The vast, conserved mammalian lincRNome

Area of Science:

• Genomics
• Non-coding RNA Biology

Background:

• Long intergenic non-coding RNAs (lincRNAs) are a large class of transcripts with diverse regulatory roles.
• The full extent and evolutionary conservation of the lincRNome remain largely uncharacterized.

Purpose of the Study:

• To estimate the total number of lincRNA genes in human and mouse.
• To quantify the conserved fraction of the lincRNome between these species.
• To assess the evolutionary conservation of lincRNA genes and infer potential shared functions.

Main Methods:

• Comparative analysis of experimentally validated lincRNAs from human and mouse.
• Application of a maximum likelihood approach to estimate lincRNome size and conservation.
• Assessment of lincRNA gene orthology and sequence conservation.

Main Results:

• Estimated total lincRNome size at 40,000–50,000 genes per species, exceeding protein-coding gene counts.
• Identified that lincRNAs occupy a larger fraction of the euchromatic genome than protein-coding sequences.
• Found unexpectedly high orthology (60–70%) between human and mouse lincRNA genes, despite lower sequence conservation.
• Predicted conserved functional roles for thousands of lincRNAs.

Conclusions:

• The lincRNome is substantially larger and more genomically prevalent than previously thought.
• A significant portion of lincRNAs are conserved between human and mouse, indicating evolutionary importance.
• Thousands of conserved lincRNAs likely possess essential, yet uncharacterized, functional roles that warrant further investigation.