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Updated: Jul 18, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
Identifying Cis-Regulatory Binding Sites in Promoter Regions of miRNA Genes: A Step-by-Step Protocol
Judith Jazmin Bernal-Gallardo1, Stefan de Folter2
1Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Guanajuato, México.
Abstract:
Plant microRNAs (miRNAs) are often regulated by transcription factors (TFs) binding to specific cis-regulatory sequences in their promoter regions. This protocol provides a user-friendly method for finding TF binding sites in miRNA promoters using MEME Suite and TOMTOM, accessible also to those with minimal programming skills. It offers both manual and automated approaches for sequence retrieval and analysis. MEME Suite helps motif discovery, while TOMTOM compares these motifs to TF binding site databases. This protocol enables efficient analysis of miRNA promoter regions, enhancing understanding of gene regulation.
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