ArticleGenome research2012
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 444 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
444 citing papers in PubMed, 826 citations in OpenAlex.
- Alternative splicing acts as a strategic switch for heat shock network diversification under escalating heat stress.Plant cell reports · 2026Article
- Arabidopsis Heterotrimeric G Beta Variants Shape Plant Development and Modulate Responses to Endoplasmic Reticulum Stress and Salt Stress.Plant, cell & environment · 2026Article
- The Role of Small Segmental Duplications in Generating Identical Isoforms Through Alternative Splicing Sites.Biochemical genetics · 2026Article
- PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development.eLife · 2026Article
- Intron retention dominates alternative splicing reprogramming during anaerobic stress in Chlamydomonas reinhardtii.Planta · 2026Article
- Infection-responsive alternative splicing of GhZDS is associated with Verticillium wilt resistance in cotton.BMC plant biology · 2026Article
- Impact of alternative splicing on Arabidopsis proteome.Nucleic acids research · 2026Article
- Loss of LEFKOTHEA Leads to Global Transcriptional and Post-Transcriptional Changes in Gene Expression During Early Light Response.Plants (Basel, Switzerland) · 2026Article
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- TaPP2C-a5 fine-tunes wheat seed dormancy and germination with a Triticeae-specific, alternatively spliced transcript.Journal of advanced research · 2026Article
- Comparative transcriptomic and transcript-based network analyses revealed genotype-specific alternative splicing induced by Sclerotinia sclerotiorum in Brassica napus.BMC plant biology · 2026Article
- Alternative splicing: an underexplored layer in immune receptor regulation, systemic resistance and priming.Frontiers in plant science · 2026Article
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- Identification of the Splicing FactorInternational journal of molecular sciences · 2025Article
- Impact of U2-type introns on splice site prediction in A. thaliana species using deep learning.BMC bioinformatics · 2025Article
- The implications of alternative splicing regulation for maximum lifespan.Nature communications · 2025Article
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- Conservation and Remodeling of Alternative Splicing Landscapes in the Evolution ofPlants (Basel, Switzerland) · 2025Article
- Impact of alternative splicing on Arabidopsis proteome.bioRxiv : the preprint server for biology · 2025Article
- The Role of Alternative Splicing in Polyploids in Response to Abiotic Stress.International journal of molecular sciences · 2025Review
384 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis. We detect ∼150,000 splice junctions derived mostly from typical plant introns, including an eightfold increase in the number of U12 introns (2069). Around 61% of multiexonic genes are alternatively spliced under normal growth conditions. Moreover, we provide experimental validation of 540 AS transcripts (from 256 genes coding for important regulatory factors) using high-resolution RT-PCR and Sanger sequencing. Intron retention (IR) is the most frequent AS event (∼40%), but many IRs have relatively low read coverage and are less well-represented in assembled transcripts. Additionally, ∼51% of Arabidopsis genes produce AS transcripts which do not involve IR. Therefore, the significance of IR in generating transcript diversity was generally overestimated in previous assessments. IR analysis allowed the identification of a large set of cryptic introns inside annotated coding exons. Importantly, a significant fraction of these cryptic introns are spliced out in frame, indicating a role in protein diversity. Furthermore, we show extensive AS coupled to nonsense-mediated decay in AFC2, encoding a highly conserved LAMMER kinase which phosphorylates splicing factors, thus establishing a complex loop in AS regulation. We provide the most comprehensive analysis of AS to date which will serve as a valuable resource for the plant community to study transcriptome complexity and gene regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.