scholarly journals FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs

2020 ◽  
Vol 6 (4) ◽  
pp. 41
Author(s):  
Mihnea P. Dragomir ◽  
Ganiraju C. Manyam ◽  
Leonie Florence Ott ◽  
Léa Berland ◽  
Erik Knutsen ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Start Codon ◽  
Small Peptides ◽  
Reading Frame ◽  
Cellular Processes ◽  
New Class ◽  
Web Resource ◽  
Non Coding Rnas ◽  
Functional Peptides ◽  
Small Open Reading Frames

Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section.

scholarly journals Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1673
Author(s):  
Bernardo Bonilauri ◽  
Fabiola Barbieri Holetz ◽  
Bruno Dallagiovanna
Keyword(s):  
Stem Cells ◽  
Ribosome Profiling ◽  
Open Reading Frames ◽  
Adipose Derived Stem Cells ◽  
Translational Machinery ◽  
Bona Fide ◽  
Non Coding Rnas ◽  
Functional Peptides ◽  
Small Open Reading Frames

Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.

scholarly journals Functional Peptides Encoded by Long Non-Coding RNAs in Gastrointestinal Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Yao Chen ◽  
Weili Long ◽  
Liqiong Yang ◽  
Yueshui Zhao ◽  
Xu Wu ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Gastrointestinal Cancer ◽  
Open Reading Frame ◽  
Chromatin Modifications ◽  
Small Peptides ◽  
Common Cause ◽  
Reading Frame ◽  
Non Coding Rnas ◽  
Functional Peptides ◽  
Common Malignancy

Gastrointestinal cancer is by far the most common malignancy and the most common cause of cancer-related deaths worldwide. Recent studies have shown that long non-coding RNAs (lncRNAs) play an important role in the epigenetic regulation of cancer cells and regulate tumor progression by affecting chromatin modifications, gene transcription, translation, and sponge to miRNAs. In particular, lncRNA has recently been found to possess open reading frame (ORF), which can encode functional small peptides or proteins. These peptides interact with its targets to regulate transcription or the signal axis, thus promoting or inhibiting the occurrence and development of tumors. In this review, we summarize the involvement of lncRNAs and the function of lncRNAs encoded small peptides in gastrointestinal cancer.

scholarly journals Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Julie L Aspden ◽  
Ying Chen Eyre-Walker ◽  
Rose J Phillips ◽  
Unum Amin ◽  
Muhammad Ali S Mumtaz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Open Reading Frames ◽  
Small Peptides ◽  
Functional Roles ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Reading Frames ◽  
Small Open Reading Frames

Thousands of small Open Reading Frames (smORFs) with the potential to encode small peptides of fewer than 100 amino acids exist in our genomes. However, the number of smORFs actually translated, and their molecular and functional roles are still unclear. In this study, we present a genome-wide assessment of smORF translation by ribosomal profiling of polysomal fractions in Drosophila. We detect two types of smORFs bound by multiple ribosomes and thus undergoing productive translation. The ‘longer’ smORFs of around 80 amino acids resemble canonical proteins in translational metrics and conservation, and display a propensity to contain transmembrane motifs. The ‘dwarf’ smORFs are in general shorter (around 20 amino-acid long), are mostly found in 5′-UTRs and non-coding RNAs, are less well conserved, and have no bioinformatic indicators of peptide function. Our findings indicate that thousands of smORFs are translated in metazoan genomes, reinforcing the idea that smORFs are an abundant and fundamental genome component.

scholarly journals The product of the H19 gene may function as an RNA.

