A database of plant splice sites and splicing signals. Recent genomewide analysis of as using rnaseq has revealed that as is highly pervasive in plants. In this study we addressed the functional impact of alternative splicing in plants using a comparative analysis approach. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. Genomewide analysis of alternative splicing of premrna. Atubl5 regulates growth and development through premrna. Alternative splicing shapes transcriptome but not proteome. We downloaded tomato rnaseq sequence data from the ncbi sra database. Skip controls flowering time via the alternative splicing of. Those databases contain fulllength cdna sequences and partial ests from different types of libraries, but neither. In this paper, we collected all the known alternatively spliced genes in plants and developed a webbased relational database, the plant alternative splicing database. Although plenty of analyses of as in plants have been presented and a huge quantity of data produced, it is necessary to think about the most efficient way to display these data. Tools search against intron, exon and junction sequences in arabidopsis and rice.
Identification of spliced transcripts plays an important role in understanding the ecotypic responses and also has played fundamental role in understanding the regulome of plant species. Alternative splicing is coupled to rna surveillance and processing mechanisms, including nonsense mediated decay. Genetics of alternative splicing evolution during sunflower. Alternative splicing, or alternative rna splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. Database and analyses of known alternatively spliced genes in. An algorithm, based on expressed sequence tag est pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ests to search for as. Alternative splicing is required for stage differentiation in. Genomewide analyses of alternative splicing have established its nearly ubiquitous role in gene regulation in many organisms. Splicing decisions are affected by the combinatorial behavior of different splicing factors that bind to multiple binding sites in exons and introns. Plants versus animals article pdf available in frontiers in plant science 10 june 2019 with 355 reads how we measure reads. Alternative splicing is a phenomenon where different mature transcripts are created from a single premrna species. There are numerous factors that affect the process, but splice sites themselves along with the adjacent splicing signals are critical here. The impact of as alternative splicing is wellrecognized in animal systems as a key regulator of gene expression and proteome complexity. An increase in temperature promotes changes in plant morphology as well as the transition from the vegetative to the reproductive.
To understand how these sequence changes affect splicing, we created a database of these mutations. In a more recent study that combined data from a large collection of estcdna, 21. Although rna splicing is a conserved premrna processing event in eukaryotes, there are many plantspecific features of this process, including a low proportion of genes undergoing alternative splicing, a high level of intron retention and low level of exon skipping es, a small number of introns. Genomewide comparative analysis of alternative splicing in. The wrst section of this article discusses theoretical aspects of the problem. Skip controls flowering time via the alternative splicing.
Two arabidopsis r2r3type myb genes, atmyb59 and atmyb48, were found to undergo similar alternative splicing. Genomewide analysis of mrna splicing variants in higher plants. Mapping transcripts including mrna sequences, ests, and rnaseq reads to the genome allows identifying premrna alternative splicing. The specific pages associated with the cereal plants offer. Alternative splicing regulation in plants view all 15 articles. Based on these results, we showed that atubl5b positively regulates plant root elongation and development through premrna splicing with atprp38c in a. In eukaryotes, one premrna can generate multiple mrna transcripts by alternative splicing as, which expands transcriptome and proteome diversity. Extensive divergence in alternative splicing patterns after.
U12 splice site data were downloaded from u12db alioto 2007. This study is one of the first to investigate variation in alternative splicing during a major evolutionary transition. Alternative splicing in plants is largely an unexplored area of gene expression, as this phenomenon used to be considered rare. Similar to other eukaryotes, splicing is emerging as an important process affecting development and stress tolerance in plants. Light is one of the most important factors regulating plant growth and development. Cryptic peroxisomal targeting via alternative splicing and. Alternative splicing as plays a critical regulatory role in modulating transcriptome and proteome. Tomato solanum lycopersicum is an important vegetable and fruit crop. It is also partly supported by a grantinaid genome science for scientific research on priority areas from the ministry of education, science, sports, and culture in japan. The circadian clock is a complex piece of cellular machinery that can regulate. Alternative splicing as1 is a widespread mechanism increasing transcriptome complexity and proteome diversity. Alternative splicing has been found during abiotic and biotic stress and during development. Comparative crossspecies alternative splicing in plants.
