Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends.

Julia H Chariker,Eric C Rouchka,Donald M Miller,Fenfei Leng

doi:10.1371/journal.pone.0165101

Julia H Chariker, Eric C Rouchka + Show 2 more

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https://doi.org/10.1371/journal.pone.0165101

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Journal: PloS one	Publication Date: Oct 24, 2016
Citations: 16	License type: CC BY 4.0

Affiliation: University of Louisville, James Graham Brown Foundation

Abstract

G-quadruplex structures (G4) are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.

Highlights

G-quadruplex structures, often referred to as G4, are a form of non-B DNA involved in a variety of molecular processes [1,2,3,4,5,6,7,8,9]
One might expect a relationship between G-rich structures and alternating GC content across cytobands, the G4 banding patterns were not entirely related to the GC content across different cytobands categories
Just as cytobands serve as a unique signature for identifying chromosomes, the banding patterns of G4 do so as well

Summary

Introduction

G-quadruplex structures, often referred to as G4, are a form of non-B DNA involved in a variety of molecular processes [1,2,3,4,5,6,7,8,9] They are defined by sequences of DNA or RNA that consist of four tracts of guanine bases separated by short (3–7 bp) runs of non-specific nucleotide sequences. The sequence folds to form a three-dimensional structure in which the guanine tracts form stacks of planar structures, known as G-tetrads, while short segments separating the guanine tracts form connecting loops in the three-dimensional structure (see Fig 1). These structures are highly polymorphic, and variations often involve different numbers of G-tetrads and different connecting loop lengths. The configuration that results from the folding process is relevant to the stability and the function of the three-dimensional structure [10].

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