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

Author:

Uemura Kohei1,Ohyama Takashi12

Affiliation:

1. Waseda University Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, , 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

2. Waseda University Department of Biology, Faculty of Education and Integrated Arts and Sciences, , 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan

Abstract

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.

Funder

JST SPRING

JSPS KAKENHI

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Biochemistry,General Medicine

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