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      Alternative Splicing and Protein Diversity: Plants Versus Animals

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          Abstract

          Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.

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          Most cited references113

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          The evolutionary landscape of alternative splicing in vertebrate species.

          How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.
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            Understanding alternative splicing: towards a cellular code.

            In violation of the 'one gene, one polypeptide' rule, alternative splicing allows individual genes to produce multiple protein isoforms - thereby playing a central part in generating complex proteomes. Alternative splicing also has a largely hidden function in quantitative gene control, by targeting RNAs for nonsense-mediated decay. Traditional gene-by-gene investigations of alternative splicing mechanisms are now being complemented by global approaches. These promise to reveal details of the nature and operation of cellular codes that are constituted by combinations of regulatory elements in pre-mRNA substrates and by cellular complements of splicing regulators, which together determine regulated splicing pathways.
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              The Arabidopsis Information Resource (TAIR): gene structure and function annotation

              The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submissions from the research community. New developments at TAIR include the addition of the GBrowse genome viewer to the TAIR site, a redesigned home page, navigation structure and portal pages to make the site more intuitive and easier to use, the launch of several TAIR web services and a new genome annotation release (TAIR7) in April 2007. A combination of manual and computational methods were used to generate this release, which contains 27 029 protein-coding genes, 3889 pseudogenes or transposable elements and 1123 ncRNAs (32 041 genes in all, 37 019 gene models). A total of 681 new genes and 1002 new splice variants were added. Overall, 10 098 loci (one-third of all loci from the previous TAIR6 release) were updated for the TAIR7 release.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                12 June 2019
                2019
                : 10
                : 708
                Affiliations
                [1] 1School of Human and Life Sciences, Canterbury Christ Church University , Canterbury, United Kingdom
                [2] 2Department of Biology and Program in Cell and Molecular Biology, Colorado State University , Fort Collins, CO, United States
                Author notes

                Edited by: Ezequiel Petrillo, CONICET Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Argentina

                Reviewed by: Federico Damian Ariel, Instituto de Agrobiotecnología del Litoral (IAL), Argentina; John William Slessor Brown, University of Dundee, United Kingdom

                *Correspondence: Naeem H. Syed, naeem.syed@ 123456canterbury.ac.uk

                These authors have contributed equally to this work

                This article was submitted to Plant Physiology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2019.00708
                6581706
                31244866
                3b852367-4cf3-4739-a90c-0eae547a15f3
                Copyright © 2019 Chaudhary, Khokhar, Jabre, Reddy, Byrne, Wilson and Syed.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 08 March 2019
                : 13 May 2019
                Page count
                Figures: 3, Tables: 1, Equations: 0, References: 153, Pages: 14, Words: 0
                Categories
                Plant Science
                Review

                Plant science & Botany
                alternative splicing,co-transcriptional splicing,protein diversity,intron retention,nmd,splicing memory,epigenetic modifications

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