LC Sciences News

Next-gen sequencing has provided new insight into the microRNAome, is accerating the rate of discovery of new small RNAs, and is responsible for many of the changes to the miRBase sequence database in recent updates. But a miRBase update is not merely the adding of new sequences.  Though that is a large part of it, sequences are also updated, corrected, or in some cases deleted.

Deleting Sequences

• Misannotated sequences are deleted – next-gen sequencing data will enable more of this
• Cases of duplicate entries mapping to a single genomic locus are cleaned up – some enabled by new genome assembly releases
• Ex – Drosophila pseudoobscura V18 – 211 database entries, V19 – 210 database entries.

Renaming Sequences

• The process of retiring the miR/miR* nomenclature, in favour of the -5p/-3p nomenclature began with version 17 of the database.
• Version 17 – Drosophila sequences renamed.
• Version 18 – Human, Mouse, and Zebrafish sequences renamed.
• Version 19 – the miR* nomenclature is finally retired for all species.
• The miRBase curators note that the names are meant to be useful, but are not formally stable. They recommend that sequence names shouldn’t be used to convey complex information. Instead they recommend to use miRNA accession numbers, which do remain stable between releases, or you can always quote the sequence to be truly unambiguous. (miRBase Blog post regarding naming)

Adding Sequences

• Version 19 includes 3171 new hairpins and 3625 novel mature products.  That’s an 18% increase in the database size in a single update.

Because the rate of increase in size of the database is accelerating, it is making it more and more difficult for array manufacturers (that use the miRBase sequence database for probe content) to keep their microarrays up-to-date with the latest sequence information.  Often, pre-made arrays, sitting on the shelf, contain only a fraction of the known content for a particular species.

In comparison, LC Sciences’ microRNA microarrays are produced only as needed. This is made possible by our µParaflo® Biochip Technology – a high performance microfluidic custom microarray platform, enables on demand synthesis of microarrays.

Our microRNA arrays cover all species for which sequence data are available in the miRBase Sequence Database and the Plant MicroRNA Database.

Comparison of miRBase Versions

A comparison of the array versions available from various suppliers shows a significant amount of miRNA expression information is missed when using these out of date arrays for miRNA expression profiling analysis.

Comparison of miRBase Coverage