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Clusters of internally primed transcripts reveal novel long noncoding RNAs.

Masaaki Furuno1, Ken C Pang, Noriko Ninomiya

  • 1Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America.

Plos Genetics
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Researchers discovered numerous large non-coding RNAs (macro ncRNAs) in the mouse genome. These novel macro ncRNAs, similar to Xist and Air, play significant regulatory roles and are predominantly found in the nucleus.

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Area of Science:

  • Genomics
  • Molecular Biology
  • RNA Biology

Background:

  • Non-protein-coding RNAs (ncRNAs) are crucial for gene regulation.
  • While microRNAs are well-studied, larger functional ncRNAs (macro ncRNAs) like Xist and Air are less understood.
  • Existing data suggested macro ncRNAs might be fragmented in cDNA libraries.

Purpose of the Study:

  • To identify novel macro ncRNA candidates using a genome-wide approach.
  • To characterize the nature and location of these potential macro ncRNAs.
  • To validate the existence and size of newly identified ncRNAs.

Main Methods:

  • Analysis of FANTOM3 mouse cDNA clones to identify clusters of short, unspliced transcripts.
  • Genome-wide search for regional cDNA clusters outside protein-coding genes.
  • In silico analysis for imprinting, antisense transcription, and association with microRNAs and CNS transcripts.
  • Experimental validation using northern blot and RT-PCR for selected candidates.

Main Results:

  • Identified 66 novel regions containing macro ncRNA candidates, with a mean length of 92 Kb.
  • Confirmed the presence of known long ncRNAs within these regions.
  • Experimental validation confirmed the majority of selected regions represent previously unrecognized noncoding transcripts (≥10 Kb) localized in the nucleus.
  • Found associations with microRNAs and central nervous system transcripts.

Conclusions:

  • The study identified numerous novel macro ncRNAs, expanding the known repertoire of regulatory RNAs.
  • The findings suggest a vast number of undiscovered macro ncRNAs exist in the mouse genome.
  • Macro ncRNAs like Xist and Air are more prevalent than previously thought and play significant roles in gene regulation.