Article abstract

Nature Structural & Molecular Biology 16, 183 - 189 (2009)
Published online: 18 January 2009 | doi:10.1038/nsmb.1536

A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordate

Weiyang Shi1,2, David Hendrix1,2, Mike Levine1 & Benjamin Haley1

MicroRNAs (miRNAs) have been implicated in various cellular processes. They are thought to function primarily as inhibitors of gene activity by attenuating translation or promoting mRNA degradation. A typical miRNA gene produces a predominant approx21-nucleotide (nt) RNA (the miRNA) along with a less abundant miRNA* product. We sought to identify miRNAs from the simple chordate Ciona intestinalis through comprehensive sequencing of small RNA libraries created from different developmental stages. Unexpectedly, half of the identified miRNA loci encode up to four distinct, stable small RNAs. The additional RNAs, miRNA-offset RNAs (moRs), are generated from sequences immediately adjacent to the predicted approx60-nt pre-miRNA. moRs seem to be produced by RNAse III–like processing, are approx20 nt long and, like miRNAs, are observed at specific developmental stages. We present evidence suggesting that the biogenesis of moRs results from an intrinsic property of the miRNA processing machinery in C. intestinalis.

  1. Department of Molecular Cell Biology, Division of Genetics, Genomics, and Development, Center for Integrative Genomics, University of California, Berkeley, California 94720-3200, USA.
  2. These authors contributed equally to the work.

Correspondence to: Mike Levine1 e-mail:

Correspondence to: Benjamin Haley1 e-mail:


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