Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5'-flanking regions of tRNA genes

Abstract

Numerous noncoding (nc)RNAs have been identified. Similar to the transcription of protein-coding (mRNA) genes, long noncoding (lnc)RNA genes and most of micro (mi)RNA genes are transcribed by RNA polymerase II (Pol II). In the transcription of mRNA genes, core promoters play an indispensable role; they support the assembly of the preinitiation complex (PIC). However, the structural and/or physical properties of the core promoters of lncRNA and miRNA genes remain largely unexplored, in contrast with those of mRNA genes. Using the core promoters of human genes, we analyzed the repertoire and population ratios of residing core promoter elements (CPEs) and calculated the following five DNA physical properties (DPPs): duplex DNA free energy, base stacking energy, protein-induced deformability, rigidity and stabilizing energy of Z-DNA. Here, we show that their CPE and DPP profiles are similar to those of mRNA gene promoters. Importantly, the core promoters of these three classes of genes have two highly distinctive sites in their DPP profiles around the TSS and position -27. Similar characteristics in DPPs are also found in the 5'-flanking regions of tRNA genes, indicating their common essential roles in transcription initiation over the kingdom of RNA polymerases.

Keywords: Core promoter; lncRNA; miRNA; physical properties of DNA; protein-coding gene; tRNA.

Graphical Abstract

Figure 1

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Fig. 1

CPEs and DPPs of human lncRNA gene promoters. (A) The numbers of lncRNA genes in 16 categorized groups. The data of Extended Fig. 1c of Hon et al. (25) were modified. Definitions of the genomic context and the DHS type by Hon et al. (25) are as follows. ‘Divergent from mRNA’ (‘divergent lncRNAs’ in their study): the lncRNA genes occurring on the opposite strand of any mRNA genes or pseudogenes. ‘Sense-intronic lncRNA’: representatively, the lncRNA genes starting within the intron of another gene or those with at least 1/2 of their genic region overlapping with the genic region of any another gene. For the other species, see Hon et al. (25). ‘Antisense to mRNA’ (‘antisense lncRNAs’ in their study): ≥50% genic regions of the lncRNA genes overlapping with those of mRNA genes or pseudogenes on the opposite strand. ‘Intergenic’ (‘intergenic lncRNAs’ in their study): the lncRNA genes on the outside of the above categories. The DHS types of lncRNA genes depend on where the DNase I hypersensitive sites (DHSs) occur and were classified as promoter, enhancer and 'dyadic' (25). Among them, the term 'dyadic' is used when the category can be both promoter and enhancer. (B) Classification of promoters by CPEs. The classification was performed group by group. The term ‘core-less’ refers to the promoters that lack CPEs. Only the percentages of the top five promoter ‘species’ are shown. (C, D) Average DPP profiles: C, profiles of 27,919 unsorted promoters; D, profiles of 15,820 core-less promoters. The five DPPs were duplex DNA free energy (28), base stacking energy (29), protein-induced deformability (30), rigidity (31), and stabilizing energy of Z-DNA (AS) (32). Promoters were aligned with the TSSs assigned at 0. Only mean values are shown. Two vertical dotted lines indicate positions 0 and −27, respectively. For the profiles of a wider DNA range and the data for SD, see Supplementary Figs. S1A, B and Supplementary Materials S4A-J, respectively.

Fig. 2

CPEs and DPPs of human miRNA gene promoters. (A) Classification of promoters by CPEs. The human miRNA genes were divided into two groups: intergenic and intronic (16). The classification was performed group by group. Only the percentages of the top five promoter species are shown. For all data, see Supplementary Material S2. (B, C) Average DPP profiles: B, profiles of 1005 unsorted promoters; C, profiles of 587 core-less promoters. Promoters were aligned with the TSSs assigned at 0. Only mean values are shown. Two vertical dotted lines indicate positions 0 and −27, respectively. For the profiles of a wider DNA range and the data for SD, see Supplementary Figs. S2A, B and Supplementary Materials S5A-J, respectively.

Fig. 3

CPEs and DPPs of human mRNA gene promoters. (A) Classification of promoters by CPEs. Randomly selected promoters (n = 3000) were subjected to the analysis. Only the percentages of the top five promoter species are shown. For all data, see Supplementary Material S3. (B, C) Average DPP profiles: B, profiles of the 3000 unsorted promoters; C, profiles of 1677 core-less promoters. Promoters were aligned with the TSSs assigned at 0. Means ± SD are shown. Two vertical dotted lines indicate positions 0 and −27, respectively. For the profiles of a wider DNA range, see Supplementary Figs. S3A, B.

Fig. 4

Average DPP profiles of 5′-flanking and internal promoter regions of human tRNA genes. (A) Diagram illustrating the three regions used for the acquisition of DPP profiles. (B) Profiles of the region spanning from the TSS to position −50 relative to the TSS (defined as 0). The number of samples was 445. Means ± SD are shown. Two vertical dotted lines indicate positions 0 and −27, respectively. (C) Profiles of the A-box-containing region spanning from the position corresponding to the 5′-end of the tRNA (defined as 0) to +30, relative to position 0. The A-box region is indicated with a dashed line. (D) Profiles of the B-box-containing region spanning from the position corresponding to the discriminator base of the tRNA (defined as 0) to −30, relative to position 0. The B-box region is indicated with a dashed line.