ArticleGenome biology2022
An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
- Domain compositions of Arabidopsis Toll/Interleukin-1 Receptor/Resistance domain-containing TX14 proteins affect localization and induction of the hypersensitive response.Journal of experimental botany · 2026Article
- Splicing Factors in Plant Abiotic Stress Responses: Regulatory Mechanisms and Perspectives.Plants (Basel, Switzerland) · 2026Review
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- Loss of LEFKOTHEA Leads to Global Transcriptional and Post-Transcriptional Changes in Gene Expression During Early Light Response.Plants (Basel, Switzerland) · 2026Article
- Cotyledon opening during seedling deetiolation is determined by ABA-mediated splicing regulation.EMBO reports · 2025Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis.Nature communications · 2024Article
- Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.The Plant cell · 2024Article
- SYNAPTOTAGMIN 4 is expressed mainly in the phloem and participates in abiotic stress tolerance in Arabidopsis.Frontiers in plant science · 2024Article
- The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis.Plants (Basel, Switzerland) · 2023Article
- The Function ofGenes · 2022Article
- Arabidopsis B-box transcription factors BBX20-22 promote UVR8 photoreceptor-mediated UV-B responses.The Plant journal : for cell and molecular biology · 2022Article
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- How alternative splicing changes the properties of plant proteins.Quantitative plant biology · 2022Review
- Transcript Complexity and New Insights of Restorer Line in CMS-D8 Cotton Through Full-Length Transcriptomic Analysis.Frontiers in plant science · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLight switches on the photomorphogenic development of young plant seedlings, allowing young seedlings to acquire photosynthetic capacities and gain survival fitness. Light regulates gene expression at all levels of the central dogma, including alternative splicing (AS) during the photomorphogenic development. However, accurate determination of full-length (FL) splicing variants has been greatly hampered by short-read RNA sequencing technologies.
resultIn this study, we adopt PacBio isoform sequencing (Iso-seq) to overcome the limitation of the short-read RNA-seq technologies. Normalized cDNA libraries used for Iso-seq allows for comprehensive and effective identification of FL AS variants. Our analyses reveal more than 30,000 splicing variant models from approximately 16,500 gene loci and additionally identify approximately 700 previously unannotated genes. Among the variants, approximately 12,000 represent new gene models. Intron retention (IR) is the most frequently observed form of variants, and many IR-containing AS variants show evidence of engagement in translation. Our study reveals the formation of heterodimers of transcription factors composed of annotated and IR-containing AS variants. Moreover, transgenic plants overexpressing the IR forms of two B-BOX DOMAIN PROTEINs exhibits light-hypersensitive phenotypes, suggesting their regulatory roles in modulating optimal light responses.
conclusionsThis study provides an accurate and comprehensive portrait of full-length transcript isoforms and experimentally confirms the presence of de novo synthesized AS variants that impose regulatory functions in photomorphogenic development in Arabidopsis.
Indexed as
Identifiers
What OpenQuestion holds
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.