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Current Opinion in Neurobiology Aug 2020The synaptotagmin family of molecules is known for regulating calcium-dependent membrane fusion events. Mice and humans express 17 synaptotagmin isoforms, where most... (Review)
Review
The synaptotagmin family of molecules is known for regulating calcium-dependent membrane fusion events. Mice and humans express 17 synaptotagmin isoforms, where most studies have focused on isoforms 1, 2, and 7, which are involved in synaptic vesicle exocytosis. Recent work has highlighted how brain function relies on additional isoforms, with roles in postsynaptic receptor endocytosis, vesicle trafficking, membrane repair, synaptic plasticity, and protection against neurodegeneration, for example, in addition to the traditional concept of synaptotagmin-mediated neurotransmitter release - in neurons as well as glia, and at different timepoints. In fact, it is not uncommon for the same isoform to feature several splice isoforms, form homo- and heterodimers, and function in different subcellular locations and cell types. This review aims to highlight the diversity of synaptotagmins, offers a concise summary of key findings on all isoforms, and discusses different ways of grouping these.
Topics: Animals; Calcium; Exocytosis; Humans; Membrane Fusion; Mice; Nerve Tissue Proteins; Protein Isoforms; Synaptotagmin I; Synaptotagmins
PubMed: 32663762
DOI: 10.1016/j.conb.2020.04.006 -
Nature Methods Apr 2022
Topics: Amino Acid Sequence; Protein Isoforms
PubMed: 35396478
DOI: 10.1038/s41592-022-01472-9 -
Journal of Molecular Biology Aug 2017Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among... (Review)
Review
Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.
Topics: Aging; Animals; Gene Expression Profiling; Gene Expression Regulation; Humans; Protein Isoforms; RNA Splicing
PubMed: 28684248
DOI: 10.1016/j.jmb.2017.06.019 -
Handbook of Experimental Pharmacology 2017Actin is the central building block of the actin cytoskeleton, a highly regulated filamentous network enabling dynamic processes of cells and simultaneously providing... (Review)
Review
Actin is the central building block of the actin cytoskeleton, a highly regulated filamentous network enabling dynamic processes of cells and simultaneously providing structure. Mammals have six actin isoforms that are very conserved and thus share common functions. Tissue-specific expression in part underlies their differential roles, but actin isoforms also coexist in various cell types and tissues, suggesting specific functions and preferential interaction partners. Gene deletion models, antibody-based staining patterns, gene silencing effects, and the occurrence of isoform-specific mutations in certain diseases have provided clues for specificity on the subcellular level and its consequences on the organism level. Yet, the differential actin isoform functions are still far from understood in detail. Biochemical studies on the different isoforms in pure form are just emerging, and investigations in cells have to deal with a complex and regulated system, including compensatory actin isoform expression.
Topics: Actins; Animals; Humans; Mutation; Protein Isoforms
PubMed: 27757757
DOI: 10.1007/164_2016_43 -
Genome Biology Mar 2022The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the...
BACKGROUND
The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g., PacBio or Oxford Nanopore) provides full-length transcripts which can be used to predict full-length protein isoforms.
RESULTS
We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data to enable detection of protein isoforms previously intractable to MS-based detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis.
CONCLUSIONS
Our work suggests that the incorporation of long-read sequencing and proteomic data can facilitate improved characterization of human protein isoform diversity. Our first-generation pipeline provides a strong foundation for future development of long-read proteogenomics and its adoption for both basic and translational research.
Topics: Alternative Splicing; Humans; Protein Isoforms; Proteogenomics; Proteomics; Sequence Analysis, RNA; Transcriptome
PubMed: 35241129
DOI: 10.1186/s13059-022-02624-y -
Bioinformatics (Oxford, England) Feb 2022RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not...
MOTIVATION
RNA expression at isoform level is biologically more informative than at gene level and can potentially reveal cellular subsets and corresponding biomarkers that are not visible at gene level. However, due to the strong 3' bias sequencing protocol, mRNA quantification for high-throughput single-cell RNA sequencing such as Chromium Single Cell 3' 10× Genomics is currently performed at the gene level.
