Journal ArticleDOI
Structure and function of long noncoding RNAs in epigenetic regulation
Tim R. Mercer,John S. Mattick +1 more
TLDR
This work focuses on the well-characterized ability for lncRNAs to function as epigenetic modulators, and suggests that lnc RNAs may be part of a broad epigenetic regulatory network.Abstract:
Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this diverse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network.read more
Citations
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TGF-β: the master regulator of fibrosis
TL;DR: Studies over the past 5 years have identified additional mechanisms that regulate the action of TGF-β1/Smad signalling in fibrosis, including short and long noncoding RNA molecules and epigenetic modifications of DNA and histone proteins.
Journal ArticleDOI
Long Noncoding RNA and Cancer: A New Paradigm.
TL;DR: The emerging functions and association of lncRNAs in different types of cancer and their potential implications in cancer diagnosis and therapy are reviewed.
Journal ArticleDOI
Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches
TL;DR: This review guides the reader through important aspects of non-coding RNA biology, including their biogenesis, mode of actions, physiological function, as well as their role in the disease context (such as in cancer or the cardiovascular system).
Journal ArticleDOI
RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts
Sarah Geisler,Jeff Coller +1 more
TL;DR: A paradigm in which lncRNAs regulate transcription via chromatin modulation is supported, but new functions are steadily emerging, including post-transcriptional regulation, organization of protein complexes, cell-cell signalling and allosteric regulation of proteins.
Journal ArticleDOI
The rise of regulatory RNA.
Kevin V. Morris,John S. Mattick +1 more
TL;DR: A central role for RNA in human evolution and ontogeny is suggested and the emergence of the previously unsuspected world of regulatory RNA from a historical perspective is reviewed.
References
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Journal ArticleDOI
Network biology: understanding the cell's functional organization
TL;DR: This work states that rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize the view of biology and disease pathologies in the twenty-first century.
Journal ArticleDOI
Landscape of transcription in human cells
Sarah Djebali,Carrie A. Davis,Angelika Merkel,Alexander Dobin,Timo Lassmann,Ali Mortazavi,Ali Mortazavi,Andrea Tanzer,Julien Lagarde,Wei Lin,Felix Schlesinger,Chenghai Xue,Georgi K. Marinov,Jainab Khatun,Brian A. Williams,Chris Zaleski,Joel Rozowsky,Marion S. Röder,Felix Kokocinski,Rehab F. Abdelhamid,Tyler Alioto,Igor Antoshechkin,Michael T. Baer,Nadav Bar,Philippe Batut,Kimberly Bell,Ian Bell,Sudipto K. Chakrabortty,Xian Chen,Jacqueline Chrast,Joao Curado,Thomas Derrien,Jorg Drenkow,Erica Dumais,Jacqueline Dumais,Radha Duttagupta,Emilie Falconnet,Meagan Fastuca,Kata Fejes-Toth,Pedro G. Ferreira,Sylvain Foissac,Melissa J. Fullwood,Hui Gao,David Gonzalez,Assaf Gordon,Harsha P. Gunawardena,Cédric Howald,Sonali Jha,Rory Johnson,Philipp Kapranov,Brandon King,Colin Kingswood,Oscar Junhong Luo,Eddie Park,Kimberly Persaud,Jonathan B. Preall,Paolo Ribeca,Brian A. Risk,Daniel Robyr,Michael Sammeth,Lorian Schaffer,Lei-Hoon See,Atif Shahab,Jørgen Skancke,Ana Maria Suzuki,Hazuki Takahashi,Hagen Tilgner,Diane Trout,Nathalie Walters,Huaien Wang,John A. Wrobel,Yanbao Yu,Xiaoan Ruan,Yoshihide Hayashizaki,Jennifer Harrow,Mark Gerstein,Tim Hubbard,Alexandre Reymond,Stylianos E. Antonarakis,Gregory J. Hannon,Morgan C. Giddings,Morgan C. Giddings,Yijun Ruan,Barbara J. Wold,Piero Carninci,Roderic Guigó,Thomas R. Gingeras,Thomas R. Gingeras +87 more
TL;DR: Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
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
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
John L. Rinn,Michael Kertesz,Jordon K. Wang,Sharon L. Squazzo,Xiao Xu,Samantha A. Brugmann,L. Henry Goodnough,Jill A. Helms,Peggy J. Farnham,Eran Segal,Howard Y. Chang +10 more
TL;DR: The transcriptional landscape of the four human HOX loci is characterized at five base pair resolution in 11 anatomic sites and 231 HOX ncRNAs are identified that extend known transcribed regions by more than 30 kilobases, suggesting transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance.
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.
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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
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