scholarly journals Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e109443 ◽  
Author(s):  
Tanvir Alam ◽  
Yulia A. Medvedeva ◽  
Hui Jia ◽  
James B. Brown ◽  
Leonard Lipovich ◽  
...  
Keyword(s):  
Promoter Analysis ◽  
Differential Regulation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Long Non Coding Rna

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

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 .

scholarly journals Clinical significance of long non-coding RNA DUXAP8 and its protein coding genes in hepatocellular carcinoma

2020 ◽  
Vol 11 (20) ◽  
pp. 6140-6156
Author(s):  
Xiang-Kun Wang ◽  
Xi-Wen Liao ◽  
Rui Huang ◽  
Jian-Lu Huang ◽  
Zi-Jun Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Clinical Significance ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Long non-coding RNAs and splicing

2021 ◽  
Author(s):  
David Staněk
Keyword(s):  
Dominant Role ◽  
Splice Sites ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Splicing Efficiency ◽  
Non Coding Rnas ◽  
Intron Removal ◽  
Long Non Coding Rna

Abstract In this review I focus on the role of splicing in long non-coding RNA (lncRNA) life. First, I summarize differences between the splicing efficiency of protein-coding genes and lncRNAs and discuss why non-coding RNAs are spliced less efficiently. In the second half of the review, I speculate why splice sites are the most conserved sequences in lncRNAs and what additional roles could splicing play in lncRNA metabolism. I discuss the hypothesis that the splicing machinery can, besides its dominant role in intron removal and exon joining, protect cells from undesired transcripts.

scholarly journals Beyond protein-coding genes

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anna Lozano-Ureña ◽  
Sacri R Ferrón
Keyword(s):  
Intellectual Disabilities ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Neuronal Genes ◽  
Long Non Coding Rna

A long non-coding RNA called lnc-NR2F1 regulates several neuronal genes, including some involved in autism and intellectual disabilities.

scholarly journals Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes

2019 ◽  
Vol 21 (2) ◽  
pp. 637-648 ◽  
Author(s):  
Aritro Nath ◽  
Paul Geeleher ◽  
R Stephanie Huang
Keyword(s):  
Expression Patterns ◽  
Imputation Accuracy ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Cancer Tissues ◽  
Long Non Coding Rna

Abstract Long non-coding RNAs (lncRNAs) play an important role in gene regulation and are increasingly being recognized as crucial mediators of disease pathogenesis. However, the vast majority of published transcriptome datasets lack high-quality lncRNA profiles compared to protein-coding genes (PCGs). Here we propose a framework to harnesses the correlative expression patterns between lncRNA and PCGs to impute unknown lncRNA profiles. The lncRNA expression imputation (LEXI) framework enables characterization of lncRNA transcriptome of samples lacking any lncRNA data using only their PCG profiles. We compare various machine learning and missing value imputation algorithms to implement LEXI and demonstrate the feasibility of this approach to impute lncRNA transcriptome of normal and cancer tissues. Additionally, we determine the factors that influence imputation accuracy and provide guidelines for implementing this approach.

scholarly journals HSF2 Co-regulates Protein-coding and Long Non-coding RNA Genes Specific to Black Tissues of the Black Chicken, Yeonsan Ogye

2017 ◽  
Author(s):  
Hyosun Hong ◽  
Han-Ha Chai ◽  
Kyoungwoo Nam ◽  
Dajeong Lim ◽  
Kyung-Tai Lee ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Entire Body ◽  
Specific Expression ◽  
Protein Coding ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Black Coloring ◽  
Long Non Coding Rna

AbstractThe Yeonsan Ogye (Ogye) is a rare Korean domestic chicken breed, the entire body of which, including its feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been globally investigated. In this study, high-throughput RNA sequencing and DNA methylation sequencing were performed to dissect the expression landscape of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes along with DNA methylation landscape in twenty different Ogye tissues. About 75% of Ogye lncRNAs showed tissue-specific expression whereas about 45% of protein-coding genes did. For some genes, the tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. About 39% of the tissue-specific lncRNAs displayed functional association with proximal or distal protein-coding genes. In particular, heat shock transcription factor 2 (HSF2)-associated lncRNAs were discovered to be functionally linked to protein-coding genes that are specifically expressed in black skin tissues, tended to be more syntenically conserved in mammals, and were differentially expressed in black tissues relative to white tissues. Our results not only facilitate understanding how the non-coding genome regulates unique phenotypes but also should be of use for future genomic breeding of chickens.

