scholarly journals Netrin Family: Role for Protein Isoforms in Cancer

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Caroline Suzanne Bruikman ◽  
Huayu Zhang ◽  
Anneli Maite Kemper ◽  
Janine Maria van Gils
Keyword(s):  
Cell Migration ◽  
Alternative Splicing ◽  
Special Interest ◽  
Tumor Biology ◽  
Family Members ◽  
Axonal Guidance ◽  
Protein Isoforms ◽  
Family Role ◽  
Associated Proteins

Netrins form a family of secreted and membrane-associated proteins. Netrins are involved in processes for axonal guidance, morphogenesis, and angiogenesis by regulating cell migration and survival. These processes are of special interest in tumor biology. From the netrin genes various isoforms are translated and regulated by alternative splicing. We review here the diversity of isoforms of the netrin family members and their known and potential roles in cancer.

scholarly journals Splicing Regulators and Their Roles in Cancer Biology and Therapy

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Maria Roméria da Silva ◽  
Gabriela Alves Moreira ◽  
Ronni Anderson Gonçalves da Silva ◽  
Éverton de Almeida Alves Barbosa ◽  
Raoni Pais Siqueira ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cancer Biology ◽  
Single Gene ◽  
Tumor Biology ◽  
Sr Proteins ◽  
Protein Isoforms ◽  
Protein Expression Pattern ◽  
Regulatory Factors ◽  
Impact Pathways ◽  
Splicing Regulators

Alternative splicing allows cells to expand the encoding potential of their genomes. In this elegant mechanism, a single gene can yield protein isoforms with even antagonistic functions depending on the cellular physiological context. Alterations in splicing regulatory factors activity in cancer cells, however, can generate an abnormal protein expression pattern that promotes growth, survival, and other processes, which are relevant to tumor biology. In this review, we discuss dysregulated alternative splicing events and regulatory factors that impact pathways related to cancer. The SR proteins and their regulatory kinases SRPKs and CLKs have been frequently found altered in tumors and are examined in more detail. Finally, perspectives that support splicing machinery as target for the development of novel anticancer therapies are discussed.

Alternative splicing in plant abiotic stress responses

2020 ◽  
Vol 48 (5) ◽  
pp. 2117-2126
Author(s):  
Paola Punzo ◽  
Stefania Grillo ◽  
Giorgia Batelli
Keyword(s):  
Abiotic Stress ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Environmental Changes ◽  
Single Gene ◽  
Plant Stress ◽  
Protein Isoforms ◽  
Stress Adaptation ◽  
Associated Proteins ◽  
Stress Related Genes

Modifications of the cellular proteome pool upon stress allow plants to tolerate environmental changes. Alternative splicing is the most significant mechanism responsible for the production of multiple protein isoforms from a single gene. The spliceosome, a large ribonucleoprotein complex, together with several associated proteins, controls this pre-mRNA processing, adding an additional level of regulation to gene expression. Deep sequencing of transcriptomes revealed that this co- or post-transcriptional mechanism is highly induced by abiotic stress, and concerns vast numbers of stress-related genes. Confirming the importance of splicing in plant stress adaptation, key players of stress signaling have been shown to encode alternative transcripts, whereas mutants lacking splicing factors or associated components show a modified sensitivity and defective responses to abiotic stress. Here, we examine recent literature on alternative splicing and splicing alterations in response to environmental stresses, focusing on its role in stress adaptation and analyzing the future perspectives and directions for research.

Computation-assisted targeted proteomics of alternative splicing protein isoforms in the human heart

2021 ◽  
Vol 154 ◽  
pp. 92-96
Author(s):  
Yu Han ◽  
Silas D. Wood ◽  
Julianna M. Wright ◽  
Vishantie Dostal ◽  
Edward Lau ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Human Heart ◽  
Protein Isoforms ◽  
Targeted Proteomics

scholarly journals Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Dorothea Emig ◽  
Melissa S. Cline ◽  
Karsten Klein ◽  
Anne Kunert ◽  
Petra Mutzel ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Protein Interactions ◽  
Visual Analysis ◽  
Protein Isoforms ◽  
Interaction Networks ◽  
Protein Domain ◽  
Domain Interaction ◽  
Exon Arrays ◽  
Exon Expression ◽  
Splicing Patterns

