Normalized frequency distribution profile of CCAAT-box with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of CCAAT-box frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath - solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of CCAAT-box based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of CCAAT-box element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma-solid purple). Genome-wide functional distribution profile of CCAAT-box based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the CCAAT-box element.</p

Normalized frequency distribution profile of DCE-S2 with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of DCE-S2 frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath-solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of DCE-S2 based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of DCE-S2 element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of DCE-S2 based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the DCE-S2 element.</p

Normalized frequency distribution profile of Y-patch with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of Y-patch element frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath - solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of Y-patch based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of Y-patch element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of Y-patch based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the Y-patch element.</p

Functional annotation based on gene ontology molecular functions and biological processes of TATAless genes in <i>Arabidopsis thaliana</i>.

<p>Significantly overrepresented GO terms based on GO molecular functions and biological processes were visualized in Cytoscape. The size of a node is proportional to the number of genes in the GO category. The color represents enrichment significance - the deeper the color on a color scale, the higher the enrichment significance. White color nodes are not enriched but show the hierarchical relationship among the enriched ontology branches.</p

Normalized frequency distribution profile of BREd with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of BREd element frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath - solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of BREd based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of BREd element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of BREd based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the BREd element.</p

Normalized frequency distribution profile of Inr with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of Inr frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath - solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of Inr based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of Inr element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of Inr based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the Inr element.</p

Functional annotation based on gene ontology molecular functions and biological processes of TATA containing genes in <i>Arabidopsis thaliana</i>.

<p>Significantly overrepresented GO terms based on GO molecular functions and biological processes were visualized in Cytoscape. The size of a node is proportional to the number of genes in the GO category. The color represents enrichment significance - the deeper the color on a color scale, the higher the enrichment significance. White color nodes are not enriched but show the hierarchical relationship among the enriched ontology branches.</p

Normalized frequency distribution profile of BREu with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of BREu element frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath -solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green). Genome-wide functional distribution profile of BREu based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of BREu element frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of BREu based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the BREu element.</p

Genome-wide distribution of promoter-region DNA free energy profiles across eight plant genomes.

<p>Panel A: DNA free energy distribution profile of the core promoter-region across four dicots -<i>Arabidopsis thaliana</i> (Ath - solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi -solid blue green) and four monocots - <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). The dicots showed higher average free energy than the monocots and their free energy profiles were distinctly separated from monocot energy profiles. The core promoter region between two vertical dotted black lines (around TSS) shows a sharp peak of instability near the TSS, against an overall trend of increasing stability going from upstream to downstream of the TSS. Panel B: The DNA free energy distribution of random 1000-bp windows of genomic sequence for the same species, showing flat profiles.</p

Normalized frequency distribution profile of DPE with respect to TSS across monocots and dicots.

<p>Panel A: Genome-wide positional distribution of DPE frequency profile across four dicots: <i>Arabidopsis thaliana</i> (Ath-solid navy blue), <i>Glycine max</i> (Gma-solid dark blue), <i>Populus trichocarpa</i> (Ptr –solid blue sapphire), and <i>Vitis vinifera</i> (Vvi-solid blue green). Genome-wide functional distribution profile of DPE based on the ortholog mapping of Ath with rest of the dicots (Ath:Gma, Ath:Ptr, and Ath:Vvi) is shown in dotted brown colored line. Panel B: Genome-wide positional distribution of DPE frequency profile across four monocots: <i>Brachypodium distachyon</i> (Bdi-solid bronze yellow), <i>Oryza sativa ssp. japonica</i> (Osa-solid red), <i>Sorghum bicolor</i> (Sbi-solid bronze), and <i>Zea mays</i> (Zma -solid purple). Genome-wide functional distribution profile of DPE based on the ortholog mapping of Osa with rest of the monocots (Osa:Bdi, Osa:Sbi, and Osa:Zma) is shown in dotted brown colored line. X-axis shows [−500,+500 with respect to TSS] that is binned into 20 base-pair bins, where each bin is represented by the bin-center. Y-axis shows the normalized frequency distribution of the DPE.</p