Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prevalence of alternative ATG and non-ATG translation initiators and their regulatory effects across plants

ABSTRACT: We report the global profile of ribosome profilig to study the relationship between alternative translation initaiton sites and gene expression in tomato.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE143311 | GEO | 2020/08/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Prevalence of alternative ATG and non-ATG translation initiators and their regulatory effects across plants

Project description:Prevalence of alternative ATG and non-ATG translation initiators and their regulatory effects across plants

| PRJNA599965 | ENA

Translation initiation landscape of tomato-infecting virus

Project description:We report the global profile of ribosome profilig to reveal the in vivo translation initiation sites of tomato-infecting virus.

2022-05-04 | GSE160907 | GEO

Selective translation by alternative bacterial ribosomes

Project description:Selective translation by alternative bacterial ribosomes

| PRJNA525595 | ENA

Cell type specific profiling of alternative translation identifies novel protein isoforms in the mouse brain

Project description:Translation canonically begins at a single AUG and terminates at the stop codon, generating one protein species per transcript. However, some transcripts may use alternative initiation sites or sustain translation past their stop codon, generating multiple protein isoforms. Through other mechanisms such as alternative splicing, both neurons and glia exhibit remarkable transcriptional diversity, and these other forms of post-transcriptional regulation are impacted by neural activity and disease. Here, using ribosome footprinting, we demonstrate that alternative translation is likewise abundant in the central nervous system and modulated by stimulation and disease. First, in neuron/glia mixed cultures we identify hundreds of transcripts with alternative initiation sites and confirm the protein isoforms corresponding to a subset of these sites by mass spectrometry. Many of them modulate their alternative initiation in response to KCl stimulation, indicating activity-dependent regulation of this phenomenon. Next, we detect several transcripts undergoing stop codon readthrough thus generating novel C-terminally-extended protein isoforms in vitro. Further, by coupling Translating Ribosome Affinity Purification to ribosome footprinting to enable cell-type specific analysis in vivo, we find that several of both neuronal and astrocytic transcripts undergo readthrough in the mouse brain. Functional analyses of one of these transcripts, Aqp4, reveals readthrough confers perivascular localization, indicating readthrough can be a conserved mechanism to modulate protein function. Finally, we show that AQP4 readthrough is disrupted in multiple gliotic disease models. Our study demonstrates the extensive and regulated use of alternative translational events in the brain and indicates that some of these events alter key protein properties. [NOTE: this GEO series only contains in vivo data]

2019-01-14 | GSE115483 | GEO

N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

Project description:The integrated stress response (ISR) facilitates cellular adaptation to a variety of stress conditions via phosphorylation of the common target eIF2α. During ISR, the translation of certain stress-related mRNAs is upregulated in spite of global suppression of protein synthesis.The selective translation often relieson alternative mechanisms, such as leaky scanning or reinitiation, but the underlying mechanism remains incompletely understood. Here we report that,in response to amino acid starvation, the reinitiation of ATF4 is not only governed by eIF2α-controlled ternary complex availability, but is also subjected to regulation by mRNA methylation in the form of N6-methyladenosine (m6A). We demonstrate that m6A in the 5' untranslated region (5’ UTR) controls ribosome scanning and subsequent start codonselection. Global profiling of initiating ribosomes reveals widespread alternative translation events influenced by mRNA methylation. Consistently, Fto-transgenic mice manifest enhanced ATF4 expression, highlighting the critical role of 5’ UTR methylation in translational regulation of ISR at cellular and organismal levels.

2017-08-15 | GSE102659 | GEO

Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants.

Project description:Translation initiation is a key step determining protein synthesis. Studies have uncovered a number of alternative translation initiation sites (TISs) in mammalian mRNAs and showed their roles in reshaping the proteome. However, the extent to which alternative TISs affect gene expression across plants remains largely unclear. Here, by profiling initiating ribosome positions, we globally identified in vivo TISs in tomato and Arabidopsis and found thousands of genes with more than one TIS. Of the identified TISs, >19% and >20% were located at unannotated AUG and non-AUG sites, respectively. CUG and ACG were the most frequently observed codons at non-AUG TISs, a phenomenon also found in mammals. In addition, although alternative TISs were usually found in both orthologous genes, the TIS sequences were not conserved, suggesting the conservation of alternative initiation mechanisms but flexibility in using TISs. Unlike upstream AUG TISs, the presence of upstream non-AUG TISs was not correlated with the translational repression of main open reading frames, a pattern observed across plants. Also, the generation of proteins with diverse N-terminal regions through the use of alternative TISs contributes to differential subcellular localization, as mutating alternative TISs resulted in the loss of organelle localization. Our findings uncovered the hidden coding potential of plant genomes and, importantly, the constraint and flexibility of translational initiation mechanisms in the regulation of gene expression across plant species.

| S-EPMC7605272 | biostudies-literature

Selective translation by alternative bacterial ribosomes

Project description:Mycobacteria encode several additional alternative ribosomal proteins (AltRP) and the funtion of AltRP invovling in translation is little known. In this study, we investigate the different translation landscape of AltRibo and CanRibo and found AltRibo have a relative 5' reads accumlation and preferential codon usage.

2019-04-11 | GSE127827 | GEO

eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation

Project description:eIF1-eIF4G1 inhibitors uncover alternative translation activation of stress-response genes via enhanced ribosome loading and 5’UTR translation

| PRJNA701891 | ENA

CERES is an eIF4E-interacting protein that forms non-canonical translation initiation complexes and modulates translation during the diel cycle in plants

Project description:Translation is a fundamental step in gene expression that regulates multiple developmental and stress responses. One key step of translation is the association between eIF4E and eIF4G. This process is regulated in different eukaryotes by proteins which bind to eIF4E and block the formation of the eIF4E/eIF4G complex. Here, we report the discovery of CERES, the first functional eIF4E regulator described in plants. CERES is a modular protein that contains a LRR domain and a canonical eIF4E binding site (4E-BS), critical for CERES interaction with eIF4E in planta. CERES/eIF4E interaction excludes eIF4G from the complex. Despite this observation, CERES promotes translation in vivo interacts with eIF4A and with eIF3 in vivo and cosediments with translation initiation complexes in sucrose gradients. Moreover, ceres mutants display a sharp increase of the 80S peak and a reduction of polysome content at specific periods of the diel cycle. Super-resolution ribosome profiling demonstrates that these mutants show a change of translation efficiency of mRNAs related to light response and glucose management. Consistently, these mutants show a hypersensitive response to glucose. These data show that CERES is a “non canonical” translation initiation factor that, through the formation of alternative translation initiation complexes, modulates translation during the light cycle in plants.

2019-12-04 | GSE124290 | GEO

Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells

Project description:Ribosome profiling with translation inhibitors reveals pervasive translation in murine ES cells. Ribosome profiling or stranded RNAseq (ribominus) with murine embryonic stem cells treated with either DMD-pateamineA, Puromycin, Harringtonine or vehicle (no drug control). Two replicates per condition.

2016-01-12 | E-GEOD-67741 | 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