SummaryProteins and their interactions are essential for the functioning of all organisms and for understanding biological processes. Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells. Splicing events that alter the protein structure and the domain composition can be responsible for the regulation of protein interactions and the functional diversity of different tissues. Discovering the occurrence of splicing events and studying protein isoforms have become feasible using Affymetrix Exon Arrays. Therefore, we have developed the versatile Cytoscape plugin DomainGraph that allows for the visual analysis of protein domain interaction networks and their integration with exon expression data. Protein domains affected by alternative splicing are highlighted and splicing patterns can be compared.

scholarly journals Estrogen-related Receptor β (ERRβ) – Renaissance Receptor or Receptor Renaissance?

2016 ◽  
Vol 14 (1) ◽  
pp. nrs.14002 ◽  
Author(s):  
Shailaja D. Divekar ◽  
Deanna M. Tiek ◽  
Aileen Fernandez ◽  
Rebecca B. Riggins
Keyword(s):  
Alternative Splicing ◽  
Nuclear Receptor ◽  
Family Members ◽  
Structure And Function ◽  
The Other ◽  
Orphan Nuclear Receptor ◽  
Nuclear Receptor Superfamily ◽  
And Function ◽  
The Impact ◽  
Estrogen Related Receptor

Estrogen-related receptors (ERRs) are founding members of the orphan nuclear receptor (ONR) subgroup of the nuclear receptor superfamily. Twenty-seven years of study have yet to identify cognate ligands for the ERRs, though they have firmly placed ERRα (ESRRA) and ERRγ (ESRRG) at the intersection of cellular metabolism and oncogenesis. The pace of discovery for novel functions of ERRβ (ESRRB), however, has until recently been somewhat slower than that of its family members. ERRβ has also been largely ignored in summaries and perspectives of the ONR literature. Here, we provide an overview of established and emerging knowledge of ERRβ in mouse, man, and other species, highlighting unique aspects of ERRβ biology that set it apart from the other two estrogen-related receptors, with a focus on the impact of alternative splicing on the structure and function of this receptor.

scholarly journals Drosophila p53 isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Ananya Chakravarti ◽  
Heshani N Thirimanne ◽  
Savanna Brown ◽  
Brian R Calvi
Keyword(s):  
Quality Control ◽  
Family Members ◽  
P53 Gene ◽  
Genotoxic Stress ◽  
Oocyte Quality ◽  
Protein Isoforms ◽  
Dna Breaks ◽  
P53 Family ◽  
Dna Lesion ◽  
P53 Isoforms

p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B are both required for the normal repair of meiotic DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is also required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.

scholarly journals Nonsense-associated alternative splicing as a putative reno-protective mechanism in Pkhd1cyli/Pkhd1cyli mutant mice

2021 ◽  
Author(s):  
Chaozhe Yang ◽  
Naoe Harafuji ◽  
Maryanne C. Odinakashukwu ◽  
Ljubica Caldovic ◽  
Ravindra Boddu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Kidney Disease ◽  
Protein Isoforms ◽  
Mutant Mice ◽  
Chromosome 1 ◽  
Recessive Mutation ◽  
Protective Mechanism ◽  
Biliary Disease ◽  
Polycystic Kidney ◽  
Cystic Liver

Autosomal recessive polycystic kidney disease (ARPKD) is a hereditary hepato-renal fibrocystic disorder and a significant genetic cause of childhood morbidity and mortality. Mutations in the Polycystic Kidney and Hepatic Disease 1 (PKHD1) gene cause all typical forms of ARPKD. Several mouse strains carrying diverse genetically engineered disruptions in the orthologous Pkhd1 gene have been generated. The current study describes a novel spontaneous mouse recessive mutation causing a cystic liver phenotype resembling the hepato-biliary disease characteristic of human ARPKD. Here we describe mapping of the cystic liver mutation to the Pkhd1 interval on Chromosome 1 and identification of a frameshift mutation within Pkhd1 exon 48 predicted to result in premature translation termination. Mice homozygous for the new mutation, symbollzed Pkhd1cyli, lack renal pathology, consistent with previously generated Pkhd1 mouse mutants that fail to recapitulate human kidney disease. We have identified a profile of alternatively spliced Pkhd1 renal transcripts that are distinct in normal versus mutant mice. The Pkhd1 transcript profile in mutant kidneys is consistent with predicted outcomes of nonsense-associated alternative splicing (NAS) and nonsense mediated decay (NMD). Overall levels of Pkhd1 transcripts in mutant mouse kidneys were reduced compared to kidneys of normal mice, and Pkhd1 encoded protein in mutant kidneys was undetectable by immunoblotting. We suggest that in Pkhd1cyli/Pkhd1cyli (cyli) mice, mutation-promoted Pkhd1 alternative splicing in the kidney yields transcripts encoding low-abundance protein isoforms lacking exon 48 encoded amino acid sequences that are sufficiently functional so as to attenuate expression of a renal cystic disease phenotype.

