Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development

Abstract

Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which depends on the orchestrated accessibility of regulatory proteins to promoters and other cis-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the developmental process. To understand the regulatory mechanism and functional elements modulating morphological and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites (DHSs) from the fruit tissues of the tomato cultivar "Moneymaker" at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening.

Profiling of chromatin accessibility across Aspergillus species and identification of transcription factor binding sites in the Aspergillus genome using filamentous fungi ATAC-seq

“…Overall, the identified accessible regions were mostly enriched around the TSSs (Fig. 1D), which is consistent with the fact that these regions usually contain active regulatory cis- elements (Qiu et al 2016). The signal intensity of accessible regions became weaker as the distance from the TSS became greater in both the Watson and Crick strands (Fig.…”

“…The chromatin accessibility regions of A. niger CBS513.88 and SH2 were similarly distributed across the various elements of the genome; the chromatin accessibility regions were found in a high proportion at TSSs (∼70%) and in a low proportion at intergenic regions (∼5%). The proportional distribution of accessible regions is different from what is observed in humans (Ackermann et al 2016), Arabidopsis (Tannenbaum et al 2018) and tomato (Qiu et al 2016), which show a high distribution in intergenic regions and gene bodies. This difference may reflect the smaller size of the A. niger genome (35 Mb) compared with the larger and less compact genomes of humans (750 Mb), Arabidopsis (125 Mb) and tomato (900 Mb).…”

“…This result may be caused by three factors: (i) None of these TFs are pioneers that change chromatin accessibility, and the vacancies caused by TF defects are filled by other non-functional proteins. (ii) TF regulation is a complex dynamic process in vivo (Qiu et al 2016; Wu et al 2016), so that even if a TF was knocked out, there may be different TFs with alternate binding at the same DNA site. For example, the AmyR recognizing motif 5’-CGGN8(C/A)GG-3’ and the PrtT recognizing motif CCG(H)CGG compete for the binding sites in the same target gene during nitrogen and carbon source metabolism regulation (Chen et al 2014).…”

“…Transcription factors (TFs) are key regulators of biological processes that function by binding to transcriptional regulatory regions to control the expression of target genes. The CREs related to TF binding play pivotal roles in the regulation of gene expression, and each TF recognizes a collection of similar DNA sequences, known as binding site motifs (Felsenfeld 1992; Qiu et al 2016). Therefore, the ability to identify these CREs and TF motifs throughout Aspergillus genomes is an important step in understanding the regulatory functions of TF binding and gene expression.…”

Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome

“…These technologies were successfully applied to identify functional CREs in several model animal species, including humans (The ENCODE Project Consortium, 2004), mouse (Stamatoyannopoulos et al, 2012), Caenorhabditis elegans, and Drosophila melanogaster (Hesselberth et al, 2009;Gerstein et al, 2010). Similar efforts have recently been reported in plants (Zhang et al, 2012a;Zhang et al, 2012b;Pajoro et al, 2014;Sullivan et al, 2014;Cumbie et al, 2015;Qiu et al, 2016), which showed that open chromatin possesses unique epigenetic modifications (Zhang et al, 2012a) and is associated with DNA sequences bound to transcription factors (TFs; Zhang et al, 2012b) and with enhancer function (Zhu et al, 2015). These studies provided insights on the regulatory landscape and transcription factor networks in plant species.…”