines remains a major challenge. Previously, mouse lncRNAs were identified using transcriptome sequencing (RNA-seq) data from a limited number of tissues or cell lines. Additionally, associating a few hundred lncRNA promoters with chromatin states in a single mouse cell line has identified two classes of chromatin-associated lncRNA. However, the discovery and classification of lncRNAs is still pending in many other tissues in mouse. To address this, we built a comprehensive catalog of lncRNAs by combining known lncRNAs with high-confidence novel lncRNAs identified by mapping and de novo assembling billions of RNA-seq reads from eight tissues and a primary cell line in mouse. Next, we integrated this catalog of lncRNAs with multiple genome-wide chromatin state maps and found two different classes of chromatin state-associated lncRNAs, including promoter-associated (plncRNAs) and enhancer-associated (elncRNAs) lncRNAs, across various tissues. Experimental knockdown of an elncRNA resulted in the downregulation of the neighboring protein-coding Kdm8 gene, encoding a histone demethylase. Our findings provide 2,803 novel lncRNAs and a comprehensive catalog of chromatin-associated lncRNAs across different tissues in mouse.
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Affiliation(s)
- Gireesh K Bogu
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Bioinformatics and Genomics Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Pedro Vizán
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lawrence W Stanton
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore Stem Cell and Developmental Biology Group, Genome Institute of Singapore, Singapore, Singapore
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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107
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Albrecht AS, Ørom UA. Bidirectional expression of long ncRNA/protein-coding gene pairs in cancer. Brief Funct Genomics 2015; 15:167-73. [DOI: 10.1093/bfgp/elv048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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108
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Hartono SR, Korf IF, Chédin F. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res 2015; 43:9729-41. [PMID: 26253743 PMCID: PMC4787789 DOI: 10.1093/nar/gkv811] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 07/29/2015] [Indexed: 01/18/2023] Open
Abstract
GC skew is a measure of the strand asymmetry in the distribution of guanines and cytosines. GC skew favors R-loops, a type of three stranded nucleic acid structures that form upon annealing of an RNA strand to one strand of DNA, creating a persistent RNA:DNA hybrid. Previous studies show that GC skew is prevalent at thousands of human CpG island (CGI) promoters and transcription termination regions, which correspond to hotspots of R-loop formation. Here, we investigated the conservation of GC skew patterns in 60 sequenced chordates genomes. We report that GC skew is a conserved sequence characteristic of the CGI promoter class in vertebrates. Furthermore, we reveal that promoter GC skew peaks at the exon 1/ intron1 junction and that it is highly correlated with gene age and CGI promoter strength. Our data also show that GC skew is predictive of unmethylated CGI promoters in a range of vertebrate species and that it imparts significant DNA hypomethylation for promoters with intermediate CpG densities. Finally, we observed that terminal GC skew is conserved for a subset of vertebrate genes that tend to be located significantly closer to their downstream neighbors, consistent with a role for R-loop formation in transcription termination.
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Affiliation(s)
- Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA 95616, United States
| | - Ian F Korf
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA 95616, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA 95616, United States
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109
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Chen JY, Shen QS, Zhou WZ, Peng J, He BZ, Li Y, Liu CJ, Luan X, Ding W, Li S, Chen C, Tan BCM, Zhang YE, He A, Li CY. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PLoS Genet 2015; 11:e1005391. [PMID: 26177073 PMCID: PMC4503675 DOI: 10.1371/journal.pgen.1005391] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/24/2015] [Indexed: 01/08/2023] Open
Abstract
While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts. Although gene duplication has been believed as a predominant mechanism for creating new genes, recent reports suggested that new proteins could evolve “de novo” from non-coding DNA regions. These de novo genes are also named as “motherless” genes due to their lack of ancestral proteins as precursors, while recently we and others found that lncRNAs may represent an intermediate stage of their origination. To further elucidate this lncRNA-protein transition process, here we identified 64 hominoid-specific de novo genes and report a new mechanism for the origination of functional de novo proteins from ancestral non-coding transcripts: These non-coding “precursors” are generally not more selectively constrained than other lncRNA loci; and the existence of these de novo proteins is not beyond anticipation under neutral expectation; however, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution.