1990 ◽  
Vol 10 (1) ◽  
pp. 28-36 ◽  
Author(s):  
C I Brannan ◽  
E C Dees ◽  
R S Ingram ◽  
S M Tilghman
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Translation Termination ◽  
Sedimentation Coefficient ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Translational Machinery ◽  
H19 Gene ◽  
Reading Frames ◽  
Small Open Reading Frames

The mouse H19 gene was identified as an abundant hepatic fetal-specific mRNA under the transcriptional control of a trans-acting locus termed raf. The protein this gene encoded was not apparent from an analysis of its nucleotide sequence, since the mRNA contained multiple translation termination signals in all three reading frames. As a means of assessing which of the 35 small open reading frames might be important to the function of the gene, the human H19 gene was cloned and sequenced. Comparison of the two homologs revealed no conserved open reading frame. Cellular fractionation showed that H19 RNA is cytoplasmic but not associated with the translational machinery. Instead, it is located in a particle with a sedimentation coefficient of approximately 28S. Despite the fact that it is transcribed by RNA polymerase II and is spliced and polyadenylated, we suggest that the H19 RNA is not a classical mRNA. Instead, the product of this unusual gene may be an RNA molecule.

scholarly journals Small Open Reading Frames, Non-Coding RNAs and Repetitive Elements in Bradyrhizobium japonicum USDA 110

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0165429 ◽  
Author(s):  
Julia Hahn ◽  
Olga V. Tsoy ◽  
Sebastian Thalmann ◽  
Jelena Čuklina ◽  
Mikhail S. Gelfand ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Repetitive Elements ◽  
Open Reading Frames ◽  
Non Coding Rnas ◽  
Reading Frames ◽  
Small Open Reading Frames

scholarly journals Blotched Snakehead Virus Is a New Aquatic Birnavirus That Is Slightly More Related to Avibirnavirus Than to Aquabirnavirus

2003 ◽  
Vol 77 (1) ◽  
pp. 719-725 ◽  
Author(s):  
Bruno Da Costa ◽  
Stéphanie Soignier ◽  
Christophe Chevalier ◽  
Celine Henry ◽  
Corinne Thory ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Cleavage Sites ◽  
Genomic Segment ◽  
Small Peptides ◽  
Viral Protease ◽  
Reading Frame ◽  
Polyprotein Processing ◽  
Viral Particles ◽  
Catalytic Dyad ◽  
Reading Frames

ABSTRACT By different approaches, we characterized the birnavirus blotched snakehead virus (BSNV). The sequence of genomic segment A revealed the presence of two open reading frames (ORFs): a large ORF with a 3,207-bp-long nucleotide sequence and a 417-nucleotide-long small ORF located within the N-terminal half of the large ORF, but in a different reading frame. The large ORF was found to encode a polyprotein cotranslationally processed by the viral protease VP4 to generate pVP2 (the VP2 precursor), a 71-amino-acid-long peptide ([X]), VP4, and VP3. The two cleavage sites at the [X]-VP4 and VP4-VP3 junctions were identified by N-terminal sequencing. We showed that the processing of pVP2 generated VP2 and several small peptides (amino acids [aa] 418 to 460, 461 to 467, 468 to 474, and 475 to 486). Two of these peptides (aa 418 to 460 and 475 to 486) were positively identified in the viral particles with 10 additional peptides derived from further processing of the peptide aa 418 to 460. The results suggest that VP4 cleaves multiple Pro-X-Ala↓Ala motifs, with the notable exception of the VP4-VP3 junction. Replacement of the members of the predicted VP4 catalytic dyad (Ser-692 and Lys-729) confirmed their indispensability in the polyprotein processing. The genomic segment B sequence revealed a single large ORF encoding a putative polymerase, VP1. Our results demonstrate that BSNV should be considered a new aquatic birnavirus species, slightly more related to IBDV than to IPNV.

scholarly journals attI1-Located Small Open Reading Frames ORF-17 and ORF-11 in a Class 1 Integron Affect Expression of a Gene Cassette Possessing a Canonical Shine-Dalgarno Sequence

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Costas C. Papagiannitsis ◽  
Leonidas S. Tzouvelekis ◽  
Eva Tzelepi ◽  
Vivi Miriagou
Keyword(s):  
Single Gene ◽  
Gene Cassette ◽  
Open Reading Frames ◽  
Translation Initiation Region ◽  
Class 1 Integron ◽  
Reading Frame ◽  
Class 1 ◽  
Shine Dalgarno Sequence ◽  
Reading Frames ◽  
Small Open Reading Frames

