ORIGINAL ARTICLE ASR5 is involved in the regulation of miRNA expression in rice Lauro Bu ¨ cker Neto 1 • Rafael Augusto Arenhart 3 • Luiz Felipe Valter de Oliveira 2 • Ju ´lio Cesar de Lima 4 • Maria Helena Bodanese-Zanettini 1 • Rogerio Margis 2 • Ma ´rcia Margis-Pinheiro 1 Received: 24 April 2015 / Revised: 25 June 2015 / Accepted: 30 June 2015 Ó Springer-Verlag Berlin Heidelberg 2015 Abstract Key message The work describes an ASR knockdown transcriptomic analysis by deep sequencing of rice root seedlings and the transactivation of ASR cis-acting elements in the upstream region of a MIR gene. Abstract MicroRNAs are key regulators of gene expres- sion that guide post-transcriptional control of plant devel- opment and responses to environmental stresses. ASR (ABA, Stress and Ripening) proteins are plant-specific transcription factors with key roles in different biological processes. In rice, ASR proteins have been suggested to participate in the regulation of stress response genes. This work describes the transcriptomic analysis by deep sequencing two libraries, comparing miRNA abundance from the roots of transgenic ASR5 knockdown rice seedlings with that of the roots of wild-type non-trans- formed rice seedlings. Members of 59 miRNA families were detected, and 276 mature miRNAs were identified. Our analysis detected 112 miRNAs that were differentially expressed between the two libraries. A predicted inverse correlation between miR167abc and its target gene (LOC_Os07g29820) was confirmed using RT-qPCR. Pro- toplast transactivation assays showed that ASR5 is able to recognize binding sites upstream of the MIR167a gene and drive its expression in vivo. Together, our data establish a comparative study of miRNAome profiles and is the first study to suggest the involvement of ASR proteins in miRNA gene regulation. Keywords MiRNAome Á Gene expression profile Á Transcription factor Á Roots Communicated by M. Menossi. Electronic supplementary material The online version of this article (doi:10.1007/s00299-015-1836-3) contains supplementary material, which is available to authorized users. & Ma ´rcia Margis-Pinheiro marcia.margis@ufrgs.br Lauro Bu ¨cker Neto laurobucker@gmail.com Rafael Augusto Arenhart rafaarenhart@yahoo.com.br Luiz Felipe Valter de Oliveira scryrps@gmail.com Ju ´lio Cesar de Lima juliocesarlima@upf.br Maria Helena Bodanese-Zanettini maria.zanettini@ufrgs.br Rogerio Margis rogerio.margis@ufrgs.br 1 Programa de Po ´s-Graduac ¸a ˜o em Gene ´tica e Biologia Molecular, Departamento de Gene ´tica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonc ¸alves 9500, pre ´dio 43312, Porto Alegre, RS 91501-970, Brazil 2 Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonc ¸alves 9500, pre ´dio 43431, Porto Alegre, RS 91501-970, Brazil 3 Centro Nacional de Pesquisa de Uva e Vinho, Empresa Brasileira de Pesquisa Agropecua ´ria, Rua Livramento 515, Bento Gonc ¸alves, RS 95700-000, Brazil 4 Universidade de Passo Fundo, Laborato ´rio de Gene ´tica Molecular, BR285, Passo Fundo, RS 99052-900, Brazil 123 Plant Cell Rep DOI 10.1007/s00299-015-1836-3