Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames

ABSTRACT: All species continuously evolve small open reading frames (sORFs) that can be templated for protein synthesis and may provide raw material for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionary young and emerged de novo. We additionally discovered 221 yet uncataloged peptides smaller than 16 amino acids, for which we found evidence of translation in human and rodent tissues. To investigate the potential bioactivity of microproteins and peptides translated from young and very small ORFs we established MiPRISMA: a mass spectrometry-based interactome screen with sequence motif resolution. We assessed 266 candidates and implicated several in essential cellular processes including splicing, translational regulation, and endocytosis, a subset of which we validate in cellular assays. MiPRISMA provides a scalable platform to characterize small and evolutionarily young proteins, shedding light on a largely unexplored territory of the putative human proteome.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Heart

SUBMITTER: Marieluise Kirchner

LAB HEAD: Philipp Mertins

PROVIDER: PXD036997 | Pride | 2023-02-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	220922_Nano_MP_LysC_List1_Hek_HeLa_K652.skyd	Other
	220922_Nano_MP_LysC_List1_allHearts.skyd	Other
	220922_Nano_MP_LysC_List2_HEK_HeLa_K562_allHearts.skyd	Other
	220922_Nano_MP_LysC_List3_HEK_HeLa_K562_allHearts.skyd	Other
	220922_Nano_MP_Trypsin_List1_HEK_HeLa_K562_allHearts.skyd	Other

Items per page:

1 - 5 of 103

Similar Datasets

MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part1

Project description:All species continuously evolve small open reading frames (sORFs) that can be templated for protein synthesis and may provide raw material for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionary young and emerged de novo. We additionally discovered 221 yet uncataloged peptides smaller than 16 amino acids, for which we found evidence of translation in human and rodent tissues. To investigate the potential bioactivity of microproteins and peptides translated from young and very small ORFs we established MiPRISMA: a mass spectrometry-based interactome screen with sequence motif resolution. We assessed 266 candidates and implicated several in essential cellular processes including splicing, translational regulation, and endocytosis, a subset of which we validate in cellular assays. MiPRISMA provides a scalable platform to characterize small and evolutionarily young proteins, shedding light on a largely unexplored territory of the putative human proteome.

2023-02-17 | PXD033651 | Pride

MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part4

2023-02-17 | PXD033631 | Pride

MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part3

2023-02-17 | PXD033630 | Pride

MiPRISMA: Interactome profiling of small peptides and young microproteins translated from human short open reading frames Part2

2023-02-17 | PXD033629 | Pride

Expression analysis of Shigella flexneri 2a strain 301

Project description:Investigation of whole genome gene expression to identify overlooked sRNAs and sORFs. Background The completion of numerous genome sequences has introduced an era of whole-genome study. However, many real genes, including small RNAs (sRNAs) and small ORFs (sORFs), are missed in genome annotation. In order to improve genome annotation, we sought to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery or shigellosis. Results Firstly, we identified 64 sRNAs in Shigella which is experimentally validated in other bacteria based on sequence conservation. Secondly, among possible approaches to search for sRNAs, we employed computer-based and tiling array based methods, followed by RT-PCR and northern blots. This allowed us to identify 12 sRNAs in Shigella flexneri strain 301. We also find 29 candidate sORFs. Conclusions This investigation provides an updated and comprehensive annotation of the Shigella genome, increases the expected numbers of sORFs and sRNAs with the corresponding impact on future functional genomics and proteomics studies. Our method can be used for the large scale reannotation of sRNAs and sORFs in any microbe whose genome sequence is available. Study using total RNA recovered from five conditions.

2011-06-27 | E-GEOD-22800 | biostudies-arrayexpress

The small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:Ribosome profiling was applied for the first time on S. meliloti to generate a translatome map. Our work reveals active translation for several ORFs including small ORFs (sORFs). In addition, our ribosome profiling data led to the discovery of several translated non-annotated sORFs. Translation of these non-annotated sORFs was validated by proteomics and western blotting.

2023-02-14 | GSE206492 | GEO

Expression analysis of Shigella flexneri 2a strain 301

2011-06-27 | GSE22800 | GEO

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryo reveals hundreds of conserved translating sORFs

Project description:Identification of translating small open reading frames (sORFs) through deep sequecing of ribosome-associated poly-adenylated RNA and conservation analysis in early Drosophila embryo

2017-03-05 | E-MTAB-4571 | biostudies-arrayexpress

TINCR lncRNA encodes a ubiquitin-like protein that activates CDC42, promotes epithelial differentiation and suppresses tumor growth

Project description:The human transcriptome contains thousands of small open reading frames (sORFs) that have been largely overlooked because of their small size. Some of these sORFs code for bioactive small proteins although none have been associated to the regulation of cell identity. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein with a SUMO interacting motif (SIM) that is expressed in many epithelia. pTINCR binds to SUMO and modifies global cell SUMOylation patterns. One of its main targets is CDC42, a Rho-GTPase critical for actin cytoskeleton remodeling and for epidermal differentiation. pTINCR increases CDC42 SUMOylation and promotes its activation in a SIM-dependent manner. pTINCR is necessary and sufficient for epithelial cell differentiation in vitro, and promotes epidermal differentiation in vivo. Consistent with its pro-differentiation role, pTINCR expression is lost in human cutaneous squamous cell carcinomas (cSCC), and its overexpression reduces cSCC growth in vitro and in vivo. Moreover, pTINCR is a target of the tumor suppressor p53, and the expression of pTINCR in epithelial cancers correlates with better prognosis. Our results identify pTINCR as a novel regulator of epithelial differentiation with tumor suppressor activity. More generally, our findings suggest that the proteome encoded by previously assumed non-coding RNAs can indeed be a source of new regulators of cell identity relevant for cancer.

2022-09-28 | GSE175463 | GEO

Deep sequencing of small RNAs of the pig brain

Project description:Small RNAs have been emerged as gene regulators in variety of biological pathways and functions including physiological stress and anxiety response system. In this study, we profiled and cataloged small non-coding RNAs of the pig brain in three different brain regions; the amygdala, hippocampus and hypothalamus obtained from 20 adult pigs. In addition, the adrenal gland was also included in the analysis.

2020-12-01 | E-MTAB-7499 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data