RESULTS
We have developed an isoform-level quantification method for high-throughput single-cell RNA sequencing by exploiting the concepts of transcription clusters and isoform paralogs. The method, called Scasa, compares well in simulations against competing approaches including Alevin, Cellranger, Kallisto, Salmon, Terminus and STARsolo at both isoform- and gene-level expression. The reanalysis of a CITE-Seq dataset with isoform-based Scasa reveals a subgroup of CD14 monocytes missed by gene-based methods.
AVAILABILITY AND IMPLEMENTATION
Implementation of Scasa including source code, documentation, tutorials and test data supporting this study is available at Github: https://github.com/eudoraleer/scasa and Zenodo: https://doi.org/10.5281/zenodo.5712503.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Gene Expression Profiling; Sequence Analysis, RNA; Protein Isoforms; Software; RNA, Messenger; RNA
PubMed: 34864849
DOI: 10.1093/bioinformatics/btab807 -
Cell Reports Methods Sep 2021Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal... (Review)
Review
Transcription start site (TSS) selection influences transcript stability and translation as well as protein sequence. Alternative TSS usage is pervasive in organismal development, is a major contributor to transcript isoform diversity in humans, and is frequently observed in human diseases including cancer. In this review, we discuss the breadth of techniques that have been used to globally profile TSSs and the resulting insights into gene regulation, as well as future prospects in this area of inquiry.
Topics: Humans; Promoter Regions, Genetic; Gene Expression Regulation; Protein Isoforms
PubMed: 34632443
DOI: 10.1016/j.crmeth.2021.100081 -
Cells Dec 2023Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying... (Review)
Review
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
Topics: Humans; Alternative Splicing; RNA, Messenger; Protein Isoforms; RNA Splicing Factors; Aging; Nonsense Mediated mRNA Decay
PubMed: 38132139
DOI: 10.3390/cells12242819 -
EMBO Reports Dec 2021All living organisms have developed processes to sense and address environmental changes to maintain a stable internal state (homeostasis). When activated, the p53... (Review)
Review
All living organisms have developed processes to sense and address environmental changes to maintain a stable internal state (homeostasis). When activated, the p53 tumour suppressor maintains cell and organ integrity and functions in response to homeostasis disruptors (stresses) such as infection, metabolic alterations and cellular damage. Thus, p53 plays a fundamental physiological role in maintaining organismal homeostasis. The TP53 gene encodes a network of proteins (p53 isoforms) with similar and distinct biochemical functions. The p53 network carries out multiple biological activities enabling cooperation between individual cells required for long-term survival of multicellular organisms (animals) in response to an ever-changing environment caused by mutation, infection, metabolic alteration or damage. In this review, we suggest that the p53 network has evolved as an adaptive response to pathogen infections and other environmental selection pressures.
Topics: Animals; Genes, p53; Homeostasis; Infections; Mutation; Protein Isoforms; Stress, Physiological; Tumor Suppressor Protein p53
PubMed: 34779563
DOI: 10.15252/embr.202153085 -
International Journal of Molecular... Nov 2018The insulin receptor (IR) mediates both metabolic and mitogenic effects especially when overexpressed or in clinical conditions with compensatory hyperinsulinemia, due... (Review)
Review
The insulin receptor (IR) mediates both metabolic and mitogenic effects especially when overexpressed or in clinical conditions with compensatory hyperinsulinemia, due to the metabolic pathway resistance, as obesity diabetes. In many cancers, IR is overexpressed preferentially as IR-A isoform, derived by alternative splicing of exon 11. The IR-A overexpression, and the increased IR-A:IR-B ratio, are mechanisms that promote the mitogenic response of cancer cells to insulin and IGF-2, which is produced locally by both epithelial and stromal cancer cells. In cancer IR-A, isoform predominance may occur for dysregulation at both mRNA transcription and post-transcription levels, including splicing factors, non-coding RNAs and protein degradation. The mechanisms that regulate IR isoform expression are complex and not fully understood. The IR isoform overexpression may play a role in cancer cell stemness, in tumor progression and in resistance to target therapies. From a clinical point of view, the IR-A overexpression in cancer may be a determinant factor for the resistance to IGF-1R target therapies for this issue. IR isoform expression in cancers may have the meaning of a predictive biomarker and co-targeting IGF-1R and IR-A may represent a new more efficacious treatment strategy.
Topics: Animals; Gene Expression Regulation, Neoplastic; Humans; Models, Biological; Neoplasms; Protein Isoforms; Receptor, Insulin
PubMed: 30453495
DOI: 10.3390/ijms19113615