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Affiliation(s)
- Jia-Yu Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
| | - Jiguang Peng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Bin Z. He
- FAS Center for Systems Biology & Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yumei Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chu-Jun Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xuke Luan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Wanqiu Ding
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shuxian Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
- * E-mail: (AH); (CYL)
| | - Chuan-Yun Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
- * E-mail: (AH); (CYL)
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110
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Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 2015; 161:541-554. [PMID: 25910208 DOI: 10.1016/j.cell.2015.03.010] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/26/2014] [Accepted: 02/18/2015] [Indexed: 01/12/2023]
Abstract
Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide resolution. We developed a simple and powerful approach for performing native elongating transcript sequencing (NET-seq) in human cells that globally maps strand-specific Pol II density at nucleotide resolution. NET-seq exposes a mode of antisense transcription that originates downstream and converges on transcription from the canonical promoter. Convergent transcription is associated with a distinctive chromatin configuration and is characteristic of lower-expressed genes. Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coincident with transcription factor occupancy. Finally, exons retained in mature transcripts display Pol II pausing signatures that differ markedly from skipped exons, indicating an intrinsic capacity for Pol II to recognize exons with different processing fates. Together, human NET-seq exposes the topography and regulatory complexity of human gene expression.
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111
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Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet 2015; 31:426-33. [PMID: 26073855 DOI: 10.1016/j.tig.2015.05.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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112
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Giannakakis A, Zhang J, Jenjaroenpun P, Nama S, Zainolabidin N, Aau MY, Yarmishyn AA, Vaz C, Ivshina AV, Grinchuk OV, Voorhoeve M, Vardy LA, Sampath P, Kuznetsov VA, Kurochkin IV, Guccione E. Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress. Sci Rep 2015; 5:9737. [PMID: 26024509 PMCID: PMC4448690 DOI: 10.1038/srep09737] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/04/2015] [Indexed: 12/27/2022] Open
Abstract
Oxidative stress (OS) is caused by an imbalance between pro- and anti-oxidant reactions leading to accumulation of reactive oxygen species within cells. We here investigate the effect of OS on the transcriptome of human fibroblasts. OS causes a rapid and transient global induction of transcription characterized by pausing of RNA polymerase II (PolII) in both directions, at specific promoters, within 30 minutes of the OS response. In contrast to protein-coding genes, which are commonly down-regulated, this novel divergent, PolII pausing-phenomenon leads to the generation of thousands of long noncoding RNAs (lncRNAs) with promoter-associated antisense lncRNAs transcripts (si-paancRNAs) representing the major group of stress-induced transcripts. OS causes transient dynamics of si-lncRNAs in nucleus and cytosol, leading to their accumulation at polysomes, in contrast to mRNAs, which get depleted from polysomes. We propose that si-lncRNAs represent a novel component of the transcriptional stress that is known to determine the outcome of immediate-early and later cellular stress responses and we provide insights on the fate of those novel mature lncRNA transcripts by showing that their association with polysomal complexes is significantly increased in OS.