Alternative splicing events occur in almost all physiological responses. Histone h3 lysine 36 methylation affects temperatureinduced. Most plant genes are interrupted by introns and the corresponding transcripts need to undergo premrna splicing to remove these intervening sequences. The specific pages associated with the cereal plants offer several endusers functionalities such as querying using the put id, gene id, keywords in functional annotation, pfam, or as event types as query fields. Here, using transcriptome and proteome profiling data, we analyzed as in two life forms of. Alternative splicing plays a critical role in maintaining. In particular, it increases the functional diversity of proteins. Global cotranscriptional splicing in arabidopsis and the.
Dec 30, 2014 in this study, we provide clear evidence that phytochrome controls not only transcription, but also alternative splicing in arabidopsis. Frontiers expanding alternative splicing identification by. Our results demonstrate that phytochrome simultaneously regulates two different aspects of gene expression, namely transcription and alternative splicing to mediate light responses in plants. Comparative crossspecies alternative splicing in plants ncbi nih. Light regulates plant alternative splicing through the. Sablok g, powell b, braessler j, yu f, min xj 2017 comparative landscape of alternative splicing in fruit plants. Genomewide analysis of heatsensitive alternative splicing. Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. This serves as control for alternative mrna splicing decisions, which demonstrates that coupling between transcription and splicing is important for a whole organism to respond to environmental cues. Mechanistic details and functional consequences of alternative splicing are discussed with a focus on the model plant arabidopsis thaliana. In the second section, we present two simple contexts in which to test and illuminate the principles and issues. We generated rna deep sequencing data rnaseq to measure genomewide mrna expression at the exon and genelevel. Plant alternative splicing database a catalog of alternatively splicing as events in cereal crops. Identification, evolution and alternative splicing profile.
Comparative landscape of alternative splicing in fruit plants. Alternative splicing in plan ts coming of age naeem 2 h. Alternative splicing as plays a critical regulatory role in modulating transcriptome and proteome diversity. In the current version, it provides data for eight plant species. Because of its genomic complexity, and because no genomic information is available in the public genbank database, the complete structure of the mrna transcript is unclear and there are limited molecular mechanism studies for ananas. It is widely believed that upon absorbing red light, phytochrome induces plant light responses by regulating the transcription of numerous target genes. To clarify this role, we obtained whole transcriptome rna sequencing data from rice oryza sativa roots grown in the presence or absence of. Brown1,3 1division 2 ofplant sciences, university dundeeat the james hutton institute, invergowrie, dd2 5da, scotland, uk. Oct 01, 2017 one difficulty when identifying alternative splicing as events in plants is distinguishing functional as from splicing noise. Alternative splicing as is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. Although genomewide studies have revealed complex as1 patterns in plants, whether as1.
To analyze global changes in as under salt stress, we obtained highcoverage 200 times rna sequencing data from arabidopsis thaliana seedlings that were treated. Detection and measurement of alternative splicing using. Pdf manipulating mrna splicing by base editing in plants. According to the ascribed role of as as a mechanism for expanding proteome diversity, a gene can become polymorph in its expression through an additional splice variant that encodes a different, yet functional protein. We thus took advantage of our rnaseq data to further examine alternative spicing events. May 28, 2019 tomato solanum lycopersicum is an important vegetable and fruit crop. The production of proteins with diverse domain rearrangements from the same gene is the main alternative splicing mechanism for pathogenresistance genes. Frontiers expanding alternative splicing identification.
Furthermore, it has been suggested that most as events are subject to tissuespecific regulation. Alternative splicing of premessenger rnas in plants in the. Alternative splicing of premessenger rna mrna is an important mechanism underlying ambient temperaturecontrolled responses in plants, yet its regulation is poorly understood. Alternative splicing plays crucial roles by influencing the diversity of the transcriptome and proteome and regulating protein structurefunction and gene expression. Alternative splicing is required for stage differentiation. Volker brendel, major professor thomas peterson philip becraft xun gu. Enter database browse the alternative splicing events in arabidopsis and rice. Alternative splicing as produces multiple mrna splicing variants from a single precursor transcript. Identification of alternative splicing events by rna. Mar 18, 2020 alternative splicing as plays a critical regulatory role in modulating transcriptome and proteome diversity. October 2008 update were used to find introns in the genes that are alternatively spliced. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Approximately 56% of these events are intron retention intronr, and only 8% are exon. Alternative splicing as can add significantly to genome complexity.
