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Functional transcriptomics in the post-ENCODE era.

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The human transcriptome is more complex than previously understood, with many novel transcripts discovered. Determining the functional significance of this complexity is an ongoing challenge for genome scientists.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • The human genome sequence annotation has revealed a vast and complex human transcriptome.
  • This complexity includes alternative splicing and numerous long noncoding RNAs.
  • Existing transcript models are often incomplete, and many transcripts may remain undiscovered.

Purpose of the Study:

  • To discuss the current state of human transcriptome annotation.
  • To highlight knowledge gaps in transcript functionality.
  • To consider strategies for assessing transcript functionality.

Main Methods:

  • Drawing on experience from generating the GENCODE gene annotation set.
  • Reviewing computational and experimental strategies for annotation.
  • Proposing an integrated strategy combining experimental resources.

Main Results:

  • The human transcriptome is far larger and more complex than previously appreciated.
  • Significant numbers of human transcripts may still be unannotated or incompletely described.
  • The functional proportion of this transcriptional complexity remains an open question.

Conclusions:

  • Understanding the full functional scope of the human transcriptome is a long-term endeavor.
  • An integrated strategy combining diverse experimental resources is crucial.
  • Significant progress can be made by systematically assessing transcript functionality.