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Affiliation(s)
- Antonis Giannakakis
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Jingxian Zhang
- 1] Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore [2] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore
| | - Piroon Jenjaroenpun
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Srikanth Nama
- Institute of Medical Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Norliyana Zainolabidin
- 1] Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore [2] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore
| | - Mei Yee Aau
- Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Aliaksandr A Yarmishyn
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Candida Vaz
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Anna V Ivshina
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Oleg V Grinchuk
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Mathijs Voorhoeve
- 1] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore [2] Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore
| | - Leah A Vardy
- 1] Institute of Medical Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore [2] School of Biological Sciences, Nanyang Technological University, 138673, Singapore
| | - Prabha Sampath
- 1] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore [2] Institute of Medical Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore [3] Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore
| | - Vladimir A Kuznetsov
- 1] Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore [2] School of Computer Engineering, Nanyang Technological University, 639798, Singapore
| | - Igor V Kurochkin
- Division of Genome and Gene Expression Data analysis, Bioinformatics Institute A*STAR (Agency for Science, Technology and Research), 138671, Singapore
| | - Ernesto Guccione
- 1] Division of Cancer Genetics and Therapeutics, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 138673, Singapore [2] Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore
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113
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Bornelöv S, Komorowski J, Wadelius C. Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription. BMC Genomics 2015; 16:300. [PMID: 25881024 PMCID: PMC4446127 DOI: 10.1186/s12864-015-1485-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several post-translational histone modifications are mainly found in gene promoters and are associated with the promoter activity. It has been hypothesized that histone modifications regulate the transcription, as opposed to the traditional view with transcription factors as the key regulators. Promoters of most active genes do not only initiate transcription of the coding sequence, but also a substantial amount of transcription of the antisense strand upstream of the transcription start site (TSS). This promoter feature has generally not been considered in previous studies of histone modifications and transcription factor binding. RESULTS We annotated protein-coding genes as bi- or unidirectional depending on their mode of transcription and compared histone modifications and transcription factor occurrences between them. We found that H3K4me3, H3K9ac, and H3K27ac were significantly more enriched upstream of the TSS in bidirectional genes compared with the unidirectional ones. In contrast, the downstream histone modification signals were similar, suggesting that the upstream histone modifications might be a consequence of transcription rather than a cause. Notably, we found well-positioned CTCF and RAD21 peaks approximately 60-80 bp upstream of the TSS in the unidirectional genes. The peak heights were related to the amount of antisense transcription and we hypothesized that CTCF and cohesin act as a barrier against antisense transcription. CONCLUSIONS Our results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction.
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Affiliation(s)
- Susanne Bornelöv
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden.
- Current affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden.
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, 01-248, Poland.
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 08, Sweden.
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114
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Hu W, Criscione F, Liang S, Tu Z. MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi. INSECT MOLECULAR BIOLOGY 2015; 24:240-52. [PMID: 25420875 PMCID: PMC4361387 DOI: 10.1111/imb.12152] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, single-stranded small RNAs that have important regulatory functions at the post-transcriptional level. In the present study, we characterize miRNAs in two divergent mosquito species, Aedes aegypti and Anopheles stephensi, through deep sequencing of small RNAs spanning all developmental stages. We discovered eight novel miRNAs in Ae. aegypti and 20 novel miRNAs in An. stephensi, which enabled the first systematic analysis of miRNA evolution in mosquitos. We traced the phylogenetic history of all miRNAs in both species and report a rate of 0.055-0.13 miRNA net gain per million years. Most novel miRNAs originate de novo. Duplications that produced miRNA clusters and families are more common in Ae. aegypti than in An. stephensi. We also identified arm-switch as a source of new miRNAs. Expression profile analysis identified mosquito-specific miRNAs that showed strong stage-specific expression in one or both lineages. For example, the aae-miR-2941/2946 family represents the most abundant maternally deposited and zygotically transcribed miRNAs in Ae. aegypti. miR-2943 is a highly expressed zygotic miRNA in both Ae. aegypti and An. stephensi. Such information provides the basis from which to study the function of these miRNAs in biology common to all mosquitos or unique to one particular lineage.
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Affiliation(s)
- W Hu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
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115
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Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci 2015; 40:165-71. [PMID: 25680757 DOI: 10.1016/j.tibs.2015.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 12/11/2022]
Abstract
Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.
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Affiliation(s)
- Ananda L Roy
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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116
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Sun M, Kraus WL. From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease. Endocr Rev 2015; 36:25-64. [PMID: 25426780 PMCID: PMC4309736 DOI: 10.1210/er.2014-1034] [Citation(s) in RCA: 311] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases.
