Tandem array–based expression screens identify host mRNA targets of virus-encoded microRNAs

Abstract

MicroRNAs (miRNAs) are short non-coding RNAs of cellular1 and viral origin2-7 that post-transcriptionally regulate gene expression through imperfect base pairing to their mRNA targets. Because the recognition sequences of miRNAs for their targets are short and may be discontinuous, bioinformatic prediction of targets is difficult. Here we present an approach to the experimental identification of the mRNA targets of miRNAs encoded by the Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV encodes 17 miRNAs, derived from 12 pre-miRNAs expressed from a single locus during viral latency2,5-10. Our approach is based upon multiple screens that examine small changes in transcript abundance under different conditions of miRNA expression or inhibition, followed by searching the identified transcripts for seed sequence matches. This strategy led to the identification of the Bcl2-associated factor BCLAF1 as a target for miR-K5, and further analysis revealed that several other KSHV miRNAs also target this gene product. Our results support that this type of expression profiling provides a potentially general approach to the identification of miRNA targets.

The role of RNAi and microRNAs in animal virus replication and antiviral immunity

“…Cold Spring Harbor Laboratory Press on May 11, 2018 -Published by genesdev.cshlp.org Downloaded from miR-K9, and miR-K10 (Ziegelbauer et al 2009). BCLAF1 can apparently function as a pro-or anti-apoptotic factor, depending on its cellular context.…”

Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs

“…Detailed functional roles of the KSHV miRNAs during bona fide infection are lacking. However, several mRNA targets that are repressed by the KSHV miRNAs have been identified (Gottwein et al 2007;Samols et al 2007;Skalsky et al 2007;Whitby 2009;Ziegelbauer et al 2009). Some of these targets include host genes that play a role in angiogenesis, transformation, and apoptosis, suggesting that the KSHV miRNA may be involved in the pathogenesis associated with KSHV infection.…”

BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells

“…However, the role in apoptotic pathway remains controversial, as cells from BCLAF1-deficient mice do not have obvious defects in apoptosis 2 . Indeed, multiple functions have been described for BCLAF1 by different groups, such as in posttranscriptional processes 3,4 , production of Kaposi's sarcoma-associated herpesvirus 5 and human cytomegalovirus infection 6 , lung development and T-cell activation 2,7 .…”