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A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms

Noronha Fernandes-Brum, Christiane ; Marinho Rezende, Pâmela ; Cherubino Ribeiro, Thales Henrique ; Ricon de Oliveira, Raphael ; Cunha de Sousa Cardoso, Thaís ; Rodrigues do Amaral, Laurence ; de Souza Gomes, Matheus ; Chalfun-Junior, Antonio Lu, Rui

PloS one, 2017-04, Vol.12 (4), p.e0176333-e0176333 [Periódico revisado por pares]

United States: Public Library of Science

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A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms
Autor: Noronha Fernandes-Brum, Christiane ; Marinho Rezende, Pâmela ; Cherubino Ribeiro, Thales Henrique ; Ricon de Oliveira, Raphael ; Cunha de Sousa Cardoso, Thaís ; Rodrigues do Amaral, Laurence ; de Souza Gomes, Matheus ; Chalfun-Junior, Antonio
Lu, Rui
Assuntos: Agricultural economics ; Arabidopsis thaliana ; Base Sequence ; Biochemistry ; Bioinformatics ; Biology ; Biology and life sciences ; Biosynthesis ; Catalysis ; Coffea canephora ; Coffee ; Coffee - genetics ; Computer and Information Sciences ; Computer applications ; Deoxyribonucleic acid ; DNA ; DNA methylation ; DNA-directed RNA polymerase ; Double-stranded RNA ; Economic models ; Gene expression ; Gene regulation ; Gene Silencing ; Genomes ; Genomics ; Kinases ; Laboratories ; Loci ; MicroRNAs ; miRNA ; Pathways ; Physiology ; Polymerase ; Post-transcription ; Proteins ; Regulatory mechanisms (biology) ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA polymerase ; RNA, Small Interfering - genetics ; RNA-directed RNA polymerase ; RNA-mediated interference ; siRNA ; Structure-function relationships ; Transcription factors
É parte de: PloS one, 2017-04, Vol.12 (4), p.e0176333-e0176333
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Conceptualization: CNFB MSG ACJ.Data curation: CNFB PMR THCR TCSC LRA MSG.Formal analysis: CNFB PMR THCR TCSC LRA MSG.Funding acquisition: ACJ MSG.Investigation: CNFB PMR THCR TCSC LRA MSG.Methodology: LRA MSG.Project administration: CNFB.Resources: ACJ MSG LRA.Software: PMR THCR LRA MSG.Supervision: ACJ MSG.Validation: RRO.Visualization: CNFB PMR THCR.Writing – original draft: CNFB.Writing – review & editing: RRO MSG ACJ.
Competing Interests: The authors have declared that no competing interests exist.
Descrição: microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated), and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA) pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.
Editor: United States: Public Library of Science
Idioma: Inglês

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A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms

Noronha Fernandes-Brum, Christiane ; Marinho Rezende, Pâmela ; Cherubino Ribeiro, Thales Henrique ; Ricon de Oliveira, Raphael ; Cunha de Sousa Cardoso, Thaís ; Rodrigues do Amaral, Laurence ; de Souza Gomes, Matheus ; Chalfun-Junior, Antonio Lu, Rui

United States: Public Library of Science

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