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Dissection of Hippocampal Dentate Gyrus from Adult Mouse

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Published on: November 17, 2009

Creating reference gene annotation for the mouse C57BL6/J genome assembly.

Jonathan M Mudge¹, Jennifer Harrow²

¹Wellcome Trust Sanger Institute, Cambridge, UK. jm12@sanger.ac.uk.

Mammalian Genome : Official Journal of the International Mammalian Genome Society

|July 19, 2015

Summary

The GENCODE mouse annotation project enhances the C57BL6/J reference genome by integrating manual and computational methods. This effort now includes non-coding RNAs and uses new sequencing data to improve gene identification and strain variation analysis.

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Area of Science:

Genomics
Transcriptomics
Bioinformatics

Background:

The C57BL6/J mouse genome annotation is a continuous effort.
Initial focus was on protein-coding genes, expanding to non-coding RNAs and pseudogenes.

Purpose of the Study:

To report progress on the GENCODE mouse annotation project.
To detail the integration of diverse datasets and validation pipelines.
To explore the utility of the genebuild for comparative genomics.

Main Methods:

Combined manual annotation (HAVANA) with Ensembl computational annotation.
Utilized experimental and in silico validation pipelines.
Incorporated next-generation sequencing and mass-spectrometry data.

Main Results:

Significant progress in annotating protein-coding genes, long non-coding RNAs, small RNAs, and pseudogenes.
Demonstrated the use of mass-spectrometry for novel protein-coding gene discovery.
Established a comprehensive genebuild for the C57BL6/J mouse.

Conclusions:

The GENCODE project provides a robust mouse genome annotation.
Advanced annotation includes diverse RNA types and pseudogenes.
The C57BL6/J genebuild facilitates insights into genetic variations across mouse strains and species.