Abstract
Postranscriptional regulation has been widely shown to be regulated by several classes of small non-coding RNAs; most abundantly, microRNAs, which have been shown to be the first dominant class and has been widely characterized as post-transcriptional regulators. In addition to microRNAs, triggered by miRNAs, transcripts called as PHAS (or TAS) generate abundant class of small RNAs in 21-nt manner, which is a pattern formed by DICER-LIKE 4 (DCL4) processing. Although PHAS can be identified by aligning transcripts to reported PHAS in other species, the most sensitive and accurate way to discovery them is by mapping of the smallRNAs taking into account the transcript coordinates. Here, we describe a workflow that can be used for the identification PHAS and corresponding phasiRNAs in Brachypodium distachyon using publically availabe smallRNAs datasets.
References
Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159
Zhai J, Zhang H, Arikit S, Huang K, Nan GL, Walbot V, Meyers BC (2015) Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci U S A 112:3146–3151
Fan Y, Yang J, Mathioni SM, Yu J, Shen J, Yang X, Wang L, Zhang Q, Cai Z, Xu C, Li X, Xiao J, Meyers BC, Zhang Q (2016) PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice. Proc Natl Acad Sci U S A 113:15144–15149
Johnson C et al (2009) Clusters and superclusters of phased small RNAs in the de-veloping inflorescence of rice. Genome Res 19(8):1429–1440
Komiya R et al (2014) Rice germline-specific argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant J 78(3):385–397
Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C (2016) Novel meiotic miRNAs and indications for a role of PhasiRNAs in meiosis. Front Plant Sci 7:762
Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y et al (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev 25(23):2540–2553
Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18(19):2368–2379
Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC et al (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16(1):69–79
Yoshikawa M, Peragine A, Park MY, Poethig RS (2005) A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19(18):2164–2175
Zheng Y, Wang Y, Wu J, Ding B, Fei Z (2015) A dynamic evolutionary and functional landscape of plant phased small interfering RNAs. BMC Biol 13(1):1
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Yang, K., Wen, X., Sablok, G. (2018). Method for the Large-Scale Identification of phasiRNAs in Brachypodium distachyon . In: Sablok, G., Budak, H., Ralph, P. (eds) Brachypodium Genomics. Methods in Molecular Biology, vol 1667. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7278-4_14
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DOI: https://doi.org/10.1007/978-1-4939-7278-4_14
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