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Long non-coding RNAs: new players in cell differentiation and development
Alessandro Fatica,Irene Bozzoni +1 more
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TLDR
The function of lncRNAs in developmental processes, such as in dosage compensation, genomic imprinting, cell differentiation and organogenesis, with a particular emphasis on mammalian development are described.Abstract:
Genomes of multicellular organisms are characterized by the pervasive expression of different types of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs) belong to a novel heterogeneous class of ncRNAs that includes thousands of different species. lncRNAs have crucial roles in gene expression control during both developmental and differentiation processes, and the number of lncRNA species increases in genomes of developmentally complex organisms, which highlights the importance of RNA-based levels of control in the evolution of multicellular organisms. In this Review, we describe the function of lncRNAs in developmental processes, such as in dosage compensation, genomic imprinting, cell differentiation and organogenesis, with a particular emphasis on mammalian development.read more
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Gene regulation by long non-coding RNAs and its biological functions.
TL;DR: A review of the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications is presented in this article.
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).
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LncRNA-mediated regulation of cell signaling in cancer.
TL;DR: The latest developments primarily in important cell signaling pathways regulated by lncRNAs in cancer are discussed, including changes in transcription, translation, protein modification and the formation of RNA–protein or protein–protein complexes.
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A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals
Stefan Washietl,Pouya Kheradpour,Jason Ernst,Lucas D. Ward,Irwin Jungreis,Matthew D. Rasmussen,Manolis Kellis +6 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation as mentioned in this paper, which reveals a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons.
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Transition from inflammation to proliferation: a critical step during wound healing
TL;DR: This review summarizes mechanisms regulating the inflammation–proliferation transition at cellular and molecular levels and proposes that identification of such mechanisms will reveal promising targets for development of more effective therapies.
References
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Journal ArticleDOI
A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster
Xueqing Zhang,Zheng Lian,Carolyn Padden,Mark Gerstein,Joel Rozowsky,Michael Snyder,Thomas R. Gingeras,Philipp Kapranov,Sherman M. Weissman,Peter E. Newburger +9 more
TL;DR: Findings suggest that HOTAIRM1 plays a role in the myelopoiesis through modulation of gene expression in the HOXA cluster.
Journal ArticleDOI
Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
TL;DR: It is demonstrated that these lncRNAs are not merely controlled by mESC transcription factors, but that they themselves regulate developmental state: knockdown and overexpression of these transcripts lead to robust changes in Oct4 and Nanog mRNA levels, in addition to alterations in cellular lineage-specific gene expression and in the pluripotency of mESCs.
Journal ArticleDOI
R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus
TL;DR: A homeodomain protein, AtNDX, is identified that regulates COOLAIR, a set of antisense transcripts originating from the 3′ end of Arabidopsis FLOWERING LOCUS C (FLC), and R-loop stabilization mediated by AtNDx inhibits COOL AIR transcription, which in turn modifies FLC expression.
Journal ArticleDOI
The transcriptional activity of human Chromosome 22
John L. Rinn,Ghia Euskirchen,Paul Bertone,Rebecca Martone,Nicholas M. Luscombe,Stephen Hartman,Paul M. Harrison,F. Kenneth Nelson,Perry L. Miller,Mark Gerstein,Sherman M. Weissman,Michael Snyder +11 more
TL;DR: A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)(+) RNA and revealed twice as many transcribed bases as have been reported previously.
Journal ArticleDOI
Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression
Lingjie Li,Bo Liu,Orly L. Wapinski,Miao-Chih Tsai,Kun Qu,Jiajing Zhang,Jeffrey C. Carlson,Meihong Lin,Fengqin Fang,Rajnish A. Gupta,Jill A. Helms,Howard Y. Chang +11 more
TL;DR: It is shown that targeted deletion of mouse Hotair lncRNA leads to derepression of hundreds of genes, resulting in homeotic transformation of the spine and malformation of metacarpal-carpal bones.
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