Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD006638
PROVIDER: PRJNA401719 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6000350.fastq.gz | Fastqsanger.gz | |||
| SRR6000360.fastq.gz | Fastqsanger.gz | |||
| SRR6000351.fastq.gz | Fastqsanger.gz | |||
| SRR6000361.fastq.gz | Fastqsanger.gz | |||
| SRR6000352.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition. The levels of iMet retention are inversely correlated with cellular proliferation rates. Further, despite the increased MetAP2 expression observed upon MetAP1 deletion and as inferred from the iMet retention profiles observed, MetAP2 was unable to restore processing of MS-, MP- and MA- N-termini, indicating the higher activity of MetAP1 over these N-termini. Proteome and transcriptome expression profiling point to differential expression of proteins implicated in lipid metabolism, cytoskeleton organization, cell proliferation and protein synthesis upon perturbation of MetAP activity.
2018-01-12 | GSE103405 | GEO
Project description:To understand the impact of alternative translation initiation on a proteome, we performed the first study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes. Overall, we monitored the stability of 1,941 human N-terminal proteoforms, including 147 N-terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine. Ribosome profiling of lactimidomycin and cycloheximide treated human Jurkat T-lymphocytes
2015-10-23 | E-GEOD-74279 | biostudies-arrayexpress
Project description:To understand the impact of alternative translation initiation on a proteome, we performed the first study on protein turnover using positional proteomics and ribosome profiling to distinguish between N-terminal proteoforms of individual genes. Overall, we monitored the stability of 1,941 human N-terminal proteoforms, including 147 N-terminal proteoform pairs that originate from alternative translation initiation, alternative splicing or incomplete processing of the initiator methionine.
2015-10-23 | GSE74279 | GEO
Project description:Excision of the N-terminal initiator methionine (iMet) from nascent peptide chains is an essential and omnipresent protein modification carried out by Methionine aminopetidases (MetAPs) and accounting for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of MetAP1 deletion and MetAP inhibition in general. While the levels of iMet retention are inversely correlated with cellular proliferation rates, deletion of MetAP1 was in part rescued by the increased MetAP2 expression and activity profiles observed.
2018-01-10 | PXD006638 | Pride
Project description:While previous studies suggest that many mRNAs containing more than one translation initiation site (TIS), the biological significance of most alternative TISs and their protein isoform (proteoform) products remains undetermined. Here we show that alternative translation initiation at a CUG and an AUG TIS in neuronal pentraxin receptor (NPR) mRNA produces two proteoforms, and their relative abundance is regulated by both neuronal activity as well as an adjacent RNA secondary structure. Downstream AUG initiation transformed the N-terminal transmembrane domain into a signal peptide, thereby converting NPR to a secreted factor sufficient to promote synaptic clustering of AMPA-type glutamate receptors. Changing the relative proteoform ratio, but not the overall NPR abundance reduces AMPA receptor in parvalbumin (PV)-positive interneurons and induces changes in learning behaviors in mice. In addition to NPR, N-terminal extensions of C1q-like synaptic organizers, mediated by upstream AUU start codons, anchor these otherwise secreted factors to the membrane. Thus, our results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a widespread mechanism to diversify protein localization and functions.
2024-09-23 | GSE255191 | GEO
Project description:Various forms of the protein, called proteoform, are generated by co- or post-translational modification, alternative splicing and alternative translation initiation site, resulting in interactions between ribosomes, mRNAs, tRNAs, and various enzymes. Here, we introduce a N-terminal peptide enrichment method (Nrich) using a negative selection on filter for the N-terminal peptides with two chemical reagents for labeling free amine and two endoproteases. We identified 6,525 acetylated (or partially acetylated) and 6,570 free protein N-termini from 5,727 proteins. The protein N-termini can be classified into nine groups, such as initial methionine removed or retained, non-terminal residue, signal/transit/pro-peptide removal, putative alternative translational initiation site (methionine removed or retained) and unknown processing, suggesting various proteoform in vivo. In addition, novel protein N-termini was identified in 5`-UTR sequence with pseudo start codon using customized database. Nrich can obtain information about protein stability, localization and function through the observation of finished N-terminal sequence of mature protein.
2017-08-17 | PXD005583 | Pride
Project description:To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we monitored the stability of 1,941human N-terminal proteoforms, including 147 proteoform pairs with heterogeneous N-termini originating from the same gene that result from alternative translation initiation and incomplete processing of the initiator methionine. N-terminally truncated proteoforms were on average less abundant than canonical proteoforms, many had different stabilities and exhibited both faster and slower turnover rates compared to their canonical counterparts. These differences in stability did not depend on the length of truncation but on individual protein characteristics. In silico simulation of N-terminal proteoforms in macromolecular complexes revealed possible consequences for complex integrity such as replacement of unstable canonical subunits. The extent of intrinsic disorder in N-terminal protein structures correlated with turnover times, indicating that a change in the structural flexibility of protein N-termini in truncated proteoforms might impact proteoform stability. Interestingly, removal of the initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms while susceptibility for N-terminal acetylation, another common co-translational modification, did not seem to impact on turnover rates. Taken together, our findings reveal differences in protein stability between N-terminal proteoforms and point to a role for alternative translation initiation and co-translational initiator methionine removal in the overall regulation of proteome homeostasis.
2013-03-14 | PXD002091 | Pride
Project description:We report the application of RNA-seq for profiling gene transcription upon treatment of methyl bestatin (MeBs, aminopeptidase inhibitor) or brefeldin A (BFA, ER-to-Golgi transport inhibitor), compared to DMSO control. We found MeBs and BFA similarly upregulated genes pertinent to proteotoxic stress.
2022-11-15 | GSE200454 | GEO
Project description:Positional proteomics reveals differences in N-terminal proteoform stability
| PRJNA299254 | ENA
Project description:To understand the impact of alternative translation initiation on a proteome, we performed the first large-scale study of protein turnover rates in which we distinguish between N-terminal proteoforms pointing to translation initiation events. Using pulsed SILAC combined with N-terminal COFRADIC we monitored the stability of 1,941human N-terminal proteoforms, including 147 proteoform pairs with heterogeneous N-termini originating from the same gene that result from alternative translation initiation and incomplete processing of the initiator methionine. N-terminally truncated proteoforms were on average less abundant than canonical proteoforms, many had different stabilities and exhibited both faster and slower turnover rates compared to their canonical counterparts. These differences in stability did not depend on the length of truncation but on individual protein characteristics. In silico simulation of N-terminal proteoforms in macromolecular complexes revealed possible consequences for complex integrity such as replacement of unstable canonical subunits. The extent of intrinsic disorder in N-terminal protein structures correlated with turnover times, indicating that a change in the structural flexibility of protein N-termini in truncated proteoforms might impact proteoform stability. Interestingly, removal of the initiator methionine by methionine aminopeptidases reduced the stability of processed proteoforms while susceptibility for N-terminal acetylation, another common co-translational modification, did not seem to impact on turnover rates. Taken together, our findings reveal differences in protein stability between N-terminal proteoforms and point to a role for alternative translation initiation and co-translational initiator methionine removal in the overall regulation of proteome homeostasis.
2019-03-13 | MSV000083565 | MassIVE