Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures

Abstract

Background: Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.

Mid-Range Inhomogeneity of Eukaryotic Genomes

“…We start considering mid-range genomic compositional patterns from the most-studied case: G+C-rich and A+T-rich regions. These G+C-rich and A+T-rich regions of various lengths from 30 to several thousand nucleotides are four to 20 times over-represented in the mammalian genomes compared to random expectation [6,7]. Among G+C-rich genomic segments, CpG islands have drawn the most public attention, due to their functional properties and involvement in gene expression regulation [8].…”

“…According to nucleic acid nomenclature, G or T nucleotides are also known as Keto or K, while A or C are known as Imino or M. Thus, sometimes these regions are referred to as K.M tracks or motifs [39]. Bechtel and coauthors demonstrated that G+T regions are about five times more abundant in the mammalian genomes compared to random expectation [7]. Moreover, these regions practically do not intersect with interspersed DNA repeats at all.…”

“…We call such compositional extremes genomic mid-range inhomogeneity (or MRI) if they stretch at least 30 bp, but <10,000 bp. To characterize genomic MRI patterns, a public computational resource (Genomic MRI) has been created that allows us to detect sequence regions with any type of extreme composition [7]. Using this resource, it was demonstrated that various MRI regions occupy up to a quarter of the human genome and their existence is maintained via strong fixation bias [56].…”

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

“…The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al 2009). Here we demonstrate a freely available Internet resource --the Genomic MRI program package --designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences.…”

“…Here we demonstrate a freely available Internet resource --the Genomic MRI program package --designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences.…”