scholarly journals Involvement of transposable elements in neurogenesis

2020 ◽  
Vol 24 (2) ◽  
pp. 209-218
Author(s):  
R. N. Mustafin ◽  
E. K. Khusnutdinova
Keyword(s):  
Stem Cells ◽  
Transposable Elements ◽  
Human Brain ◽  
Significant Activity ◽  
Protein Coding ◽  
Neuronal Stem Cells ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Long Non Coding Rna

The article is about the role of transposons in the regulation of functioning of neuronal stem cells and mature neurons of the human brain. Starting from the first division of the zygote, embryonic development is governed by regular activations of transposable elements, which are necessary for the sequential regulation of the expression of genes specific for each cell type. These processes include differentiation of neuronal stem cells, which requires the finest tuning of expression of neuron genes in various regions of the brain. Therefore, in the hippocampus, the center of human neurogenesis, the highest transposon activity has been identified, which causes somatic mosai cism of cells during the formation of specific brain structures. Similar data were obtained in studies on experimental animals. Mobile genetic elements are the most important sources of long non-coding RNAs that are coexpressed with important brain protein-coding genes. Significant activity of long non-coding RNA was detected in the hippocampus, which confirms the role of transposons in the regulation of brain function. MicroRNAs, many of which arise from transposon transcripts, also play an important role in regulating the differentiation of neuronal stem cells. Therefore, transposons, through their own processed transcripts, take an active part in the epigenetic regulation of differentiation of neurons. The global regulatory role of transposons in the human brain is due to the emergence of protein-coding genes in evolution by their exonization, duplication and domestication. These genes are involved in an epigenetic regulatory network with the participation of transposons, since they contain nucleotide sequences complementary to miRNA and long non-coding RNA formed from transposons. In the memory formation, the role of the exchange of virus-like mRNA with the help of the Arc protein of endogenous retroviruses HERV between neurons has been revealed. A possible mechanism for the implementation of this mechanism may be reverse transcription of mRNA and site-specific insertion into the genome with a regulatory effect on the genes involved in the memory.  

scholarly journals The Growth-Arrest-Specific (GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers

2019 ◽  
Vol 5 (3) ◽  
pp. 46 ◽  
Author(s):  
Anton Goustin ◽  
Pattaraporn Thepsuwan ◽  
Mary Kosir ◽  
Leonard Lipovich
Keyword(s):  
Genomic Dna ◽  
Growth Arrest ◽  
Evolutionary Conservation ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Mammalian Genomes ◽  
Long Non Coding Rna ◽  
Reading Frames

Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading frames (smORFs) that may encode short proteins. Any given lncRNA may have more than one of these functions. This review focuses on one fascinating case—the growth-arrest-specific (GAS)-5 gene, encoding a complicated repertoire of alternatively-spliced lncRNA isoforms. GAS5 is also a host gene of numerous small nucleolar (sno) RNAs, which are processed from its introns. Publications about this lncRNA date back over three decades, covering its role in cell proliferation, cell differentiation, and cancer. The GAS5 story has drawn in contributions from prominent molecular geneticists who attempted to define its tumor suppressor function in mechanistic terms. The evidence suggests that rodent Gas5 and human GAS5 functions may be different, despite the conserved multi-exonic architecture featuring intronic snoRNAs, and positional conservation on syntenic chromosomal regions indicating that the rodent Gas5 gene is the true ortholog of the GAS5 gene in man and other apes. There is no single answer to the molecular mechanism of GAS5 action. Our goal here is to summarize competing, not mutually exclusive, mechanistic explanations of GAS5 function that have compelling experimental support.

scholarly journals Long non-coding RNA gene regulation and trait associations across human tissues

2019 ◽  
Author(s):  
O. M. de Goede ◽  
N. M. Ferraro ◽  
D. C. Nachun ◽  
A. S. Rao ◽  
F. Aguet ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcriptional Activity ◽  
Biological Function ◽  
Cell Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Regulation Network ◽  
Long Non Coding Rna ◽  
Trait Associations

AbstractLong non-coding RNA (lncRNA) genes are known to have diverse impacts on gene regulation. However, it is still a major challenge to distinguish functional lncRNAs from those that are byproducts of surrounding transcriptional activity. To systematically identify hallmarks of biological function, we used the GTEx v8 data to profile the expression, regulation, network relationships and trait associations of lncRNA genes across 49 tissues encompassing 87 distinct traits. In addition to revealing widespread differences in regulatory patterns between lncRNA and protein-coding genes, we identified novel disease-associated lncRNAs, such as C6orf3 for psoriasis and LINC01475/RP11-129J12.1 for ulcerative colitis. This work provides a comprehensive resource to interrogate lncRNA genes of interest and annotate cell type and human trait relevance.One Sentence SummarylncRNA genes have distinctive regulatory patterns and unique trait associations compared to protein-coding genes.

Sign in / Sign up

Export Citation Format

Share Document