Profiling and identification of small rDNA-derived RNAs and their potential biological functions

PLoS One. 2013;8(2):e56842. doi: 10.1371/journal.pone.0056842. Epub 2013 Feb 13.

Abstract

Small non-coding RNAs constitute a large family of regulatory molecules with diverse functions. Notably, some small non-coding RNAs matched to rDNA have been identified as qiRNAs and small guide RNAs involved in various biological processes. However, a large number of small rDNA-derived RNAs (srRNAs) are usually neglected and yet to be investigated. We systematically investigated srRNAs using small RNA datasets generated by high-throughput sequencing, and found srRNAs are mainly mapped to rRNA coding regions in sense direction. The datasets from immunoprecipitation and high-throughput sequencing demonstrate that srRNAs are co-immunoprecipitated with Argonaute (AGO) proteins. Furthermore, the srRNA expression profile in mouse liver is affected by diabetes. Overexpression or inhibition of srRNAs in cultured cells shows that srRNAs are involved in various signaling pathways. This study presents a global view of srRNAs in total small RNA and AGO protein complex from different species, and demonstrates that srRNAs are correlated with diabetes, and involved in some biological processes. These findings provide new insights into srRNAs and their functions in various physiological and pathological processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis / genetics
  • Argonaute Proteins / genetics*
  • Argonaute Proteins / metabolism
  • Cell Line, Tumor
  • DNA, Ribosomal / genetics*
  • Diabetes Mellitus / genetics
  • Drosophila melanogaster / genetics
  • Gene Expression Profiling*
  • Gene Expression Regulation
  • Glucose-6-Phosphatase / genetics
  • Humans
  • Liver / metabolism
  • Luciferases / genetics
  • Luciferases / metabolism
  • MAP Kinase Signaling System / genetics
  • Male
  • Mice
  • Mice, Inbred C57BL
  • NIH 3T3 Cells
  • Phosphoenolpyruvate Carboxykinase (ATP) / genetics
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • RNA, Small Untranslated / genetics*
  • RNA, Small Untranslated / metabolism

Substances

  • Argonaute Proteins
  • DNA, Ribosomal
  • RNA, Plant
  • RNA, Small Untranslated
  • Luciferases
  • Glucose-6-Phosphatase
  • Phosphoenolpyruvate Carboxykinase (ATP)

Grants and funding

This research was supported by grants from National Natural Science Foundation of China (30825009, 30970619, 31030022, 81021002 and 31200591), National Basic Research Program of China (973 Program, 2009CB918403), Program of Shanghai Subject Chief Scientist (11XD1405800), Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-EW-R-09), Postdoctoral Fellowship Program of Shanghai Institutes for Biological Sciences (2011KIP511) and SA-SIBS Scholarship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.