scholarly journals The expression level of small non‐coding RNA s derived from the first exon of protein‐coding genes is predictive of cancer status

EMBO Reports ◽  
2014 ◽  
Vol 15 (4) ◽  
pp. 402-410 ◽  
Author(s):  
Athanasios Zovoilis ◽  
Andrew J Mungall ◽  
Richard Moore ◽  
Richard Varhol ◽  
Andy Chu ◽  
...  
Keyword(s):  
Expression Level ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
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 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 The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8305 ◽  
Author(s):  
Aimee Caye G. Chang ◽  
Qiang Lai ◽  
Tao Chen ◽  
Tieyao Tu ◽  
Yunhua Wang ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Plastid Genome ◽  
The Other ◽  
Protein Coding ◽  
Tropical Regions ◽  
Protein Coding Genes ◽  
Non Coding Rna ◽  
Plant Group ◽  
Slow Evolution ◽  
Cp Genome

Cycadales is an extant group of seed plants occurring in subtropical and tropical regions comprising putatively three families and 10 genera. At least one complete plastid genome sequence has been reported for all of the 10 genera except Microcycas, making it an ideal plant group to conduct comprehensive plastome comparisons at the genus level. This article reports for the first time the plastid genome of Microcycas calocoma. The plastid genome has a length of 165,688 bp with 134 annotated genes including 86 protein-coding genes, 47 non-coding RNA genes (39 tRNA and eight rRNA) and one pseudogene. Using global sequence variation analysis, the results showed that all cycad genomes share highly similar genomic profiles indicating significant slow evolution and little variation. However, identity matrices coinciding with the inverted repeat regions showed fewer similarities indicating that higher polymorphic events occur at those sites. Conserved non-coding regions also appear to be more divergent whereas variations in the exons were less discernible indicating that the latter comprises more conserved sequences. Phylogenetic analysis using 81 concatenated protein-coding genes of chloroplast (cp) genomes, obtained using maximum likelihood and Bayesian inference with high support values (>70% ML and = 1.0 BPP), confirms that Microcycas is closest to Zamia and forms a monophyletic clade with Ceratozamia and Stangeria. While Stangeria joined the Neotropical cycads Ceratozamia, Zamia and Microcyas, Bowenia grouped with the Southern Hemisphere cycads Encephalartos, Lepidozamia and Macrozamia. All Cycas species formed a distinct clade separated from the other genera. Dioon, on the other hand, was outlying from the rest of Zamiaceae encompassing two major clades—the Southern Hemisphere cycads and the Neotropical cycads. Analysis of the whole cp genomes in phylogeny also supports that the previously recognized family—Stangeriaceae—which contained Bowenia and Stangeria, is not monophyletic. Thus, the cp genome topology obtained in our study is congruent with other molecular phylogenies recognizing only a two-family classification (Cycadaceae and Zamiaceae) within extant Cycadales.

scholarly journals The role of transposable elements in the ecological morphogenesis under the influence of stress

2019 ◽  
Vol 23 (4) ◽  
pp. 380-389 ◽  
Author(s):  
R. N. Mustafin ◽  
E. K. Khusnutdinova
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Insertional Mutagenesis ◽  
Specific Protein ◽  
Regulatory Sequences ◽  
Rapid Variability ◽  
Protein Coding ◽  
Genome Variability ◽  
Protein Coding Genes ◽  
Non Coding Rna

In natural selection, insertional mutagenesis is an important source of genome variability. Transposons are sensors of environmental stress effects, which contribute to adaptation and speciation. These effects are due to changes in the mechanisms of morphogenesis, since transposons contain regulatory sequences that have cis and trans effects on specific protein-coding genes. In variability of genomes, the horizontal transfer of transposons plays an important role, because it contributes to changing the composition of transposons and the acquisition of new properties. Transposons are capable of site-specific transpositions, which lead to the activation of stress response genes. Transposons are sources of non-coding RNA, transcription factors binding sites and protein-coding genes due to domestication, exonization, and duplication. These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. Therefore, inherited features of the location and composition of transposons, along with a change in the phenotype, play an important role in the characteristics of responding to a variety of environmental stressors. This is the basis for the selection and survival of organisms with a specific composition and arrangement of transposons that contribute to adaptation under certain environmental conditions. In evolution, the capability to transpose into specific genome sites, regulate gene expression, and interact with transcription factors, along with the ability to respond to stressors, is the basis for rapid variability and speciation by altering the regulation of ontogenesis. The review presents evidence of tissue-specific and stage-specific features of transposon activation and their role in the regulation of cell differentiation to confirm their role in ecological morphogenesis.

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.

Sign in / Sign up

Export Citation Format

Share Document