ArticleGenome research2011
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 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
129 citing papers in PubMed, 215 citations in OpenAlex.
- Review
- Alternative tandem transcription initiation links noncoding variants to human disease through translational control.Nature communications · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Solid Tumors Pan Cancer Transcriptome: Tissue/Cancer specific expression groups at the Isoform-Level.bioRxiv : the preprint server for biology · 2026Article
- Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.Nature communications · 2026Article
- Maternal nutrition alters mRNA isoform expression, usage, and splicing dynamics in skeletal muscle of beef cattle offspring.Frontiers in genetics · 2026Article
- SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.Computational and structural biotechnology journal · 2026Article
- G-quadruplex structures as modulators of alternative promoter usage.NAR genomics and bioinformatics · 2025Article
- Hierarchical regulation of cerebellar neurogenesis by Sin3A-mediated gene repression.bioRxiv : the preprint server for biology · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- The generation and consequences of N-terminal proteoform diversity.Cell reports · 2025Review
- Hypoxic stimulation of DCLK1 transcription and alternative-promoter switching fuels tumor malignancy in clear cell renal cell carcinoma.Cell death & disease · 2025Article
- Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes.Genome research · 2025Article
- Plant ADH1 promoter acts as an H3K27me3-associated hyper-long cold-responsive promoter.The Plant journal : for cell and molecular biology · 2025Article
- Alternative promoter usage during organ development.PLoS genetics · 2025Article
- Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders.Nucleic acids research · 2025Article
- Aberrant histone modifications in pediatric brain tumors.Frontiers in oncology · 2025Review
- Retinal prolactin isoform PRLΔE1 sustains rod disease in inherited retinal degenerations.Cell death & disease · 2024Article
- Article
- TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups.Bioinformatics (Oxford, England) · 2024Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Despite our growing knowledge that many mammalian genes generate multiple transcript variants that may encode functionally distinct protein isoforms, the transcriptomes of various tissues and their developmental stages are poorly defined. Identifying the transcriptome and its regulation in a cell/tissue is the key to deciphering the cell/tissue-specific functions of a gene. We built a genome-wide inventory of noncoding and protein-coding transcripts (transcriptomes), their promoters (promoteromes) and histone modification states (epigenomes) for developing, and adult cerebella using integrative massive-parallel sequencing and bioinformatics approach. The data consists of 61,525 (12,796 novel) distinct mRNAs transcribed by 29,589 (4792 novel) promoters corresponding to 15,669 protein-coding and 7624 noncoding genes. Importantly, our results show that the transcript variants from a gene are predominantly generated using alternative transcriptional rather than splicing mechanisms, highlighting alternative promoters and transcriptional terminations as major sources of transcriptome diversity. Moreover, H3K4me3, and not H3K27me3, defined the use of alternative promoters, and we identified a combinatorial role of H3K4me3 and H3K27me3 in regulating the expression of transcripts, including transcript variants of a gene during development. We observed a strong bias of both H3K4me3 and H3K27me3 for CpG-rich promoters and an exponential relationship between their enrichment and corresponding transcript expression. Furthermore, the majority of genes associated with neurological diseases expressed multiple transcripts through alternative promoters, and we demonstrated aberrant use of alternative promoters in medulloblastoma, cancer arising in the cerebellum. The transcriptomes of developing and adult cerebella presented in this study emphasize the importance of analyzing gene regulation and function at the isoform level.
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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.