In the plant pathogen ustilago maydis and in aspergillus nidulans, both enzymes contain cryptic peroxisomal targeting signals that are activated by alternative splicing or translational. Alternative splicing as is an important posttranscriptional process that creates multiple mrna variants from a single premrna molecule, thereby enhancing the coding and regulatory potential of genomes. Alternative splicing as is a posttranscriptional regulatory mechanism for gene expression regulation. Pif4 and hookless1 impinge on common transcriptome and. Phytochrome controls alternative splicing to mediate light. Jun 12, 2019 alternative premrna splicing as is prevalent in plants and is involved in many interactions between plants and environmental stresses. In this study, we found that skip is required for the splicing of. Brendel v 2006 genomewide comparative analysis of alternative splicing in pl ants.
Alternative splicing as a regulator of early plant development. Genomewide analysis of splicing related genes and alternative splicing in plants by bingbing wang a dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of doctor of philosophy major. Briefly, the genome sequence for sweet orange data were downloaded from. Lee y, lee y, kim b, shin y, nam s, kim p, kim n, chung wh, kim j, lee s 2007 ecgene. Syed1, maria kalyna2, yamile marquez2, andrea barta and john w. Plants are thought to exhibit less as than animals. Recent genome sequencing analyses and increasing experimental evidence in flowering plants have revealed that as is far more prevalent than previously thought and plays crucial roles in the diversification of gene regulation. We performed highthroughput mrna sequencing to analyze light. An as database, eg, alternative splicing in plants asip, and genome browser tracks that are open source and easy to download may be the. An as database, eg, alternative splicing in plants asip, 12 and genome browser tracks that are open source and easy to download may be the best choice. Evolutionarily conserved alternative splicing across monocots.
We use a high throughput method to identify junctionbased conserved as events from rnaseq data across nine plant species. Alternative splicing as can significantly impact the transcriptome and proteome of a eukaryotic cell. Evolutionary character of alternative splicing in plants. The alternative splicing in plants database wang and brendel 2006.
A database of plant splice sites and splicing signals michal wojciech szczesniak. Genome wide comparative analysis of alternative splicing in plants. With the development of sequencing technologies, the detection of as in plants is coming of age 15. Legumes come to asip, thanks to the medicago genome sequencing project medicago and lotus data identified from samespecies and crossspecies estcdnas. Additionally, alternative splicing plays a key role in gene regulation. In plants, as is of growing importance as more genes are. Comparative analysis indicates that alternative splicing in.
Its genome was completely sequenced and there are also a large amount of available expressed sequence tags ests and short reads generated by rna sequencing rnaseq technologies. Shaping the arabidopsis transcriptome through alternative. Numerous recent studies revealed that alternative splicing allows plants to rapidly adjust to environmental. Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. First, we use a modiwed twointron yeast gene altered in the branch point of the wrst intron that. However, the role of as in maintaining mineral nutrient homeostasis in plants is largely unknown. The tomato solanum lycopersicum genome sequence was downloaded from. The work offers a comprehensive evaluation on the phylogenetics and conservation of splicing patterns of the plant spf30 splicing factor gene family. Rnasequencing of a timeseries of arabidopsis thaliana plants exposed to cold determines the timing of significant as changes. Analysis of alternative splicing in pl ants with bioinformatics tools. Download access all raw data, including genome sequences, estcdna. Plant growth and development are constantly influenced by temperature fluctuations.
