Besides Pathology: Long Non-Coding RNA in Cell and Tissue Homeostasis
Amanda Salviano-Silva,Sara Cristina Lobo-Alves,Rodrigo Coutinho de Almeida,Danielle Malheiros,Maria Luiza Petzl-Erler +4 more
TLDR
This review highlights studies identifying lncRNAs in the homeostasis of various cell and tissue types or demonstrating their effects in the expression of protein-coding or other non-c coding RNA genes.Abstract:
A significant proportion of mammalian genomes corresponds to genes that transcribe long non-coding RNAs (lncRNAs). Throughout the last decade, the number of studies concerning the roles played by lncRNAs in different biological processes has increased considerably. This intense interest in lncRNAs has produced a major shift in our understanding of gene and genome regulation and structure. It became apparent that lncRNAs regulate gene expression through several mechanisms. These RNAs function as transcriptional or post-transcriptional regulators through binding to histone-modifying complexes, to DNA, to transcription factors and other DNA binding proteins, to RNA polymerase II, to mRNA, or through the modulation of microRNA or enzyme function. Often, the lncRNA transcription itself rather than the lncRNA product appears to be regulatory. In this review, we highlight studies identifying lncRNAs in the homeostasis of various cell and tissue types or demonstrating their effects in the expression of protein-coding or other non-coding RNA genes.read more
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Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease
Juliane Cristina Ribeiro Fernandes,Stephanie Maia Acuña,Juliana Ide Aoki,Lucile Maria Floeter-Winter,Sandra Marcia Muxel +4 more
TL;DR: Key aspects of lncRNA biology are reviewed, focusing on their role as regulatory elements in gene expression modulation during physiological and disease processes, with implications in host and pathogens physiology, and their role in immune response modulation.
Journal ArticleDOI
Long non-coding RNAs: From disease code to drug role.
TL;DR: This paper has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research, and cutting-edge strategies for lncRNA modulation have been summarized.
Systematic Localization of Common Disease-Associated Variation in
Matthew T. Maurano,Richard Humbert,Eric Rynes,Robert E. Thurman,Eric Haugen,Hao Wang,Alex Reynolds,Richard Sandstrom,Hongzhu Qu,Jennifer A. Brody,Anthony Shafer,Fidencio Neri,Kristen Lee,Tanya Kutyavin,Sandra Stehling-Sun,Audra K. Johnson,Theresa K. Canfield,Erika Giste,Morgan Diegel,Daniel Bates,R. Scott Hansen,Shane Neph,Peter J. Sabo,Shelly Heimfeld,Antony Raubitschek,Steven F. Ziegler,Chris Cotsapas,Nona Sotoodehnia,Ian A. Glass,Shamil R. Sunyaev,Rajinder Kaul,John A. Stamatoyannopoulos +31 more
TL;DR: The authors found that 80% of the deoxyribonuclease I hypersensitive sites (DHSs) are active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes.
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Long non-coding RNAs in cancer: Another layer of complexity.
Jaqueline Carvalho de Oliveira,Luana Caroline Oliveira,Carolina Mathias,Gabrielle Araújo Pedroso,Débora S. Lemos,Amanda Salviano-Silva,Tayana Schultz Jucoski,Sara Cristina Lobo-Alves,Erika P. Zambalde,Gabriel Adelman Cipolla,Daniela Fiori Gradia +10 more
TL;DR: A review of the most well characterized long non-coding RNAs with important roles in hallmarks of cancer, additionally including lncRNAs with a higher potential for clinical application can be found in this paper.
Journal ArticleDOI
Long Non-Coding RNAs in Multifactorial Diseases: Another Layer of Complexity.
Gabriel Adelman Cipolla,Jaqueline Carvalho de Oliveira,Amanda Salviano-Silva,Sara Cristina Lobo-Alves,Débora S. Lemos,Luana Caroline Oliveira,Tayana Schultz Jucoski,Carolina Mathias,Gabrielle Araújo Pedroso,Erika P. Zambalde,Daniela Fiori Gradia +10 more
TL;DR: This review summarizes the involvement of some lncRNAs in the most common multifactorial diseases, with a focus on those with published functional data.
References
More filters
Journal ArticleDOI
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien,Rory Johnson,Giovanni Bussotti,Andrea Tanzer,Sarah Djebali,Hagen Tilgner,Gregory Guernec,David C. Martin,Angelika Merkel,David G. Knowles,Julien Lagarde,Lavanya Veeravalli,Xiaoan Ruan,Yijun Ruan,Timo Lassmann,Piero Carninci,James B. Brown,Leonard Lipovich,José M. González,Mark G. Thomas,Carrie A. Davis,Ramin Shiekhattar,Thomas R. Gingeras,Tim Hubbard,Cedric Notredame,Jennifer Harrow,Roderic Guigó +26 more
TL;DR: The most complete human lncRNA annotation to date is presented, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts, and expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes.