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Affiliation(s)
- Miao Sun
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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117
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Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol 2015; 16:20. [PMID: 25630241 PMCID: PMC4369099 DOI: 10.1186/s13059-015-0586-4] [Citation(s) in RCA: 476] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution. Results We use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of ‘jackpot’ cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern. Conclusions Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0586-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moran N Cabili
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Margaret C Dunagin
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Patrick D McClanahan
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Andrew Biaesch
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Olivia Padovan-Merhar
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA. .,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140, USA.
| | - John L Rinn
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Arjun Raj
- School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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118
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A long non-coding RNA links calreticulin-mediated immunogenic cell removal to RB1 transcription. Oncogene 2015; 34:5046-54. [DOI: 10.1038/onc.2014.424] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/07/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
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119
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Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS, Alt FW. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell 2014; 159:1538-48. [PMID: 25483776 PMCID: PMC4322776 DOI: 10.1016/j.cell.2014.11.014] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/01/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023]
Abstract
Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single-stranded DNA targets. Though largely specific for immunoglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. How AID is recruited to off-targets has been a long-standing mystery. Based on deep GRO-seq studies of mouse and human B lineage cells activated for CSR or SHM, we report that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge. Moreover, we found that such AID-targeting "convergent" transcription arises from antisense transcription that emanates from super-enhancers within sense transcribed gene bodies. Our findings provide an explanation for AID off-targeting to a small subset of mostly lineage-specific genes in activated B cells.
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Affiliation(s)
- Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Alexander Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jiazhi Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Qiao Wang
- Howard Hughes Medical Institute, Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, NIAMS, and Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Corina Amor
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlyn R Wasserman
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, and Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel C Nussenzweig
- Howard Hughes Medical Institute, Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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120
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Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG. microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun 2014; 5:5700. [DOI: 10.1038/ncomms6700] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/29/2014] [Indexed: 01/04/2023] Open
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121
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Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun 2014; 5:5429. [PMID: 25403355 PMCID: PMC4416701 DOI: 10.1038/ncomms6429] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/30/2014] [Indexed: 01/28/2023] Open
Abstract
Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences--including introns and several classes of noncoding RNAs (ncRNAs)--do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here we use computational methods to identify the products of non-canonical translation in mouse neurons by analysing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from antisense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential.
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Affiliation(s)
- Sudhakaran Prabakaran
- Proteomics Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston MA 02115, USA
| | - Martin Hemberg
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Ruchi Chauhan
- Proteomics Center, Boston Children’s Hospital, Boston, MA 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Dominic Winter
- Proteomics Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Ry Y. Tweedie-Cullen
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Christian Dittrich
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Elizabeth Hong
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston MA 02115, USA
| | - Hanno Steen
- Proteomics Center, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel Kreiman
- Department of Ophthalmology, Boston Children’s Hospital, Boston, MA 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Judith A. Steen
- Proteomics Center, Boston Children’s Hospital, Boston, MA 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA 02115, USA
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122
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Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 2014; 46:1311-20. [PMID: 25383968 PMCID: PMC4254663 DOI: 10.1038/ng.3142] [Citation(s) in RCA: 442] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022]
Abstract
Despite the conventional distinction between them, promoters and enhancers share
many features in mammals, including divergent transcription and similar modes of
transcription factor binding. Here, we examine the architecture of transcription
initiation through comprehensive mapping of transcription start sites (TSSs) in human
lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE
cell lines. Using a nuclear run-on protocol called GRO-cap, which captures TSSs for both
stable and unstable transcripts, we conduct detailed comparisons of thousands of promoters
and enhancers in human cells. These analyses reveal a common architecture of initiation,
including tightly spaced (110 bp) divergent initiation, similar frequencies of
core-promoter sequence elements, highly positioned flanking nucleosomes, and two modes of
transcription factor binding. Post-initiation transcript stability provides a more
fundamental distinction between promoters and enhancers than patterns of histone
modifications, transcription factors or co-activators. These results support a unified
model of transcription initiation at promoters and enhancers.
