ArticleNature communications2019
Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 61 citations in OpenAlex.
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- Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development.BMC genomics · 2024Article
- Thermoregulated transcriptomics: the molecular basis and biological significance of temperature-dependent alternative splicing.The Biochemical journal · 2024Review
- Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform.Nature communications · 2023Article
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- Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).G3 (Bethesda, Md.) · 2023Article
- Re-evaluating the impact of alternative RNA splicing on proteomic diversity.Frontiers in genetics · 2023Review
- Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells.Frontiers in genetics · 2023Article
- Context-specific regulation and function of mRNA alternative polyadenylation.Nature reviews. Molecular cell biology · 2022Review
- Targeted proteoform mapping uncovers specific Neurexin-3 variants required for dendritic inhibition.Neuron · 2022Article
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- Foster thy young: enhanced prediction of orphan genes in assembled genomes.Nucleic acids research · 2022Article
- Generation and network analysis of an RNA-seq transcriptional atlas for the rat.NAR genomics and bioinformatics · 2022Article
- Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes.BMC genomics · 2022Article
- Improved Reference Genome Annotation ofFrontiers in plant science · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies.
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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.