ABSTRACT By searching the Integrall integron and GenBank databases, a novel open reading frame (ORF) of 51 nucleotides (nts) (ORF-17) overlapping the previously described ORF-11 was identified within the attI1 site in virtually all class 1 integrons. Using a set of isogenic plasmid constructs carrying a single gene cassette (bla GES-1) and possessing a canonical translation initiation region, we found that ORF-17 contributes to GES-1 expression.

scholarly journals A STUDY OF THE ROLE OF MICRORNA IN PITUITARY ADENOMA

2018 ◽  
Vol 5 (2) ◽  
pp. 8-15
Author(s):  
I. F. Gareev ◽  
O. A. Beylerli
Keyword(s):  
Pituitary Adenoma ◽  
Target Genes ◽  
Decisive Role ◽  
Cellular Processes ◽  
New Class ◽  
Number Of Genes ◽  
Non Coding Rnas ◽  
New Biomarkers ◽  
New Evidence

MicroRNAs are a new class of small non-coding RNAs, a length of 18–22 nucleotides that play a decisive role as posttranscriptional regulators of gene expression. Due to the large number of genes, regulated microRNAs, microRNAs are involved in many cellular processes. The study of the impairment of the expression of the target genes of microRNA, often associated with changes in important biological characteristics, provides a significant understanding of the role of microRNAs in oncogenesis. New evidence suggests that aberrant microRNA expression or dysregulation of endogenous microRNAs affects the onset and development of tumors, including adenomas of the pituitary gland. In this review, the significance of some microRNAs in the pathology of the pituitary adenoma will be assessed, as well as data on the study of microRNAs as therapeutic targets and new biomarkers.

scholarly journals Small open reading frames and cellular stress responses

2019 ◽  
Vol 15 (2) ◽  
pp. 108-116 ◽  
Author(s):  
Alexandra Khitun ◽  
Travis J. Ness ◽  
Sarah A. Slavoff
Keyword(s):  
Stress Responses ◽  
Cellular Stress ◽  
Open Reading Frames ◽  
Open Reading Frame ◽  
Reading Frame ◽  
Cellular Stress Responses ◽  
Small Open Reading Frame ◽  
Reading Frames ◽  
Small Open Reading Frames

Increasing evidence suggests that some small open reading frame-encoded polypeptides (SEPs) function in prokaryotic and eukaryotic cellular stress responses.

scholarly journals Improved Identification of Small Open Reading Frames Encoded Peptides by Top-Down Proteomic Approaches and De Novo Sequencing

2021 ◽  
Vol 22 (11) ◽  
pp. 5476
Author(s):  
Bing Wang ◽  
Zhiwei Wang ◽  
Ni Pan ◽  
Jiangmei Huang ◽  
Cuihong Wan
Keyword(s):  
De Novo ◽  
Average Length ◽  
De Novo Sequencing ◽  
Open Reading Frames ◽  
Start Codon ◽  
Sequence Coverage ◽  
Top Down ◽  
Bottom Up ◽  
Reading Frames ◽  
Small Open Reading Frames

Small open reading frames (sORFs) have translational potential to produce peptides that play essential roles in various biological processes. Nevertheless, many sORF-encoded peptides (SEPs) are still on the prediction level. Here, we construct a strategy to analyze SEPs by combining top-down and de novo sequencing to improve SEP identification and sequence coverage. With de novo sequencing, we identified 1682 peptides mapping to 2544 human sORFs, which were all first characterized in this work. Two-thirds of these new sORFs have reading frame shifts and use a non-ATG start codon. The top-down approach identified 241 human SEPs, with high sequence coverage. The average length of the peptides from the bottom-up database search was 19 amino acids (AA); from de novo sequencing, it was 9 AA; and from the top-down approach, it was 25 AA. The longer peptide positively boosts the sequence coverage, more efficiently distinguishing SEPs from the known gene coding sequence. Top-down has the advantage of identifying peptides with sequential K/R or high K/R content, which is unfavorable in the bottom-up approach. Our method can explore new coding sORFs and obtain highly accurate sequences of their SEPs, which can also benefit future function research.

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