Classification and function of small open reading frames
Sign Up to like & getrecommendations! Published in 2017 at "Nature Reviews Molecular Cell Biology"
DOI: 10.1038/nrm.2017.58
Abstract: Small open reading frames (smORFs) of 100 codons or fewer are usually — if arbitrarily — excluded from proteome annotations. Despite this, the genomes of many metazoans, including humans, contain millions of smORFs, some of… read more here.
Keywords: reading frames; small open; biology; function ... See more keywords
Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-73307-6
Abstract: Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed… read more here.
Keywords: reading frames; animal genomes; upstream open; cpuorfs ... See more keywords
Evolutionary divergence of novel open reading frames in cichlids speciation
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-78555-0
Abstract: Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive… read more here.
Keywords: reading frames; speciation; novel open; evolutionary divergence ... See more keywords
Upstream open reading frames mediate autophagy-related protein translation.
Sign Up to like & getrecommendations! Published in 2022 at "Autophagy"
DOI: 10.1080/15548627.2022.2059744
Abstract: Macroautophagy/autophagy, a highly conserved catabolic pathway that maintains proper cellular homeostasis is stringently regulated by numerous autophagy-related (Atg) proteins. Many studies have investigated autophagy regulation at the transcriptional level; however, relatively little is known about… read more here.
Keywords: open reading; reading frames; autophagy related; upstream open ... See more keywords
Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac210
Abstract: Abstract Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used… read more here.
Keywords: reading frames; nucleotide diversity; periodicity; population ... See more keywords
slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbac610
Abstract: Abstract Trans-splicing of a spliced leader (SL) to the 5′ ends of mRNAs is used to produce mature mRNAs in several phyla of great importance to human health and the marine ecosystem. One of the… read more here.
Keywords: reading frames; tool; trans splicing; spliced leader ... See more keywords
uORF4u: a tool for annotation of conserved upstream open reading frames
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btad323
Abstract: Summary Upstream open reading frames (uORFs, encoding so-called leader peptides) can regulate translation and transcription of downstream main ORFs (mORFs) in prokaryotes and eukaryotes. However, annotation of novel functional uORFs is challenging due their short… read more here.
Keywords: reading frames; uorf4u tool; annotation; upstream open ... See more keywords
Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Biology and Evolution"
DOI: 10.1093/molbev/msab329
Abstract: Abstract All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized… read more here.
Keywords: coli pangenome; reading frames; gene families; escherichia coli ... See more keywords
Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkac1180
Abstract: Abstract A stop codon entering the ribosome A-site is normally decoded by release factors that induce release of the polypeptide. Certain factors influence the efficiency of the termination which is in competition with elongation in… read more here.
Keywords: stop codons; reading frames; frames downstream; termination ... See more keywords
Profiling Human Cytomegalovirus-Specific T Cell Responses Reveals Novel Immunogenic Open Reading Frames
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Virology"
DOI: 10.1128/jvi.00940-21
Abstract: To understand the crucial role of adaptive immunity in controlling cytomegalovirus infection and disease, we systematically analyzed the CMV “ORFeome” to identify new CMV epitopes targeted primarily by CD4 T cells in humans. Our study… read more here.
Keywords: open reading; reading frames; novel orfs; cmv ... See more keywords
Computational discovery and annotation of conserved small open reading frames in fungal genomes
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2550-2
Abstract: BackgroundSmall open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotated. For many genomes, a second round… read more here.
Keywords: reading frames; gene prediction; annotation; fungal genomes ... See more keywords