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Domestic Dog MicroRNA Annotation Updated

NEW YORK (GenomeWeb) – A team from the UK, the US, and Sweden has expanded the collection of microRNAs previously documented in the genome of the domestic dog, Canis familiaris.

"Our results represent a clear improvement in our knowledge of the dog genome, paving the way for further research on the evolution of gene regulation, and the contribution of microRNAs to pathological conditions," first author Luca Penso-Dolfin, a vertebrate and health genomics researcher at The Genome Analysis Centre in Norwich, said in a statement.

As they reported today in PLOS One, Penso-Dolfin and his colleagues sequenced small RNAs in nine dog tissues as part of an effort to annotate dog miRNAs. They uncovered more than 800 dog miRNAs, including 720 conserved miRNAs and 91 miRNAs not described in the past. The results are expected to serve as a resource for understanding miRNA biology, particularly for research teams using the domestic dog to model gene regulation as it relates to human traits and diseases.

"Many polymorphisms in miRNAs target sites have already been identified which are associated with pathological conditions," the authors wrote. "Investigating the functional role of these novel miRNAs has the potential of further elucidating the biology of several human diseases, and the evolution of artificially selected phenotypic traits in dog."

Domestic dogs have been gaining favor as model organisms due to their diversity and long history sharing environments with humans. That's particularly true for human diseases that overlap with conditions in one or more dog breeds, including complex traits or diseases, and dog cancers such as chronic myeloid leukemia, bladder cancer, lymphoma, or osteosarcoma.

To get a more robust view of regulatory features in the dog genome, the researchers used the Illumina HiSeq 2000 to sequence small RNA libraries representing domestic dog blood and tissues from the brain, heart, kidney, lung, ovary, skin, testes, and smooth muscle.

The team analyzed these sequences with the help of the most recent dog genome reference assembly, CanFam3.1, and sequences from several other animal species, and identified 720 conserved miRNAs — this set includes 207 conserved miRNAs described in other animals, but not previously found in the dog genome.

The researchers also identified 91 new miRNAs, along with 263 predicted piwi-interacting RNA (piRNA) clusters. They further considered tissue-specific small RNA expression and took a crack at predicting the genes targeted by domestic dog miRNAs.

The updated small RNA annotation is available online through the Broad Institute Canine Genomic Resources web site and a related University of California at Santa Cruz canine annotation track hub that hosts the data. The team is reportedly continuing to search for miRNAs in the dog as well as other domestic animals.

"We are now looking at additional data for dog and a variety of farm animals," Penso-Dolfin said, "combining microRNA discovery to the investigation of their possible role in domestication."