Bmc plant biology 2008 crossspecies est alignments. Splicing is one of the major contributors to observed spatiotemporal diversification of transcripts and proteins in metazoans. As research in plants has made substantial progress in the past 45 years. We analyzed rna from wild and domesticated sunflowers to examine differentiation in splice patterns during domestication. Although many levels of gene expression are modulated by photoreceptors, regulation at the mrna splicing step remains unclear. Nov 16, 2015 alternative splicing as regulates multiple biological processes including flowering, circadian and stress response in plant. These splicing sites can be considered as canonical, since they produce a mature mrna translated into a functional protein. It is noteworthy to highlight that the previous estimates using. It is widespread in plants, and alteration of the levels of splicing factors leads to a wide variety of growth and developmental phenotypes. Alternative splicing data rna modification analysis omicx. Frontiers evolution of alternative splicing in eudicots. May 23, 2012 in the plant pathogen ustilago maydis and in aspergillus nidulans, both enzymes contain cryptic peroxisomal targeting signals that are activated by alternative splicing or translational. Mapping transcripts including mrna sequences, ests, and rnaseq reads to the genome allows identifying premrna alternative splicing as, a. Although accumulating evidences indicate that as is developmentally regulated, how as responds to developmental cues is not well understood.
Alternative splicing as has been extensively studied in mammalian systems but much less in plants. Genomewide association between dna methylation and. Although genomewide studies have revealed complex as1 patterns in plants, whether. The extent and complexity of as has been revealed in model plants using high. These studies have also revealed that alternative splicing in plants can be regulated by cell type, developmental stage, the environment, and the circadian clock. Min xj 2017 comprehensive cataloging and analysis of alternative splicing in maize. To search against arabidopsis and rice intronsexonsexon junctions, paste your sequences here. The genomethreader gene prediction software computes gene structure predictions using a similaritybased approach where additional cdnaest andor protein sequences are used to predict gene structures via spliced alignments. The current available tools of alternative splicing work with raw data and include heavy computation. Evolutionary character of alternative splicing in plants ncbi. In some multicellular eukaryotes, alternative splicing is essential for cellular differentiation to form specific tissues.
Defects of premrna splicing in an atprp38 mutant resulted in an insufficient premrna splicing pattern in the intron of iaa1. Plants has new maps plants is trying out a new, more modern mapping system. Article pdf available in plant and cell physiology 542 january 20 with 75 reads how we measure reads. Extensive divergence in alternative splicing patterns. However, recent genomewide computational analyses have revealed that alternative splicing in flowering plants is far more prevalent than previously thought. A global survey of alternative splicing in allopolyploid. Lightsensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Erisdb is a comprehensive database of splice sites and splicing signals. Alternative splicing database this project is supported by the human frontier science program. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger rna mrna produced from that gene. The everincreasing number of plant genes with as and the processes in which they are involved point to the importance of understanding the mechanisms and regulation of as and the functions of as. Global warming severely affects flowering time and reproductive success of plants.
More than 60% of introncontaining genes undergo alternative splicing as in plants. The alternative splicing mutation database asmd serves as a repository for all exonic mutations not associated. Evolution of alternative splicing in eudicots plant science frontiers. Here we report as events deduced from estcdna analysis in two model plants.
Myb transcription factor genes play important roles in many developmental processes and in various defence responses of plants. Future challenges in alternative splicing research in plants. Alternative splicing of premessenger rnas in plants in. However, the patterns and underlying mechanisms of as evolution in plants remain unclear.
Splicing factor 30 spf30, also known as survival motor neuron domain. Skiinteracting protein skip, a splicing factor, is essential for circadian clock function and abiotic stress tolerance. A catalog of alternatively splicing as events in cereal crops. Comparative crossspecies alternative splicing in plants plant. Jun 26, 2018 alternative splicing is a form of genetic regulation that enables the production of multiple proteins from a single gene.
To respond to temperature changes, different levels of gene regulation are modulated in the cell. Early fruit growth mainly characterized by active cell division and cell expansion contributes to the formation of fruit. Here, recent advancements in the understanding of alternative splicing in higher plants are presented. Alternative splicing as of premrnas promotes transcriptome and proteome diversity and plays important roles in a wide range of biological processes. Alternative premrna splicing as is prevalent in plants and is. In this study we investigated the relationship between dna methylation, alternative splicing, and crossspecies gene conservation on a genomewide scale using genomewide transcription and dna methylation data.