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Genome-wide RNA Polymerase II binding signal in Arabidopsis thaliana

ABSTRACT: Several studies indicate that plant MIR genes are transcribed by RNA Pol II, similar to what is found in animals (Cai et al., 2004; Lee et al., 2004). By sequencing the 5' transcript ends Xie et al. (2005) mapped the transcription start sites (TSSs) for 52 MIR genes. This list was expanded upon through computational prediction of the core promoters (Zhou et al., 2007). In addition to the TATA box sequence motifs located upstream of the TSSs (Xie et al. 2005), Megraw et al. (2006) identified other transcription factor binding motifs in the promoter of Arabidopsis MIR genes. They showed that within the 800 nucleotides region upstream of TSSs, sequences resembling the binding sites for the transcription factors AtMYC2, ARF, SORLREP3, and LFY were overrepresented relative to protein-coding gene promoters and randomly sampled genomic sequences (Megraw et al. 2006). While these previous studies are instrumental in establishing our working understanding of MIR gene transcription in plants, there are several major knowledge gaps that urgently need to be addressed. Binding of RNA Pol II to the identified MIR promoter regions has not been tested. Because expression of MIR genes does not involve translation, transcriptional control by RNA Pol II might be different from protein-coding genes. In addition, few of the predicted cis elements have been functionally tested. Futher, the number of annotated miRNA genes has since increased from 199 to 232 (miRBase release 17; Kozomara and Griffiths-Jones, 2011). None of the newly identified genes have been subject to examination for promoter and regulatory sequences. Compared to the previously known miRNAs, these genes have narrower phylogenetic distribution and exhibit weaker expression level and more prominent tissue-specific expression (Rajagopalan et al., 2006; Fahlgren et al. 2007; Yang et al., 2011). Based on these observations, it has been argued that continuous gene birth and death allows beneficial miRNAs to be maintained while deleterious ones avoided (Rajagopalan et al., 2006; Fahlgren et al. 2007; Chen and Rajewsky, 2007; Axtell and Bowman, 2008). Identification of the promoter regions of these MIR genes and their comparison to those of the conserved are highly desirable to fully elucidate miRNA based gene regulation. In the current study, we performed chromatin immunoprecipitation (ChIP)-chip for the Pol II complex using the Affymetrix 'At35b_MR_v04' array. We designed a computational approach using genome-wide RPol II binding patterns to identify the promoter region and transcription start site of pri-miRNAs that are actively transcribed.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE35608 | GEO | 2012/02/10

SECONDARY ACCESSION(S): PRJNA152535

REPOSITORIES: GEO

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Genome-wide RNA Polymerase II binding signal in Arabidopsis thaliana

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