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Affiliation(s)
- Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - André L Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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123
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Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 2014; 30:439-52. [PMID: 25218058 PMCID: PMC4464757 DOI: 10.1016/j.tig.2014.08.004] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 02/08/2023]
Abstract
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.
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Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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124
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Abstract
Over the past decade there has been a greater understanding of genomic complexity in eukaryotes ushered in by the immense technological advances in high-throughput sequencing of DNA and its corresponding RNA transcripts. This has resulted in the realization that beyond protein-coding genes, there are a large number of transcripts that do not encode for proteins and, therefore, may perform their function through RNA sequences and/or through secondary and tertiary structural determinants. This review is focused on the latest findings on a class of noncoding RNAs that are relatively large (>200 nucleotides), display nuclear localization, and use different strategies to regulate transcription. These are exciting times for discovering the biological scope and the mechanism of action for these RNA molecules, which have roles in dosage compensation, imprinting, enhancer function, and transcriptional regulation, with a great impact on development and disease.
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Affiliation(s)
- Roberto Bonasio
- Department of Cell and Developmental Biology and Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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125
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Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP. Considerations when investigating lncRNA function in vivo. eLife 2014; 3:e03058. [PMID: 25124674 PMCID: PMC4132285 DOI: 10.7554/elife.03058] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although a small number of the vast array of animal long non-coding RNAs (lncRNAs) have known effects on cellular processes examined in vitro, the extent of their contributions to normal cell processes throughout development, differentiation and disease for the most part remains less clear. Phenotypes arising from deletion of an entire genomic locus cannot be unequivocally attributed either to the loss of the lncRNA per se or to the associated loss of other overlapping DNA regulatory elements. The distinction between cis- or trans-effects is also often problematic. We discuss the advantages and challenges associated with the current techniques for studying the in vivo function of lncRNAs in the light of different models of lncRNA molecular mechanism, and reflect on the design of experiments to mutate lncRNA loci. These considerations should assist in the further investigation of these transcriptional products of the genome. DOI:http://dx.doi.org/10.7554/eLife.03058.001
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Affiliation(s)
- Andrew R Bassett
- Andrew R Bassett is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.
| | - Asifa Akhtar
- Asifa Akhtar is in the Department of Chromatin Regulation, Max-Planck-Institut für Immunbiologie und Epigenetik, Freiburg im Breisgau, Germany
| | - Denise P Barlow
- Denise P Barlow is in the CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrian P Bird
- Adrian P Bird is in the Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil Brockdorff
- Neil Brockdorff is in the Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Denis Duboule
- Denis Duboule is in the School of Life Sciences, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland; Department of Genetics and Evolution, Université de Genève, Geneva, Switzerland
| | - Anne Ephrussi
- Anne Ephrussi is in the Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne C Ferguson-Smith
- Anne C Ferguson-Smith is in the Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Thomas R Gingeras
- Thomas R Gingeras is in the Functional Genomics Group, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Wilfried Haerty
- Wilfried Haerty is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- Douglas R Higgs is in the MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Eric A Miska
- Eric A Miska is in the Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris P Ponting
- Chris P Ponting is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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126
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Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 2014; 514:389-93. [PMID: 25119026 DOI: 10.1038/nature13580] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/12/2014] [Indexed: 12/21/2022]
Abstract
The vast majority of the mammalian genome has the potential to express noncoding RNA (ncRNA). The 11-subunit RNA exosome complex is the main source of cellular 3'-5' exoribonucleolytic activity and potentially regulates the mammalian noncoding transcriptome. Here we generated a mouse model in which the essential subunit Exosc3 of the RNA exosome complex can be conditionally deleted. Exosc3-deficient B cells lack the ability to undergo normal levels of class switch recombination and somatic hypermutation, two mutagenic DNA processes used to generate antibody diversity via the B-cell mutator protein activation-induced cytidine deaminase (AID). The transcriptome of Exosc3-deficient B cells has revealed the presence of many novel RNA exosome substrate ncRNAs. RNA exosome substrate RNAs include xTSS-RNAs, transcription start site (TSS)-associated antisense transcripts that can exceed 500 base pairs in length and are transcribed divergently from cognate coding gene transcripts. xTSS-RNAs are most strongly expressed at genes that accumulate AID-mediated somatic mutations and/or are frequent translocation partners of DNA double-strand breaks generated at Igh in B cells. Strikingly, translocations near TSSs or within gene bodies occur over regions of RNA exosome substrate ncRNA expression. These RNA exosome-regulated, antisense-transcribed regions of the B-cell genome recruit AID and accumulate single-strand DNA structures containing RNA-DNA hybrids. We propose that RNA exosome regulation of ncRNA recruits AID to single-strand DNA-forming sites of antisense and divergent transcription in the B-cell genome, thereby creating a link between ncRNA transcription and overall maintenance of B-cell genomic integrity.
