Expression changes in protein-coding genes and long non-coding RNAs in denatured dermis following thermal injury

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

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The dark matter rises: the expanding world of regulatory RNAs

Essays in Biochemistry ◽

10.1042/bse0540001 ◽

2013 ◽

Vol 54 ◽

pp. 1-16 ◽

Cited By ~ 51

Author(s):

Michael B. Clark ◽

Anupma Choudhary ◽

Martin A. Smith ◽

Ryan J. Taft ◽

John S. Mattick

Keyword(s):

Phenotypic Diversity ◽

Rapid Progress ◽

Major Area ◽

Protein Coding ◽

Diverse Range ◽

Protein Coding Genes ◽

Evolutionary Innovation ◽

Non Coding Rnas ◽

Cellular Pathways ◽

Regulatory Rnas

The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.

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Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

eLife ◽

10.7554/elife.60743 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Jun Yao ◽

Douglas C Wu ◽

Ryan M Nottingham ◽

Alan M Lambowitz

Keyword(s):

Human Plasma ◽

Binding Sites ◽

Full Length ◽

Peak Calling ◽

Healthy Individuals ◽

Protein Coding ◽

Protein Binding Sites ◽

Protein Coding Genes ◽

Non Coding Rnas ◽

Potential Biomarkers

Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.

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Regulation of Adaptive Tumor Immunity by Non-Coding RNAs

Cancers ◽

10.3390/cancers13225651 ◽

2021 ◽

Vol 13 (22) ◽

pp. 5651

Author(s):

Eleftheria Papaioannou ◽

María del Pilar González-Molina ◽

Ana M. Prieto-Muñoz ◽

Laura Gámez-Reche ◽

Alicia González-Martín

Keyword(s):

Immune Responses ◽

Cancer Immunotherapy ◽

Tumor Immunity ◽

Immune Cell ◽

Protein Coding ◽

Protein Coding Genes ◽

Therapeutic Value ◽

Non Coding Rnas ◽

And Function

Cancer immunology research has mainly focused on the role of protein-coding genes in regulating immune responses to tumors. However, despite more than 70% of the human genome is transcribed, less than 2% encodes proteins. Many non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have been identified as critical regulators of immune cell development and function, suggesting that they might play important roles in orchestrating immune responses against tumors. In this review, we summarize the scientific advances on the role of ncRNAs in regulating adaptive tumor immunity, and discuss their potential therapeutic value in the context of cancer immunotherapy.

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Faculty Opinions recommendation of Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717960736.793463655 ◽

2012 ◽

Author(s):

François Cambien

Keyword(s):

De Novo ◽

Protein Coding ◽

Protein Coding Genes ◽

Non Coding Rnas

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The indirect antiviral potential of long non-coding RNAs encoded by IFITM pseudogenes

Journal of Virology ◽

10.1128/jvi.00680-21 ◽

2021 ◽

Author(s):

Kazi Rahman ◽

Alex A. Compton

Keyword(s):

Influenza A ◽

Virus Entry ◽

Gene Families ◽

Mrna Levels ◽

Protein Coding ◽

Protein Coding Genes ◽

Non Coding Rna ◽

Selective Forces ◽

Non Coding Rnas ◽

Long Non Coding Rna

The interferon-induced transmembrane ( IFITM ) family performs multiple functions in immunity, including inhibition of virus entry into cells. The IFITM repertoire varies widely between species and consists of protein-coding genes and pseudogenes. The selective forces driving pseudogenization within gene families are rarely understood. In this issue, the human pseudogene IFITM4P is characterized as a virus-induced, long non-coding RNA that contributes to restriction of Influenza A virus by regulating mRNA levels of IFITM1 , IFITM2 , and IFITM3 .

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The RNA-centred view of the synapse: non-coding RNAs and synaptic plasticity

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0504 ◽

2014 ◽

Vol 369 (1652) ◽

pp. 20130504 ◽

Cited By ~ 44

Author(s):

Neil R. Smalheiser

Keyword(s):

Synaptic Plasticity ◽

Protein Translation ◽

Mammalian Brain ◽

Evolutionary Constraints ◽

Protein Coding ◽

Protein Coding Genes ◽

Simple Mapping ◽

Non Coding Rnas ◽

Species Specific ◽

Activity Dependent

If mRNAs were the only RNAs made by a neuron, there would be a simple mapping of mRNAs to proteins. However, microRNAs and other non-coding RNAs (ncRNAs; endo-siRNAs, piRNAs, BC1, BC200, antisense and long ncRNAs, repeat-related transcripts, etc.) regulate mRNAs via effects on protein translation as well as transcriptional and epigenetic mechanisms. Not only are genes ON or OFF, but their ability to be translated can be turned ON or OFF at the level of synapses, supporting an enormous increase in information capacity. Here, I review evidence that ncRNAs are expressed pervasively within dendrites in mammalian brain; that some are activity-dependent and highly enriched near synapses; and that synaptic ncRNAs participate in plasticity responses including learning and memory. Ultimately, ncRNAs can be viewed as the post-it notes of the neuron. They have no literal meaning of their own, but derive their functions from where (and to what) they are stuck. This may explain, in part, why ncRNAs differ so dramatically from protein-coding genes, both in terms of the usual indicators of functionality and in terms of evolutionary constraints. ncRNAs do not appear to be direct mediators of synaptic transmission in the manner of neurotransmitters or receptors, yet they orchestrate synaptic plasticity—and may drive species-specific changes in cognition.

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