Abstract:
:Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules such as miRNAs or siRNAs, also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-specific and depends on internal and external stimuli. Unfortunately, the mechanisms underlying RF biogenesis and function remain unclear. To better understand them, we employed RNA pull-down and mass spectrometry methods to characterize the interactions of seven RFs originating from tRNA, snoRNA and snRNA. By integrating our results with publicly available data on physical protein-protein interactions, we constructed an RF interactome network. We determined that the RF interactome comprises proteins generally different from those that interact with their parental full length RNAs. Proteins captured by the RFs were involved in mRNA splicing, tRNA processing, DNA recombination/replication, protein biosynthesis and carboxylic acid metabolism. Our data suggest that RFs can be endogenous aptamer-like molecules and potential players in recently revealed RNA-protein regulatory networks. SIGNIFICANCE: In the recent decade it has become evident that RNAs with well-known functions (for example tRNA, snoRNA or rRNA) can be cleaved to yield short fragments, whose role in cells remains only partially characterized. At the same time, unconventional interactions between mRNA and proteins without RNA-binding domains have been demonstrated, revealing novel layers of possible RNA-mediated regulation. Considering the above, we hypothesized that RNA fragments (RFs) can be endogenous aptamer-like molecules that unconventionally interact with proteins. In this study we identified protein partners of seven selected RFs. We found that RFs bind different set of proteins than their parental full length RNAs and identified proteins differentially bound by the particular RFs. These observations suggest biological relevance of the discovered interactions. Our data provide a novel perspective on the significance of RFs and point to this pool of molecules as to a rich collection of potential components of the recently discovered RNA-protein regulatory networks.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Jackowiak P,Lis A,Luczak M,Stolarek I,Figlerowicz Mdoi
10.1016/j.jprot.2018.10.007subject
Has Abstractpub_date
2019-02-20 00:00:00pages
173-183eissn
1874-3919issn
1876-7737pii
S1874-3919(18)30374-9journal_volume
193pub_type
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journal_title:Journal of proteomics
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abstract::Knowledge of the accurate copy number of HLA class I presented ligands is important in fundamental and clinical immunology. Currently, the best copy number determinations are based on mass spectrometry, employing single reaction monitoring (SRM) in combination with a known amount of isotopically labeled peptide. The m...
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2016.07.020
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journal_title:Journal of proteomics
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journal_title:Journal of proteomics
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.07.001
更新日期:2018-08-15 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章,评审
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pub_type: 杂志文章
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journal_title:Journal of proteomics
pub_type: 临床试验,杂志文章,多中心研究
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更新日期:2012-12-05 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.12.002
更新日期:2019-04-30 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.06.010
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abstract::Reproductive stage is very sensitive to various forms of environmental stresses such as drought stress. The proteomic analysis of anther during pollen development in response to drought stress was performed using a label-free quantitative shotgun proteomic technique to define the underlying molecular principles in two...
journal_title:Journal of proteomics
pub_type: 杂志文章
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2016.04.049
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.09.016
更新日期:2019-02-10 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.01.011
更新日期:2018-03-30 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2013.04.010
更新日期:2014-01-31 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章,评审
doi:10.1016/j.jprot.2017.09.010
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pub_type: 杂志文章
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2014.09.003
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2012.03.013
更新日期:2012-06-18 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2015.07.025
更新日期:2015-11-03 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2010.07.002
更新日期:2010-11-10 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2009.11.012
更新日期:2010-03-10 00:00:00
abstract:UNLABELLED:The mechanisms underlying resistance to challenge by gastrointestinal nematode parasites in sheep are complex. Using DIGE, we profiled ovine lymph proteins in lambs with host resistance (R), resilience (Ri) or susceptibility (S) to a daily trickle challenge with the nematode Trichostrongylus colubriformis. E...
journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2014.07.017
更新日期:2014-09-23 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2019.103541
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2019.02.001
更新日期:2019-03-30 00:00:00
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journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2009.12.014
更新日期:2010-03-10 00:00:00
abstract::Glycoproteins play pivotal roles in a series of biological processes and their glycosylation patterns need to be structurally and functionally characterized. However, the lack of versatile methods to release N-glycans as functionalized forms has been undermining glycomics studies. Here a novel method is developed for ...
journal_title:Journal of proteomics
pub_type: 杂志文章
doi:10.1016/j.jprot.2018.06.002
更新日期:2018-09-15 00:00:00