Difference between revisions of "Os04g0509300"
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===Function=== | ===Function=== | ||
Please input function information here. | Please input function information here. | ||
| + | Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer-Like (DCL) family, including OsDCL1, -3a, -3b and -4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4-1, we revealed that the processing of 21-nucleotide siRNAs, including trans-acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24-nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase-mediated 5¢ rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21- and 24-nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice. | ||
===Expression=== | ===Expression=== | ||
Revision as of 10:25, 4 June 2014
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Contents
Annotated Information
Function
Please input function information here. Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer-Like (DCL) family, including OsDCL1, -3a, -3b and -4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4-1, we revealed that the processing of 21-nucleotide siRNAs, including trans-acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24-nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase-mediated 5¢ rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21- and 24-nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice.
Expression
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Evolution
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Labs working on this gene
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References
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Structured Information
| Gene Name |
Os04g0509300 |
|---|---|
| Description |
Protein of unknown function DUF283 domain containing protein |
| Version |
NM_001059813.1 GI:115459355 GeneID:4336362 |
| Length |
7383 bp |
| Definition |
Oryza sativa Japonica Group Os04g0509300, complete gene. |
| Source |
Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
| Chromosome | |
| Location |
Chromosome 4:25872631..25880013 |
| Sequence Coding Region |
25872881..25873052,25874123..25874237,25874648..25874984,25875406..25875735,25876197..25876469 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008397:25872631..25880013 source=RiceChromosome04 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008397:25872631..25880013 source=RiceChromosome04 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>gagaacatttatcaagtggataacaccggtgcttccattagcactgcttgtagtgtatctctactacattgctactgcgacaaccttcctagggatatgttttttactccttccccagtgttcttctacattgatggcatcgagggaataatctgcagactaattcttccaccaaatgctgctttccgtcaagcagatggtcaaccatgtctgtcaaaagatgaagctaagagagatgcatgcttaaaggcatgcgtaaaacttcataaattgggtgctttgacagattttcttctgccgggtccaggttcaagaaagaataaagtatcagtaacaaataattcatcaaacaacaaagttgaagatgatagtctaagagaagagcttcatgagatgttaattcctgcagttctcaaaccttcgggattaaagttggattctttatcgaacttgcatttctactatgttaaatttattcccataccagaagataggcgatatcagatgtttggtctctttgtgatcaatccccttcctgtggaagctgaaacattgcaagttgatttgcatcttgctcgtggcaggattgtgaaagcaggaattaagcatttggggaaaatagcatttgagaaagagaagatgatgcttgcacacaagtttcaagagatgtgtctgaagattctcctggacagatctgagtttacttcaccccatgttaaattgggcaatgatgttacattagaaatcaattcaacattttaccttctgcttcccatcaagcaaaagtgttatggtgatagatttatgattgactggccagcagttgagcgctgtttatcatcaccgatttttaaagaccctatagatgtgtctgtgcatgcctcatattcatcaaatgagtctctgagacttcttgatggaatcttcagtaaaaccgatgtagttggcagtgtagtctttagtccccacaacaatatctttttctttgttgatggcattctggacgaaataaatgcttggagcgagcacagtggtgcaacttatgcagaacacttcaaggaaaggtttcgtattgagctatcacatcctgaacagccacttttgaaggctaaacagatcttcaacctgcgaaatttgcttcataatcggttaccggagaccacagaatcggagggccgtgaattactagagcacttcgtggagttacctccagaattatgctctttgaaggtcattgggttttcaaaagatatgggcagttccctgtccttgttaccttctttaatgtatcgtttggagaatttgctggtggctattgagttgaaggatgtgatgttatcttcttttccagaggcatctcaaattagtgcttctggtatacttgaagcgcttactactgagaaatgtttggagaggatatctttggagcgatttgaagtcctaggcgatgctttcttgaagtacgtagttggacgtcacaagtttattacatatgaaggacttgatgaagggcaattgaccaggagacgttctgatgtagtgaacaattcacatttatatgagttatcgatcagaaaaaaattgcaggtatacatacgggatcaacagtttgaaccgactcagttctttgctccaggaaggccttgtaaagttgtttgcaatactgacgtggaagtgagactacaccagatggatattcatccagataacagagaaaactgtaacctgagatgtacaaggtcacatcattggctgcataggaaagtgattgcagatgttgtcgaatcgcttattggagcatttcttgttgagggtggattcaaagctgcatttgctttcctgcattggattggaatagacgttgattttaataatccagctctctatagggtattagattcaagctccatcaatttatctcttatggactacactgacattgccgggcttgaagaattgataggttacaagttcaaacataagggtctacttctccaagcattcgtacacccttcatttagtcaacattctggaggctgctaccagagactggagtttcttggagacgctgttttggagtatgtgataacttcgtacctctactctacttatccggatataaaacctggtcaaataacagatctaagatcgttagctgttggtaatgattcgcttgcttatgcggcggttgagaaatctatccataagcatcttataaaggattcaaaccatctcacgtcagcaataagtaaatttgagatgtatgtgaagctctccaattcagagaaagacttgcttgaagaaccagcatgtcccaaggctcttggtgatattgttgaatcttgtattggcgcagtgcttttagattcaggcttcaacctgaactatgtttggaaggtaatgcttatgcttctaaagccagtattgaccttcgccaacatgcacactaatccgatgagagaacttcgagagctttgtcagtgtcatggatttgagttaggccttccgaaacctatgaaagctgatggagagtaccatgtcaaagtagaagttaacataaagagcaaaattatcatttgtactgcagcaaatcggaattcaaaagccgctagaaagtttgctgcacaagaaacactttctaaactgaagaattacggttataagcacagaaacaagtcccttgaggagattttgattgttgccaggaagagggaatcagaactgataggatataatgaagatccaatcgatgttgaggctgacatatctgtaaaaatgaagagtccacatatacatgaagagaacataccttttcaaaatacagaaacatctttcactaggagttctaaattccacaatcaaattatagcagggtctggcaaacatgatgtcaataatggaaggaacaatcaacccaagttggcaacacagagtggtcgtctgcctagtgaagcaacagagaaaagcaataaaaaggtgtatcatggtgacatggtacacaaaacagcaagatcattcctttttgaactatgtgctgcaaattattggaaacctcctgaattcaagttatgtaaagaggaagggccaagccaccttcggaagttcacttacaaggtggttgttgagatcaagggtgcttcggcgacccttttggagtgtcatagcgatggtaagcttcagaagaaggctgcacaagagcatgcggcacaaggggcgctctggtgtctcaagcaacttgggcacctaccaaaagaagaggacgttcgtgtatag</cdnaseq> |
| Protein Sequence |
