ArticleBMC genomics2017
Relatively frequent switching of transcription start sites during cerebellar development.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Transcription Start Site Choice Regulates mGenes · 2026Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Mechanism of expression regulation of head-to-head overlapping protein-coding genes INO80E and HIRIP3.Communications biology · 2025Article
- Predicting and comparing transcription start sites in single cell populations.PLoS computational biology · 2025Article
- Uncovering the dynamics and consequences of RNA isoform changes during neuronal differentiation.Molecular systems biology · 2024Article
- Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation.Nature communications · 2024Article
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- Article
- Genome-Wide Mapping of 5' Isoforms with 5'-Seq.Current protocols · 2023Article
- Article
- Genome-wide analysis of the3 Biotech · 2022Article
- Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.Entropy (Basel, Switzerland) · 2021Review
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish.Genome research · 2021Article
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.Scientific reports · 2021Article
- High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.Genome biology · 2021Article
- Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.Genome research · 2020Article
- AP-TSS: A New Method for the Analysis of RNA Expression from Particular and Challenging Transcription Start Sites.Biomolecules · 2020Article
- An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data.NAR genomics and bioinformatics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification spawned many single-gene studies on differential usages of tissue-specific or temporal-specific alternative TSSs. However, exploration of the switching usage of alternative TSS usage on a genomic level, especially in the central nervous system, is largely lacking.
resultsIn this study, We have prepared a unique set of time-course data for the developing cerebellum, as part of the FANTOM5 consortium ( http://fantom.gsc.riken.jp/5/ ) that uses their innovative capturing of 5' ends of all transcripts followed by Helicos next generation sequencing. We analyzed the usage of all transcription start sites (TSSs) at each time point during cerebellar development that provided information on multiple RNA isoforms that emerged from the same gene. We developed a mathematical method that systematically compares the expression of different TSSs of a gene to identify temporal crossover and non-crossover switching events. We identified 48,489 novel TSS switching events in 5433 genes during cerebellar development. This includes 9767 crossover TSS switching events in 1511 genes, where the dominant TSS shifts over time.
conclusionsWe observed a relatively high prevalence of TSS switching in cerebellar development where the resulting temporally-specific gene transcripts and protein products can play important regulatory and functional roles.
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