Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

ABSTRACT: We describe the identification of novel non-canonical ORFs in murine macrophages

ORGANISM(S): Mus musculus

PROVIDER: GSE120762 | GEO | 2018/12/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

The translation of non-canonical open reading frames controls mucosal immunity.

Project description: Not available

| S-EPMC6939389 | biostudies-literature

The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

Project description:The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

| PRJNA494404 | ENA

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma

Project description:A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a step-wise approach to employ multiple CRISPR-Cas9 screens to elucidate functional non-canonical ORFs implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream open reading frames (uORFs) exhibited selective functionality independent of the main coding sequence. One of these, ASNSD1-uORF or ASDURF, was upregulated, associated with the MYC family oncogenes, and was required for medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future cancer genomics studies seeking to define new cancer targets.

| EGAS00001007426 | EGA

Pervasive functional translation of noncanonical open reading frames

Project description:Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). Here, we exploit a systematic CRISPR-based screening strategy to identify hundreds of non-canonical CDSs that are essential for cellular growth and whose disruption elicit specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds that are presented by the HLA system. Interestingly, we find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same mRNA, thus revealing the diverse use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

2020-03-14 | GSE131650 | GEO

Pervasive functional micropeptides in humans encoded by non-canonical open reading frames

Project description:Protein-coding regions of the genome continue to expand beyond canonical annotations and remain incompletely understood. Despite recent reports demonstrating important cellular functions played by micropeptides from unannotated open reading frames (ORFs), there exists no systematic method to fully uncover the prevalence of functional ORFs and their encoded peptides. Here, using ribosome profiling and mass spectrometry based proteomics, we reveal pervasive translation of ORFs previously annotated as non-coding, including those encoded on long non-coding RNAs (lncRNA ORFs) and upstream regions of protein-coding messages (uORFs). Cross-validation of novel ORFs in six different cell lines via HLA peptidomics confirm their allotype-specific MHC receptor presentation and their engagement with the endogenous HLA processing machinery. We further developed systematic CRISPR-based screens to show that hundreds of these ORFs are essential for cellular growth and encode stable, functional peptides that play diverse roles in cells. By tagging with a split-GFP system, we show that many of the peptides have specific cellular localization patterns and form functional protein complexes. We uncovered uORFs encoding stable peptides that interact with the downstream protein encoded on the same mRNA, suggesting possible regulatory or feedback roles from the bicistronic message in addition to the previously assumed role of uORFs in translational repression. Our results uncover functional micropeptides encoded in the human genome with essential roles in diverse biological processes.

2020-03-06 | PXD014031 | Pride

Translation of small downstream ORFs enhances translation of canonical main open reading frames.

Project description: Not available

| S-EPMC7459409 | biostudies-literature

Identification of translated small open reading frames in lymphocytes

Project description:Open reading frames (ORFs) are the genomic DNA sequences that have the potential to be translated. Genome annotation pipelines dismiss translation products of small ORFs (smORFs) of less than 100 codons (<300 nucleotides) as being unlikely to have a biological function. In this study, we systematically characterized smORFs in mouse B and T cells under different conditions and predicted a total of 5744 unique actively translated smORFs. We then extended our analysis to ORFs of 101-200 codons in length and predicted 945 of such longer translation products. Additionally, our results have suggested the existence of candidate secreted micropeptides. Furthermore, verifying their existence and identifying their functions will be essential and potentially lead to useful applications.

2021-04-28 | GSE154491 | GEO

CRSPR/Cas9 gene knockout screen identifies colorectal cancer dependency on cryptic open reading frames

Project description:Emerging evidence suggests that the cryptic translation beyond the annotated translatome may yield proteins with important function. However, the role and function mechanism of these cryptic ORFs in complex diseases such as cancer remain largely unknown. To fill this gap, we combined ribosome profiling and CRISPR/Cas9 screen to systematically identify the colorectal cancer (CRC) dependency on cryptic ORFs.

2023-08-06 | GSE184322 | GEO

Pervasive functional translation of noncanonical human open reading frames.

Project description: Not available

| S-EPMC7289059 | biostudies-literature

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

Project description:We present a genome-wide assessment of small open reading frames (smORF) translation by ribosomal profiling of polysomal fractions in Drosophila S2 cell. In this way, mRNAs bound by multiple ribosomes and hence actively translated can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits. Ribosomal profiling of large and small polysomal fractions in Drosophila S2 cells to assess translation of smORFs

2014-09-11 | E-GEOD-60384 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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