Journal ArticleDOI
GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow,Adam Frankish,José M. González,Electra Tapanari,Mark Diekhans,Felix Kokocinski,Bronwen Aken,Daniel Barrell,Amonida Zadissa,Stephen M. J. Searle,If H. A. Barnes,Alexandra Bignell,Veronika Boychenko,Toby Hunt,M. Kay,Gaurab Mukherjee,Jeena Rajan,Gloria Despacio-Reyes,Gary Saunders,Charles A. Steward,Rachel A. Harte,Michael F. Lin,Cédric Howald,Andrea Tanzer,Thomas Derrien,Jacqueline Chrast,Nathalie Walters,Suganthi Balasubramanian,Baikang Pei,Michael L. Tress,Jose Manuel Rodriguez,Iakes Ezkurdia,Jeltje Van Baren,Michael R. Brent,David Haussler,Manolis Kellis,Alfonso Valencia,Alexandre Reymond,Mark Gerstein,Roderic Guigó,Tim Hubbard +40 more
TL;DR: This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.
Journal ArticleDOI
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
Ye Zhang,Kenian Chen,Steven A. Sloan,Mariko L. Bennett,Anja R. Scholze,Sean O'Keeffe,Hemali Phatnani,Paolo Guarnieri,Christine Caneda,Nadine Ruderisch,Shuyun Deng,Shane A. Liddelow,Chaolin Zhang,Richard Daneman,Tom Maniatis,Ben A. Barres,Jian Qian Wu +16 more
TL;DR: The authors' data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycoleytic enzyme pyruvate kinase.
Journal ArticleDOI
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Mitchell Guttman,Ido Amit,Manuel Garber,Courtney French,Michael F. Lin,David M. Feldser,Maite Huarte,Maite Huarte,Or Zuk,Bryce W. Carey,John P. Cassady,Moran N. Cabili,Rudolf Jaenisch,Tarjei S. Mikkelsen,Tyler Jacks,Nir Hacohen,Bradley E. Bernstein,Bradley E. Bernstein,Manolis Kellis,Manolis Kellis,Aviv Regev,John L. Rinn,John L. Rinn,John L. Rinn,Eric S. Lander +24 more
TL;DR: It is demonstrated that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFκB, Sox2, Oct4 (also known as Pou5f1) and Nanog, defining a unique collection of functional linc RNAs that are highly conserved and implicated in diverse biological processes.
Journal ArticleDOI
Biological properties of extracellular vesicles and their physiological functions
María Yáñez-Mó,Pia Siljander,Zoraida Andreu,Apolonija Bedina Zavec,Francesc E. Borràs,Edit I. Buzás,Krisztina Buzas,Krisztina Buzas,Enriqueta Casal,Francesco Cappello,Joana Carvalho,Joana Carvalho,Eva Colas,Anabela Cordeiro da Silva,Anabela Cordeiro da Silva,Stefano Fais,Juan M. Falcón-Pérez,Irene M. Ghobrial,Bernd Giebel,Mario Gimona,Mario Gimona,Michael W. Graner,Ihsan Gursel,Mayda Gursel,Niels H. H. Heegaard,Niels H. H. Heegaard,An Hendrix,Peter Kierulf,Katsutoshi Kokubun,Maja Kosanović,Veronika Kralj-Iglič,Eva-Maria Krämer-Albers,Saara Laitinen,Cecilia Lässer,Thomas Lener,Thomas Lener,Erzsébet Ligeti,Aija Linē,Georg Lipps,Alicia Llorente,Jan Lötvall,Mateja Manček-Keber,Antonio Marcilla,María Mittelbrunn,Irina Nazarenko,Esther N. M. Nolte-‘t Hoen,Tuula A. Nyman,Lorraine O'Driscoll,Mireia Olivan,Carla Oliveira,Carla Oliveira,Éva Pállinger,Hernando A. del Portillo,Hernando A. del Portillo,Jaume Reventós,Jaume Reventós,Marina Rigau,Eva Rohde,Eva Rohde,Marei Sammar,Francisco Sánchez-Madrid,Nuno Santarém,Nuno Santarém,Katharina Schallmoser,Katharina Schallmoser,Marie Stampe Ostenfeld,Willem Stoorvogel,Roman Štukelj,Susanne G. van der Grein,M. Helena Vasconcelos,M. Helena Vasconcelos,Marca H. M. Wauben,Olivier De Wever +72 more
TL;DR: A comprehensive overview of the current understanding of the physiological roles of EVs is provided, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia.
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