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Author Zhu,Q.H., Spriggs,A., Matthew,L., Fan,L., Kennedy,G., Gubler,F. and Helliwell,C.
Title A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
Endogenous small RNAs, including microRNAs (miRNAs) and short-interfering RNAs (siRNAs), function as post-transcriptional or transcriptional regulators in plants. miRNA function is essential for normal plant development and therefore is likely to be important in the growth of the rice grain. To investigate the roles of miRNAs in rice grain development, we carried out deep sequencing of the small RNA populations of rice grains at two developmental stages. In a data set of approximately 5.5 million sequences, we found representatives of all 20 conserved plant miRNA families. We used an approach based on the presence of miRNA and miRNA* sequences to identify 39 novel, nonconserved rice miRNA families expressed in grains. Cleavage of predicted target mRNAs was confirmed for a number of the new miRNAs. We identified a putative mirtron, indicating that plants may also use spliced introns as a source of miRNAs. We also identified a miRNA-like long hairpin that generates phased 21 nt small RNAs, strongly expressed in developing grains, and show that these small RNAs act in trans to cleave target mRNAs. Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner.
Journal Genome Res.
Country Australia
Volume 18(9)
Pages 1456-1465
Year 2008
PubMed ID 18687877
PubMed Central ID -
DOI 10.1101/gr.075572.107
Gene MIR1423 MIR1428B MIR1428C MIR1428D MIR1428E MIR1846A MIR1846B MIR1846C MIR1846D MIR1847 MIR1848 MIR1849 MIR1850 MIR1851 MIR1852 MIR1853 MIR1854 MIR1855 MIR1856 MIR1857 MIR1858A MIR1858B MIR1859 MIR1860 MIR1861A MIR1861B MIR1861C MIR1861D MIR1861E MIR1861F MIR1861G MIR1861H MIR1861I MIR1861J MIR1861K MIR1861L MIR1861M MIR1861N MIR1862A MIR1862B MIR1862C MIR1862D MIR1862E MIR1863 MIR1864 MIR1865 MIR1866 MIR1867 MIR1868 MIR1869 MIR1870 MIR1871 MIR1872 MIR1873 MIR1875 MIR1876 MIR1877 MIR1878 MIR1879 MIR1880 MIR1881 MIR1882A MIR1882B MIR1882C MIR1882D MIR1882E MIR1882F MIR1882G MIR1882H MIR1883A MIR1883B MIR529B MIR531B MIR806I_AS MIR806J_AS MIR812F MIR812G MIR812H MIR812I MIR812J TAS3A1 TAS3B1 TAS3B2 miR1874
INSD EU563913 EU563914 EU563915 EU563916 EU563917 EU563918 EU293143 EU293144 EU293145
Strain Wild Core Collection -
Induced Mutation Lines(NIG Collection) -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
Stages in Each Organ
- Muant Lines (Gene)
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -