Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant Export

@article{citeulike:3349720, abstract = {10.1073/pnas.0808066105 Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size. Most endogenous siRNAs in are dependent on - () for their biogenesis. Recent work has demonstrated that the maize () gene is a predicted ortholog of . The gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wild-type maize and in the isogenic - loss-of-function mutant by using Illumina's sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to in , in -, the 24-nucleotide (nt) endogenous heterochromatic short-interfering siRNAs were dramatically reduced, resulting in an enrichment of miRNAs and transacting siRNAs. In contrast to the mutant, the - plants retained a highly abundant heterochromatic ≈22-nt class of small RNAs, suggesting a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in - should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.}, author = {Nobuta, Kan and Lu, Cheng and Shrivastava, Roli and Pillay, Manoj and De Paoli, Emanuele and Accerbi, Monica and Arteaga-Vazquez, Mario and Sidorenko, Lyudmila and Jeong, Dong-Hoon and Yen, Yang and Green, Pamela J. and Chandler, Vicki L. and Meyers, Blake C.}, citeulike-article-id = {3349720}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0808066105}, citeulike-linkout-1 = {http://www.pnas.org/content/0808066105v1//.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/0808066105v1//.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/18815367}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=18815367}, day = {24}, doi = {10.1073/pnas.0808066105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {maize, mop1, smrna}, posted-at = {2008-11-21 21:31:57}, priority = {2}, title = {Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant}, url = {http://dx.doi.org/10.1073/pnas.0808066105}, year = {2008} }

TY - JOUR ID - citeulike:3349720 L3 - citeulike-article-id:3349720 N2 - 10.1073/pnas.0808066105 Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size. Most endogenous siRNAs in are dependent on - () for their biogenesis. Recent work has demonstrated that the maize () gene is a predicted ortholog of . The gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wild-type maize and in the isogenic - loss-of-function mutant by using Illumina's sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to in , in -, the 24-nucleotide (nt) endogenous heterochromatic short-interfering siRNAs were dramatically reduced, resulting in an enrichment of miRNAs and transacting siRNAs. In contrast to the mutant, the - plants retained a highly abundant heterochromatic ≈22-nt class of small RNAs, suggesting a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in - should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced. JF - Proceedings of the National Academy of Sciences TI - Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant KW - maize KW - mop1 KW - smrna AU - Nobuta, Kan AU - Lu, Cheng AU - Shrivastava, Roli AU - Pillay, Manoj AU - De Paoli, Emanuele AU - Accerbi, Monica AU - Arteaga-Vazquez, Mario AU - Sidorenko, Lyudmila AU - Jeong, Dong-Hoon AU - Yen, Yang AU - Green, Pamela AU - Chandler, Vicki AU - Meyers, Blake PY - 2008//24/ UR - http://dx.doi.org/10.1073/pnas.0808066105 ER -