Emerging roles of RNA processing factors in regulating long non-coding RNAs

Abstract

Long non-coding RNAs (IncRNAs) can be important regulators of various biological processes such as RNA-directed DNA methylation (RdDM). In the RdDM pathway, recruitment of the DNA methylation complex is mediated through complementary pairing between scaffold RNAs and Argonaute-associated siRNAs. Scaffold RNAs are chromatin-associated IncRNAs transcribed by RNA polymerase Pol V or Pol II, while siRNAs originate from Pol IV- or Pol II-dependent production of IncRNAs. In contrast to the vast literature on co-transcriptional and post-transcriptional processing of mRNAs, information is limited for IncRNA regulation that enables their production and function. Recently Arabidopsis RRP6L1, a plant paralog of the conserved nuclear RNA surveillance protein Rrp6, was shown to mediate RdDM through retention of IncRNAs in the chromatin, thereby revealing that accumulation of functional IncRNAs requires more than simply RNA polymerases. By focusing on the canonical RdDM pathway, here we summarize recent evidence that indicate co-transcriptional and/ or post-transcriptional regulation of IncRNAs, and highlight the emerging theme of IncRNA regulation by RNA processing factors.