Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

Yella, Venkata Rajesh and Kumar, Aditya and Bansal, Manju (2018) Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy. In: SCIENTIFIC REPORTS, 8 .

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Abstract

Transcription is an intricate mechanism and is orchestrated at the promoter region. The cognate motifs in the promoters are observed in only a subset of total genes across different domains of life. Hence, sequence-motif based promoter prediction may not be a holistic approach for whole genomes. Conversely, the DNA structural property, duplex stability is a characteristic of promoters and can be used to delineate them from other genomic sequences. In this study, we have used a DNA duplex stability based algorithm `PromPredict' for promoter prediction in a broad range of eukaryotes, representing various species of yeast, worm, fly, fish, and mammal. Efficiency of the software has been tested in promoter regions of 48 eukaryotic systems. PromPredict achieves recall values, which range from 68 to 92% in various eukaryotes. PromPredict performs well in mammals, although their core promoter regions are GC rich. `PromPredict' has also been tested for its ability to predict promoter regions for various transcript classes (coding and non-coding), TATA-containing and TATA-less promoters as well as on promoter sequences belonging to different gene expression variability categories. The results support the idea that differential DNA duplex stability is a potential predictor of promoter regions in various genomes.

Item Type:	Journal Article
Publication:	SCIENTIFIC REPORTS
Publisher:	NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
Additional Information:	Copy right for the article belong to NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	12 Apr 2018 18:49
Last Modified:	12 Apr 2018 18:49
URI:	http://eprints.iisc.ac.in/id/eprint/59522

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