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Related Concept Videos

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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Updated: Jul 27, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.

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Long-read RNA sequencing reveals extensive transcript isoform diversity in humans and mice. Most protein-coding genes exhibit changes in their primary transcript, highlighting dynamic gene expression across tissues and species.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Molecular Biology

Background:

  • Mammalian genes commonly produce multiple transcript isoforms via differential promoter use, alternative splicing, and varied 3' end processing.
  • Quantifying these diverse transcripts is challenging with traditional short-read RNA sequencing due to transcript length limitations.

Approach:

  • Utilized long-read RNA sequencing (LR-RNA-seq) on 264 PacBio libraries from 81 human and mouse samples, generating over 1 billion circular consensus reads.
  • Developed a novel gene and transcript annotation framework using triplets (transcript start site, exon junction chain, transcript end site) to represent transcript structure diversity.
  • Analyzed promoter selection, splice patterns, and 3' processing across human tissues and compared human-mouse orthologs.

Key Points:

  • Detected full-length transcripts for 87.7% of human protein-coding genes, identifying 200,000 full-length transcripts, with 40% featuring novel exon junction chains.
  • Nearly half of multi-transcript genes showed a bias towards a specific diversity mechanism (promoter, splicing, or 3' end).
  • The predominantly expressed transcript changed for 74% of protein-coding genes across samples, and 57.8% of orthologous gene pairs displayed distinct diversification mechanisms in matching tissues.

Conclusions:

  • This large-scale LR-RNA-seq survey provides a foundational resource for understanding alternative transcript usage in mammals.
  • Significant transcriptomic differences exist between human and mouse orthologs, despite global similarities in diversity mechanisms.
  • The study underscores the dynamic nature of transcript isoform expression and its evolutionary divergence.