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Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE.

Saakshi Jalali1,2, Shrey Gandhi1, Vinod Scaria3,4

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GENCODE human genome annotations are dynamic, with frequent updates to gene and transcript information, especially for long noncoding RNAs (lncRNAs). This evolution, while improving the resource, presents challenges for researchers using the data.

Keywords:
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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • Technological advancements have significantly improved genome annotation capabilities.
  • The GENCODE project is a major resource for human genome annotations.
  • Systematically annotating a comprehensive set of genes and transcripts is challenging.

Purpose of the Study:

  • To review the impact of dynamicity on GENCODE gene annotations over time.
  • To specifically examine the changes in long noncoding RNA (lncRNA) annotations within GENCODE.
  • To identify challenges and propose solutions for managing dynamic gene annotation data.

Main Methods:

  • Analysis of various GENCODE versions to track transcript annotation changes.
  • Examination of transcript consistency and biotype stability across GENCODE releases.
  • Review of literature and bio-curation experiments for comparative insights.

Main Results:

  • GENCODE annotations show significant dynamism, with continuous updates to protein-coding and lncRNA transcripts.
  • The percentage of the human genome transcribed has increased substantially across GENCODE versions.
  • Low consistency (21.7%) was observed for transcripts across different GENCODE versions, with only 17 out of 70 biotypes remaining stable.

Conclusions:

  • The dynamicity in GENCODE annotations reflects the evolving nature of gene nomenclature and understanding.
  • While updates enhance the resource's reliability, they pose challenges for users.
  • Potential methods are proposed to address the data management challenges arising from annotation changes.