scholarly journals Porcine Amelogenin: Alternative Splicing, Proteolytic Processing, Protein-Protein Interactions, and Possible Functions

2011 ◽  
Vol 53 (3) ◽  
pp. 275-283 ◽  
Author(s):  
Yasuo Yamakoshi
2016 ◽  
Author(s):  
Héctor Climente-González ◽  
Eduard Porta-Pardo ◽  
Adam Godzik ◽  
Eduardo Eyras

SummaryAlternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remains mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer and some of them could potentially be considered alternative splicing drivers (AS-drivers).


2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jessica Petko ◽  
Mathura Thileepan ◽  
Molly Sargen ◽  
Victor Canfield ◽  
Robert Levenson

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zakaria Louadi ◽  
Maria L. Elkjaer ◽  
Melissa Klug ◽  
Chit Tong Lio ◽  
Amit Fenn ◽  
...  

AbstractAlternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking. To mitigate this, we developed NEASE, a tool integrating pathways with structural annotations of protein-protein interactions to functionally characterize AS events. We show in four application cases how NEASE can identify pathways contributing to tissue identity and cell type development, and how it highlights splicing-related biomarkers. With a unique view on AS, NEASE generates unique and meaningful biological insights complementary to classical pathways analysis.


eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Daniel Dominguez ◽  
Yi-Hsuan Tsai ◽  
Robert Weatheritt ◽  
Yang Wang ◽  
Benjamin J Blencowe ◽  
...  

Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control.


2001 ◽  
Vol 114 (21) ◽  
pp. 3873-3884 ◽  
Author(s):  
Zoe Waibler ◽  
Annette Schäfer ◽  
Anna Starzinski-Powitz

ARVCF, a member of the catenin family, is thought to contribute to the morphoregulatory function of the cadherin-catenin complex. Recently, we reported the isolation and characterisation of murine ARVCF (mARVCF), particularly its interaction with M-cadherin. Here, we describe the identification of novel mARVCF isoforms that arise by alternative splicing. At the N-terminus, alternative splicing results in the inclusion or omission of a coiled-coil region probably important for protein-protein interactions. At the C-terminus, four isoforms also differ by domains potentially important for selective protein-protein interaction. The eight putative mARVCF isoforms were expressed as EGFP-fusion proteins in six different cell lines that exhibit a distinct pattern of cadherins. Apparently, binding of the mARVCF isoforms to M-, N-, or E-cadherin is generally unaffected by their altered N- and C-termini, as revealed by the MOM recruitment assay. However, mARVCF isoforms reproducibly exhibit differential localisation in distinct cellular environments. For example, mARVCF isoforms are unable to colocalise with N-cadherin in EJ28 carcinoma cells but do so in HeLa cells. Our results suggest that the subcellular localisation of mARVCF may be determined not only by the presence or absence of an appropriate interaction partner, in this case cadherins, but also by the cellular context.


2012 ◽  
Vol 18 (A) ◽  
pp. 35
Author(s):  
A Colantoni ◽  
F Ferrè ◽  
M Helmer-Citterich

1992 ◽  
Vol 3 (1) ◽  
pp. 31-36 ◽  
Author(s):  
N. C. Collier ◽  
S. P. Adams ◽  
H. Weingarten ◽  
M. J. Schlesinger

Peptides, corresponding to amino acid sequences in the cytoplasmic domains of the transmembranal glycoproteins encoded by Sindbis and vesicular stomatitis viruses, inhibited release of virus particles and infectious virus when added to infected cells for a 2h period during a one-cycle growth curve. Each inhibitory peptide was specific for its intended virus. The shortest peptide with antiviral activity for Sindbis virus contained six amino acids, and a related peptide that was acylated at the amino terminus with octanoic acid was ten-fold more potent as an inhibitor. Neither of these peptides affected the synthesis of viral structural proteins, but a third peptide inhibited proteolytic processing of the Sindbis virus E2 glycoprotein. Inhibition of vesicular stomatitis virus particle release was dose-dependent in the range of 50–400 μg ml−1 for a peptide corresponding to the G glycoprotein cytoplasmic domain. We postulate that these peptides competitively inhibit attachment of the glycoprotein to intracellular virus structures during assembly of the virion. Thus, drugs, based on peptides that mimic the protein-protein interactions required for virus assembly, may have therapeutic potential.


2012 ◽  
Vol 18 (A) ◽  
pp. 86
Author(s):  
V Bianchi ◽  
A Colantoni ◽  
M Helmer-Citterich ◽  
F Ferrè

2020 ◽  
Vol 49 (D1) ◽  
pp. D309-D318 ◽  
Author(s):  
Zakaria Louadi ◽  
Kevin Yuan ◽  
Alexander Gress ◽  
Olga Tsoy ◽  
Olga V Kalinina ◽  
...  

Abstract Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of individual exons on a systems biology level. We overcome this barrier by integrating protein-protein interactions, domain-domain interactions and residue-level interactions information to lift exon expression analysis to a network level. Our user-friendly database DIGGER is available at https://exbio.wzw.tum.de/digger and allows users to seamlessly switch between isoform and exon-centric views of the interactome and to extract sub-networks of relevant isoforms, making it an essential resource for studying mechanistic consequences of alternative splicing.


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