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127
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Abstract
The torrent of RNA-seq data becoming available not only furnishes an overview of the entire transcriptome but also provides tools to focus on specific areas of interest. Our focus on the synthesis of ribosomes asked whether the abundance of mRNAs encoding ribosomal proteins (RPs) matched the equimolar need for the RPs in the assembly of ribosomes. We were at first surprised to find, in the mapping data of ENCODE and other sources, that there were nearly 100-fold differences in the level of the mRNAs encoding the different RPs. However, after correcting for the mapping ambiguities introduced by the presence of more than 2000 pseudogenes derived from RP mRNAs, we show that for 80%-90% of the RP genes, the molar ratio of mRNAs varies less than threefold, with little tissue specificity. Nevertheless, since the RPs are needed in equimolar amounts, there must be sluggish or regulated translation of the more abundant RP mRNAs and/or substantial turnover of unused RPs. In addition, seven of the RPs have subsidiary genes, three of which are pseudogenes that have been "rescued" by the introduction of promoters and/or upstream introns. Several of these are transcribed in a tissue-specific manner, e.g., RPL10L in testis and RPL3L in muscle, leading to potential variation in ribosome structure from one tissue to another. Of the 376 introns in the RP genes, a single one is alternatively spliced in a tissue-specific manner.
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128
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Grzechnik P, Tan-Wong SM, Proudfoot NJ. Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 2014; 39:319-27. [PMID: 24928762 PMCID: PMC4085477 DOI: 10.1016/j.tibs.2014.05.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 01/28/2023]
Abstract
Transcriptional directionality is controlled by premature transcription termination. Transcriptional directionality is enforced by gene looping. mRNA-specific termination signals and factors are required for gene looping.
Bidirectional promoters are a common feature of many eukaryotic organisms from yeast to humans. RNA Polymerase II that is recruited to this type of promoter can start transcribing in either direction using alternative DNA strands as the template. Such promiscuous transcription can lead to the synthesis of unwanted transcripts that may have negative effects on gene expression. Recent studies have identified transcription termination and gene looping as critical players in the enforcement of promoter directionality. Interestingly, both mechanisms share key components. Here, we focus on recent findings relating to the transcriptional output of bidirectional promoters.
