TY - JOUR
T1 - Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development
AU - Kato, Masaomi
AU - de Lencastre, Alexandre
AU - Pincus, Zachary
AU - Slack, Frank J.
N1 - Funding Information:
We thank Ghia Euskirchen for help with Solexa sequencing and Valerie Reinke for critical reading of this manuscript. We also thank the CGC for strains. MK was partially supported by a postdoctoral fellowship from the Uehara Memorial Foundation; FS was supported by grants from the NIH to the modENCODE consortium (RFA-HG-06-006).
PY - 2009/5/21
Y1 - 2009/5/21
N2 - Background: Small non-coding RNAs, including microRNAs (miRNAs), serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of animals such as Caenorhabditis elegans. Results: We performed a deep analysis of small RNA expression in C. elegans using recent advances in sequencing technology, and found that a significant number of known miRNAs showed major changes in expression during development and between males and hermaphrodites. Additionally, we identified 66 novel miRNA candidates, about 35% of which showed transcripts from their 'star sequence', suggesting that they are bona fide miRNAs. Also, hundreds of novel Piwi-interacting RNAs (piRNAs)/ 21U-RNAs with dynamic expression during development, together with many longer transcripts encompassing 21U-RNA sequences, were detected in our libraries. Conclusions: Our analysis reveals extensive regulation of non-coding small RNAs during development of hermaphrodites and between different genders of C. elegans, and suggests that these RNAs, including novel miRNA candidates, are involved in developmental processes. These findings should lead to a better understanding of the biological roles of small RNAs in C. elegans development.
AB - Background: Small non-coding RNAs, including microRNAs (miRNAs), serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of animals such as Caenorhabditis elegans. Results: We performed a deep analysis of small RNA expression in C. elegans using recent advances in sequencing technology, and found that a significant number of known miRNAs showed major changes in expression during development and between males and hermaphrodites. Additionally, we identified 66 novel miRNA candidates, about 35% of which showed transcripts from their 'star sequence', suggesting that they are bona fide miRNAs. Also, hundreds of novel Piwi-interacting RNAs (piRNAs)/ 21U-RNAs with dynamic expression during development, together with many longer transcripts encompassing 21U-RNA sequences, were detected in our libraries. Conclusions: Our analysis reveals extensive regulation of non-coding small RNAs during development of hermaphrodites and between different genders of C. elegans, and suggests that these RNAs, including novel miRNA candidates, are involved in developmental processes. These findings should lead to a better understanding of the biological roles of small RNAs in C. elegans development.
UR - http://www.scopus.com/inward/record.url?scp=67649663873&partnerID=8YFLogxK
U2 - 10.1186/gb-2009-10-5-r54
DO - 10.1186/gb-2009-10-5-r54
M3 - Article
C2 - 19460142
AN - SCOPUS:67649663873
SN - 1474-7596
VL - 10
JO - Genome biology
JF - Genome biology
IS - 5
M1 - R54
ER -