<aaseq>ENIYQVDNTGASISTACSVSLLHCYCDNLPRDMFFTPSPVFFYI DGIEGIICRLILPPNAAFRQADGQPCLSKDEAKRDACLKACVKLHKLGALTDFLLPGP GSRKNKVSVTNNSSNNKVEDDSLREELHEMLIPAVLKPSGLKLDSLSNLHFYYVKFIP IPEDRRYQMFGLFVINPLPVEAETLQVDLHLARGRIVKAGIKHLGKIAFEKEKMMLAH KFQEMCLKILLDRSEFTSPHVKLGNDVTLEINSTFYLLLPIKQKCYGDRFMIDWPAVE RCLSSPIFKDPIDVSVHASYSSNESLRLLDGIFSKTDVVGSVVFSPHNNIFFFVDGIL DEINAWSEHSGATYAEHFKERFRIELSHPEQPLLKAKQIFNLRNLLHNRLPETTESEG RELLEHFVELPPELCSLKVIGFSKDMGSSLSLLPSLMYRLENLLVAIELKDVMLSSFP EASQISASGILEALTTEKCLERISLERFEVLGDAFLKYVVGRHKFITYEGLDEGQLTR RRSDVVNNSHLYELSIRKKLQVYIRDQQFEPTQFFAPGRPCKVVCNTDVEVRLHQMDI HPDNRENCNLRCTRSHHWLHRKVIADVVESLIGAFLVEGGFKAAFAFLHWIGIDVDFN NPALYRVLDSSSINLSLMDYTDIAGLEELIGYKFKHKGLLLQAFVHPSFSQHSGGCYQ RLEFLGDAVLEYVITSYLYSTYPDIKPGQITDLRSLAVGNDSLAYAAVEKSIHKHLIK DSNHLTSAISKFEMYVKLSNSEKDLLEEPACPKALGDIVESCIGAVLLDSGFNLNYVW KVMLMLLKPVLTFANMHTNPMRELRELCQCHGFELGLPKPMKADGEYHVKVEVNIKSK IIICTAANRNSKAARKFAAQETLSKLKNYGYKHRNKSLEEILIVARKRESELIGYNED PIDVEADISVKMKSPHIHEENIPFQNTETSFTRSSKFHNQIIAGSGKHDVNNGRNNQP KLATQSGRLPSEATEKSNKKVYHGDMVHKTARSFLFELCAANYWKPPEFKLCKEEGPS HLRKFTYKVVVEIKGASATLLECHSDGKLQKKAAQEHAAQGALWCLKQLGHLPKEEDV RV</aaseq> |
| Gene Sequence |
<dnaseqindica>6962..7133#5777..5891#5030..5366#4279..4608#3545..3817#2978..3436#2391..2600#2079..2290#1503..1603#899..1323#547..821#206..471#1..98#gagaacatttatcaagtggataacaccggtgcttccattagcactgcttgtagtgtatctctactacattgctactgcgacaaccttcctagggatatgtatgtcaagattttttttttttgctcttcagtctgtcaccaactcgccatgacaatgatttattgattagttctttgcgatgctaatataactcctttttatgaaggttttttactccttccccagtgttcttctacattgatggcatcgagggaataatctgcagactaattcttccaccaaatgctgctttccgtcaagcagatggtcaaccatgtctgtcaaaagatgaagctaagagagatgcatgcttaaaggcatgcgtaaaacttcataaattgggtgctttgacagattttcttctgccgggtccaggttcaagaaagaataaagtatcagtaacaaataattcatcaaacaacaaagttgaaggtattttcacttgttcatacagtaccataagcgcataatgctggctctggcttaactcttgtttccttgtttcagatgatagtctaagagaagagcttcatgagatgttaattcctgcagttctcaaaccttcgggattaaagttggattctttatcgaacttgcatttctactatgttaaatttattcccataccagaagataggcgatatcagatgtttggtctctttgtgatcaatccccttcctgtggaagctgaaacattgcaagttgatttgcatcttgctcgtggcaggattgtgaaagcaggaattaagcatttggggaaaatagcatttgagaaagagaaggcatcatcctgctcatctgttcaattgataacacatgattgtttgttggatattatttaatattcttttattttcagatgatgcttgcacacaagtttcaagagatgtgtctgaagattctcctggacagatctgagtttacttcaccccatgttaaattgggcaatgatgttacattagaaatcaattcaacattttaccttctgcttcccatcaagcaaaagtgttatggtgatagatttatgattgactggccagcagttgagcgctgtttatcatcaccgatttttaaagaccctatagatgtgtctgtgcatgcctcatattcatcaaatgagtctctgagacttcttgatggaatcttcagtaaaaccgatgtagttggcagtgtagtctttagtccccacaacaatatctttttctttgttgatggcattctggacgaaataaatgcttggagcgagcacagtggtgcaacttatgcagaacacttcaaggaaaggtaataagtcaattattatccgtgctcaccttcctggtttacatgtttttttaatgggattttactaaataaagtacaacattgcaatacctctattgagcattctttaaggtagatatagcaacacaatcaagtttaagagctttatacatgtcctgatgaacttatgcattaattaggtttcgtattgagctatcacatcctgaacagccacttttgaaggctaaacagatcttcaacctgcgaaatttgcttcataatcggttaccggagaccacaggttattccgttgtcccaccgtaacaagacaccttattcattacttctgattattatgacatgataaaaaatgtaatcagtatatcattatgctaccaagaatgttttgtcatccattagaccacagctcagaaagagcataataaattttatataactacatatatgtcgcggagaagttgctttgtaaacttctattatttattgtttcaaaattattgaactgcttgtggattgctttagagtttggaaactgcttgggaatcagttggatctgttatttttcctatttccttctccggcttttgtatactgggattactatagtagactagtagtacatttataatcttgggacccaatgcattactgaatcctattttgaatatcttactctgctgtgaatctttgcatggttctgatccaggtatagtacttctaatgttgttacatcttttgttattattatttttaagaatcggagggccgtgaattactagagcacttcgtggagttacctccagaattatgctctttgaaggtcattgggttttcaaaagatatgggcagttccctgtccttgttaccttctttaatgtatcgtttggagaatttgctggtggctattgagttgaaggatgtgatgttatcttcttttccagaggcatctcaaattagtgcttctggtgtaagttgcaccatcttttgtacctttgatcctgaacatctagtttgaatttgcttatccatgccgaaaatagttgtgatcttagacgggttcatttcagatacttgaagcgcttactactgagaaatgtttggagaggatatctttggagcgatttgaagtcctaggcgatgctttcttgaagtacgtagttggacgtcacaagtttattacatatgaaggacttgatgaagggcaattgaccaggagacgttctgatgtagtgaacaattcacatttatatgagttatcgatcagaaaaaaattgcaggttagttaaccttgaacccatttttttattgctaagttgtatgatctacaattctaccagaatcatcatattctgcactatctggctctttcattatgatctactacctcggtaccaaaatataagcatttctggctctgaatctagtgtccagattcagagctagacatgcttatattttggggcggaggtagtagcaatattgacaaacattttgtgacacttgtgatctattaattttgtctgcttatttatacaacggttccctttccgtttatttttagatggattccttttatcgctgtagaagatacaactttcctgtcaagtatttattgcaaaattcttaatcagcaatgctttctcgtgaaatttaggtatacatacgggatcaacagtttgaaccgactcagttctttgctccaggaaggccttgtaaagttgtttgcaatactgacgtggaagtgagactacaccagatggatattcatccagataacagagaaaactgtaacctgagatgtacaaggtcacatcattggctgcataggaaagtgattgcagatgttgtcgaatcgcttattggagcatttcttgttgagggtggattcaaagctgcatttgctttcctgcattggattggaatagacgttgattttaataatccagctctctatagggtattagattcaagctccatcaatttatctcttatggactacactgacattgccgggcttgaagaattgataggttacaagttcaaacataagggtctacttctccaagcattcgtacacccttcatttagtcaacattctggaggctgctaccaggtcagagttgcccctctctctctctctctctctctctctctctgattgcacaggtgctgtgattcttgatagttgctcacctgctatgttcttttcatttctggtcagagactggagtttcttggagacgctgttttggagtatgtgataacttcgtacctctactctacttatccggatataaaacctggtcaaataacagatctaagatcgttagctgttggtaatgattcgcttgcttatgcggcggttgagaaatctatccataagcatcttataaaggattcaaaccatctcacgtcagcaataagtaaatttgagatgtatgtgaagctctccaattcagagaaagacttgcttgaagaaccagcatgtcccaaggtattgacgttattgcagagatttttttccatctgcacctttgtagtaacccttttttagccgagaggaagaaagaccatggtcttgtggttgctccctctgtcccacaaaactcaacctagtacttgatgttgatgcatcatagtactacaaatctggacatgtctctgtctagattcctagtactaggatgtgtcaatatccaatactaggttggctttttatgggacggaaggagtactcctcaaggatactgtttaatattcaatatgataggggagatttataagttctacaaaatgagcaaaagtgttatcaataattgcaagtgtattagagaattattaatcatagctcattaccatgattgtgatcttttctgtaagcaattagttatatgtaattgattgattgattttttttatggcaaaagcttataagttttatctacaacaatacaggctcttggtgatattgttgaatcttgtattggcgcagtgcttttagattcaggcttcaacctgaactatgtttggaaggtaatgcttatgcttctaaagccagtattgaccttcgccaacatgcacactaatccgatgagagaacttcgagagctttgtcagtgtcatggatttgagttaggccttccgaaacctatgaaagctgatggagagtaccatgtcaaagtagaagttaacataaagagcaaaattatcatttgtactgcagcaaatcggaattcaaaagccgctagaaagtttgctgcacaagaaacactttctaaactgaaggtacaattttgttcccttagcattttcttctgcaattaccatgcaacacgaatgctttgctttcagttagctgcacgaagcactctctgtagtctatacagaagatatattttttgtgatttttccatttgctttacttttttgcgggaacactatttattttattattagaatgtgagtatcagaacctcagccattacaacgatctattttattttgcttaattgttgacatgaatgtgaaagatcattgatttaatagattggaaagaaactattcattgtgttcattgctttccagtccaacttgccaaatttacacaatatctctttgttgtttgtgttaatctgtccattcaaataccctgtttcttaaaatgcatgccacaaccagcttactggtccttttgtaaattatgcagaattacggttataagcacagaaacaagtcccttgaggagattttgattgttgccaggaagagggaatcagaactgataggatataatgaagatccaatcgatgttgaggctgacatatctgtaaaaatgaagagtccacatatacatgaagagaacataccttttcaaaatacagaaacatctttcactaggagttctaaattccacaatcaaattatagcagggtctggcaaacatgatgtcaataatggaaggaacaatcaacccaagttggcaacacagagtggtcgtctgcctagtgaagcaacagagaaaagcaataaaaaggtgtatcatggtatgctaaaatttcttactttaaagtgctaccattagaaaatttgaaacctggtggaagtctaaacagttacctacatattcagatttacagttacaatattgtggtgtagctcaaactaagcaattacatattccattcaactttgtagtgtacatttgacttaattttgttgcgtgtacgcgaaaaataacttaattttgttctgttgggcacaaccgcacaagtggacacataatatatgttatctctttttaactttatgtgctaaaatgtacgagattggcaaccgtgtcgttgtactaacatcattttaaactatgtgtttaccaaatactgggttcacacttcacagttttgattgtttaattttagaggaaatgccttaacactgtcaatcatcttggtaggtgacatggtacacaaaacagcaagatcattcctttttgaactatgtgctgcaaattattggaaacctcctgaattcaagttatgtaaagaggaagggccaagccaccttcggaagtaagttcatcttcttactgagagcacccgcaatagtaaagtaaggtgctatctataaaacatgtacatctcagcaataggctagattaatagtaaaccacttcaatggtatgtctatatgggtatatataactctctaatccattgcattgtttttctctatagactatttctaggttagtagatagttttgctctctctcttcatttaatatcttccaagtaggaaaatatgctgacatggatgtcttgtagagagcctatagcaggtacaatagcaggctattagccagctgtaaacatatttgtagccagctacagcacggactctaagacgcaatgtgtatataataggtgggaccatatattagtagtatagtaagcaactattgtatgaattggctattagattgactatagataaattggagctaatagtgggctatactattaaacttgctctaagggtgaaataataacctttacgtgttacgatgaaacttacgtcctacctgtactgtttcctttcctttgtgcagtaatatatacatggcctacccagagtagtagatgctcatatttaagttctttatagtctatccagaacgcaaattagcttgtacattttatgatcagaatttcgatgatgcaccttggcttttaggttaaacatggtgttctaaaatgtggattatacataatgccattctcatactaaagcttggtataagctggagcagcaatcgtttaactgacaagcagaactattaagcacgattctgtcatataataatttctatgcctagggaactagatgacacatggcttatacattttttagtaatattgtacttcctccgtttcacaatgtaagtcattctagcttttcccacattcatattcatgttaatgaatctagataaatatatatgtctagattcattaacatcaatatgaatatgggaaatgctagaatgacttacattgtgaaacggagggagtacacaactatctctgttgccacttgcatatgtacacatgcttgctaacttccctggaggaatgatacaggttcacttacaaggtggttgttgagatcaagggtgcttcggcgacccttttggagtgtcatagcgatggtaagcttcagaagaaggctgcacaagagcatgcggcacaaggggcgctctggtgtctcaagcaacttgggcacctaccaaaagaagaggacgttcgtgtatagcaacattgtcatgttttgggggtcacagtgcgaaagtacagtgatatttgtttgtccagagataaacgtgcctttctctcttttgctctgatgtccaacctcccttattaagggacgtgtataaattttcacttctccagtgccctttgaatggctagagttgtatagctagtccattattttccatgagacgtatattggtatatagttttattcttcaatagacgcatatagtattctttcaagttcc</dnaseqindica> |
| External Link(s) |
