MicroRNA promoter element discovery in Arabidopsis

Abstract

In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these elements in miRNA promoters, protein-coding gene promoters, and random genomic sequences. We report five transcription factor (TF) binding motifs that show evidence of overrepresentation in miRNA promoter regions relative to the promoter regions of protein-coding genes. This investigation is based on the analysis of 800-nucleotide regions upstream of 63 experimentally verified Transcription Start Sites (TSS) for miRNA primary transcripts in Arabidopsis. While the TATA-box binding motif was also previously reported by Xie and colleagues, the transcription factors AtMYC2, ARF, SORLREP3, and LFY are identified for the first time as overrepresented binding motifs in miRNA promoters.

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

“…These observations are consistent with past computational studies on plant miRNAs (Megraw et al, 2006) and may reflect the fact that miRNAs have multiple distinct heavily used TSS locations, which seems consistent with findings in mammalian systems that indicate miRNAs have multiple, complex transcripts that are related to the occurrence of numerous downstream miRNA processing steps (Saini et al, 2007;Bhattacharyya et al, 2012;Marco et al, 2013). In summary, our study indicates that 3PEAT is a useful model for the identification of high confidence, highly expressed TSS locations for miRNA primary transcripts in the absence of laboratory data in the region of interest.…”

“…To identify sequence elements that show TFBS enrichment, we next searched the promoters for specific upstream locations where these TFBS elements could be collectively enriched (see Methods: 3PEAT TSS Peak Prediction Model). We used a standard log-likelihood TFBS scanning technique to approximate DNA binding affinity along with a set of 200 known plant elements characterized in the literature (Grasser, 2006;Megraw et al, 2006;Bryne et al, 2008;Wingender, 2008;Civán and Svec, 2009;Yamamoto et al, 2009).…”

Genomic Analysis of MicroRNA Promoters and Their Cis-Acting Elements in Soybean

“…This finding supported the report that miRNAs might play a role in negative feedback loops that controlled their expression (Johnston et al 2005;Megraw et al 2006). The miR160 gene family in Arabidopsis was involved in feedback loops (Megraw et al 2006). However, no auxin related regulatory element was found in the miR160 family in this study.…”

“…The MBS was also found in each promoter of the miR159 family, from which was the inferred the negative feedback loop model. This finding supported the report that miRNAs might play a role in negative feedback loops that controlled their expression (Johnston et al 2005;Megraw et al 2006). The miR160 gene family in Arabidopsis was involved in feedback loops (Megraw et al 2006).…”

Illuminating microRNA Transcription from the Epigenome

“…Several helpful computational strategies for pri-miRNA characterization have been developed in the last few years [18-24]. Three of the most recent efforts, from Saini et al [22]; Wang et al [23]; and Wang et al [24], involved comprehensive genome-wide scans for known and predicted features of transcription start [22-24] and end regions [22].…”