scholarly journals DoChaP: The Domain Change Presenter

2020 ◽  
Author(s):  
Shani T. Gal-Oz ◽  
Nimrod Haiat ◽  
Dana Eliyahu ◽  
Guy Shani ◽  
Tal Shay
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Protein Domains ◽  
Visual Presentation ◽  
Structural Effect ◽  
Protein Isoforms ◽  
Multiple Transcripts ◽  
Genome Wide ◽  
Health And Disease ◽  
Specific Alternative

AbstractAlternative RNA splicing results in multiple transcripts of the same gene, possibly encoding for different protein isoforms with different protein domains and functionalities. Whereas it is possible to manually determine the effect of a specific alternative splicing event on the domain composition of a particular encoded protein, the process requires the tedious integration of several data sources; it is therefore error prone and its implementation is not feasible for genome-wide characterization of domains affected by differential splicing. To fulfill the need for an automated solution, we developed the Domain Change Presenter (DoChaP), a web server for the visualization of the exon–domain association. DoChaP visualizes all transcripts of a given gene, the domains of the proteins that they encode, and the exons encoding each domain. The visualization enables a comparison between the transcripts and between the protein isoforms they encode for. The organization and visual presentation of the information makes the structural effect of each alternative splicing event on the protein structure easily identified. To enable a study of the conservation of the exon structure, alternative splicing, and the effect of alternative splicing on protein domains, DoChaP also facilitates an inter-species comparison of domain–exon associations. DoChaP thus provides a unique and easy-to-use visualization of the exon–domain association and its conservation between transcripts and orthologous genes and will facilitate the study of the functional effects of alternative splicing in health and disease.

Mammalian skeletal muscle C-protein: purification from bovine muscle, binding to titin and the characterization of a full-length human cDNA

1992 ◽  
Vol 102 (4) ◽  
pp. 769-778
Author(s):  
D.O. Furst ◽  
U. Vinkemeier ◽  
K. Weber
Keyword(s):  
Skeletal Muscle ◽  
Protein Sequencing ◽  
Protein Isoforms ◽  
Fast Method ◽  
Mammalian Skeletal Muscle ◽  
Terminal Sequence ◽  
C Protein ◽  
Human Sequence ◽  
Associated Proteins ◽  
Bovine Skeletal Muscle

We report a fast method for the isolation of homogeneous C-protein from bovine skeletal muscle. In electron micrographs C-protein appears as short rods with a relatively uniform length of about 50 nm. Protein sequencing shows a single N-terminal sequence. Radio-labelled C-protein strongly decorates titin II and myosin rods but not myosin heads. Binding to titin II is retained in preparations lacking titin-associated proteins. Antibodies to bovine C-protein were used to screen a lambda gt11 cDNA library constructed from fetal human skeletal muscle. Clone HC38 is 3833 bp long and encodes a protein of 1138 amino acid residues. The start of the predicted sequence fits the N-terminal sequence of the bovine protein. All partial sequences obtained from the bovine protein (348 residues) and the sequence deduced from a partial chicken cDNA (Einheber and Fischman, 1990) can be aligned along the human sequence. The sequences of human and chicken C-proteins share 50% identity and 70% similarity. Along the repeat patterns of the human protein the fibronectin (Fn)-like domains are better conserved than the immunoglobulin (Ig)-like domains. Regions of strong divergence between chicken fast C-protein and human slow C-protein may represent differences in C-protein isoforms.

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