Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins

Shumate

et al. 2018

Preprint

We assembled the sequences from 9,795 RNA sequencing experiments, collected from 31 human tissues and hundreds of subjects as part of the GTEx project, to create a new, comprehensive catalog of human genes and transcripts. The new human gene database contains 43,162 genes, of which 21,306 are protein-coding and 21,856 are noncoding, and a total of 323,824 transcripts, for an average of 7.5 transcripts per gene. Our expanded gene list includes 4,998 novel genes (1,178 coding and 3,819 noncoding) and 97,511 novel splice variants of protein-coding genes as compared to the most recent human gene catalogs. We detected over 30 million additional transcripts at more than 650,000 sites, nearly all of which are likely to be nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells.

Section: Validation Using Mass Spectrometrymentioning

confidence: 95%

Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise

Shumate

et al. 2018

Preprint

“…In recent studies, thousands of alternative proteins were experimentally detected in human cell lines (Vanderperre et al 2013;Samandi et al 2017;Brunet et al 2019). In P. patens, we found tens of thousands of sORFs (CDS-sORFs) that overlapped with the CDS of protein-coding genes.…”

Section: Translation Of Sorfs In Mossmentioning

confidence: 99%

“…After this sORF BED file was intersected with the latest moss genome annotation V3.3 , the locations of the sORFs on transcripts were determined, resulting in the further classification of genic-sORFs into uORFs, dORFs, CDS-sORFs, and interlaced-sORFs. sORFs were denoted as upstream or downstream if they were fully separated from the longer protein-coding ORF as previously described (Calviello et al 2016;Samandi et al 2017).…”

Section: Sorf Classificationmentioning

confidence: 99%

Distinct types of short open reading frames are translated in plant cells

et al. 2019

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.

“…In recent studies, thousands of alternative proteins were experimentally detected in human cell lines (Vanderperre et al 2013; Samandi et al 2017). In P. patens , we found tens of thousands of sORFs (CDS-sORFs) that overlapped with the CDS of protein-coding genes, 305 of which were translatable.…”

Section: Discussionmentioning

confidence: 99%

Distinct types of short open reading frames are translated in plant cells

Fesenko

Kirov

Kniazev

et al. 2017

Preprint

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of ten plant species examined. Mass spectrometry analysis of proteomic and peptidomic datasets suggested that 584 sORFs located on distinct parts of mRNAs and long non-coding RNAs (lncRNAs) are translated, including 73 conservative sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Alternative splicing is likely involved in the excision of translatable sORFs from such transcripts. We identified a group of sORFs homologous to known protein domains and suggested they function as small interfering peptides. Functional analysis of candidate lncRNA-encoded peptides showed it to be involved in regulating growth and differentiation in moss. The high evolutionary rate and wide translation of sORFs suggest that they may provide a reservoir of potentially active peptides and their importance as a raw material for gene evolution. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.