title: Emerging roles of RNA processing factors in regulating long non-coding RNAs.
abstract: Long non-coding RNAs (lncRNAs) 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 lncRNAs transcribed by RNA polymerase Pol V or Pol II, while siRNAs originate from Pol IV- or Pol II-dependent production of lncRNAs. In contrast to the vast literature on co-transcriptional and post-transcriptional processing of mRNAs, information is limited for lncRNA 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 lncRNAs in the chromatin, thereby revealing that accumulation of functional lncRNAs 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 lncRNAs, and highlight the emerging theme of lncRNA regulation by RNA processing factors.
authors.affiliation: Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA.
authors.forename: Huiming
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA; Shanghai Center for Plant Stress Biology; Shanghai Institute of Biological Sciences; Chinese Academy of Sciences; Beijing, PR China.
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
mesh_terms: D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics; D029681:Arabidopsis Proteins / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D004268:DNA-Binding Proteins; D062085:RNA, Long Noncoding; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Long non-coding RNA; Pol IV; Pol V; RNA retention; RNA-directed DNA methylation; Rrp6; splicing; transcriptional silencing