NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs.
Nucleic Acids Res
; 48(12): 6481-6490, 2020 07 09.
Article
en En
| MEDLINE
| ID: mdl-32463462
ABSTRACT
Natural antisense transcript-derived small interfering RNAs (nat-siRNAs) are a class of functional small RNA (sRNA) that have been found in both plant and animals kingdoms. In plants, these sRNAs have been shown to suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex (RISC) to their sequence-specific mRNA target(s). Current computational tools for classification of nat-siRNAs are limited in number and can be computationally infeasible to use. In addition, current methods do not provide any indication of the function of the predicted nat-siRNAs. Here, we present a new software pipeline, called NATpare, for prediction and functional analysis of nat-siRNAs using sRNA and degradome sequencing data. Based on our benchmarking in multiple plant species, NATpare substantially reduces the time required to perform prediction with minimal resource requirements allowing for comprehensive analysis of nat-siRNAs in larger and more complex organisms for the first time. We then exemplify the use of NATpare by identifying tissue and stress specific nat-siRNAs in multiple Arabidopsis thaliana datasets.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Análisis de Secuencia de ARN
/
ARN de Planta
/
ARN Interferente Pequeño
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2020
Tipo del documento:
Article
País de afiliación:
Reino Unido