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Affiliation(s)
- Pawel Grzechnik
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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129
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Light S, Basile W, Elofsson A. Orphans and new gene origination, a structural and evolutionary perspective. Curr Opin Struct Biol 2014; 26:73-83. [DOI: 10.1016/j.sbi.2014.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/07/2014] [Accepted: 05/16/2014] [Indexed: 12/28/2022]
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130
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Wisotzkey RG, Quijano JC, Stinchfield MJ, Newfeld SJ. New gene evolution in the bonus-TIF1-γ/TRIM33 family impacted the architecture of the vertebrate dorsal-ventral patterning network. Mol Biol Evol 2014; 31:2309-21. [PMID: 24881051 DOI: 10.1093/molbev/msu175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Uncovering how a new gene acquires its function and understanding how the function of a new gene influences existing genetic networks are important topics in evolutionary biology. Here, we demonstrate nonconservation for the embryonic functions of Drosophila Bonus and its newest vertebrate relative TIF1-γ/TRIM33. We showed previously that TIF1-γ/TRIM33 functions as an ubiquitin ligase for the Smad4 signal transducer and antagonizes the Bone Morphogenetic Protein (BMP) signaling network underlying vertebrate dorsal-ventral axis formation. Here, we show that Bonus functions as an agonist of the Decapentaplegic (Dpp) signaling network underlying dorsal-ventral axis formation in flies. The absence of conservation for the roles of Bonus and TIF1-γ/TRIM33 reveals a shift in the dorsal-ventral patterning networks of flies and mice, systems that were previously considered wholly conserved. The shift occurred when the new gene TIF1-γ/TRIM33 replaced the function of the ubiquitin ligase Nedd4L in the lineage leading to vertebrates. Evidence of this replacement is our demonstration that Nedd4 performs the function of TIF1-γ/TRIM33 in flies during dorsal-ventral axis formation. The replacement allowed vertebrate Nedd4L to acquire novel functions as a ubiquitin ligase of vertebrate-specific Smad proteins. Overall our data reveal that the architecture of the Dpp/BMP dorsal-ventral patterning network continued to evolve in the vertebrate lineage, after separation from flies, via the incorporation of new genes.
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Affiliation(s)
- Robert G Wisotzkey
- Department of Biological Sciences, California State University, East Bay
| | - Janine C Quijano
- Department of Biological Sciences, California State University, East BaySchool of Life Sciences, Arizona State University
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131
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Abstract
Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions.
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Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - David Levens
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
| | - Laura Baranello
- Laboratory of Pathology; National Cancer Institute; Bethesda, MD USA
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Avila J, Gómez-Ramos A, Soriano E. Variations in brain DNA. Front Aging Neurosci 2014; 6:323. [PMID: 25505410 PMCID: PMC4243573 DOI: 10.3389/fnagi.2014.00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/06/2014] [Indexed: 12/16/2022] Open
Abstract
It is assumed that DNA sequences are conserved in the diverse cell types present in a multicellular organism like the human being. Thus, in order to compare the sequences in the genome of DNA from different individuals, nucleic acid is commonly isolated from a single tissue. In this regard, blood cells are widely used for this purpose because of their availability. Thus blood DNA has been used to study genetic familiar diseases that affect other tissues and organs, such as the liver, heart, and brain. While this approach is valid for the identification of familial diseases in which mutations are present in parental germinal cells and, therefore, in all the cells of a given organism, it is not suitable to identify sporadic diseases in which mutations might occur in specific somatic cells. This review addresses somatic DNA variations in different tissues or cells (mainly in the brain) of single individuals and discusses whether the dogma of DNA invariance between cell types is indeed correct. We will also discuss how single nucleotide somatic variations arise, focusing on the presence of specific DNA mutations in the brain.
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Affiliation(s)
- Jesús Avila
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology LaboratoryMadrid, Spain
- *Correspondence: Jesús Avila, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, 208, C/ Nicolás Cabrera no. 1, Madrid, 28049, Spain e-mail: ; Eduardo Soriano, Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de Barcelona, Baldiri i Reixac, 10, Barcelona 08028, Spain e-mail:
| | - Alberto Gómez-Ramos
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology LaboratoryMadrid, Spain
| | - Eduardo Soriano
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), ISCIIIMadrid, Spain
- Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de BarcelonaBarcelona, Spain
- Vall d’Hebrón Institut de Recerca (VHIR)Barcelona, Spain
- *Correspondence: Jesús Avila, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Neurobiology Laboratory, 208, C/ Nicolás Cabrera no. 1, Madrid, 28049, Spain e-mail: ; Eduardo Soriano, Department of Cell Biology, Faculty of Biology, University of Barcelona, Developmental Neurobiology and Regeneration Lab, Parc Científic de Barcelona, Baldiri i Reixac, 10, Barcelona 08028, Spain e-mail:
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