Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.
Bottom Line: The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks).Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio.The observed correlations may be related to the regulation of gene expression in eukaryotes.
Affiliation: Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia email@example.com.Show MeSH
Mentions: The second problem concerned the relationships between profiles characterizing DNA binding with proteins E(Z), Pc-S2, and Psc, and H3me3K27 marks in the chromosomes of D. melanogaster. E(Z), Pc-S2, and Psc belong to the polycomb group (PcG) of proteins, which are important for maintaining the transcriptional repression of homeotic genes.29–32 The corresponding processed and aggregated profiles were obtained by Schwartz et al.29 and were taken from EMBL ArrayExpress accession E-MEXP-535.33 The profiles were preliminarily filtered by the cut-off threshold mean + 2 SD and clustered with a distance in the range 50–500 nt with steps of 50 nt (Preprocessing of input genetic data). The data before and after preprocessing with a clustering distance of 50 nt are shown in Fig. 2a. The corresponding z-ratios [Equation (23)] indicate strong correlations between binding profiles for the PcG proteins and for H3me3K27 marks (Fig. 2b). The correlations strongly depend on the clustering distance (Fig. 2c and Supplementary data S5). As the characteristic binding region for the PcG proteins is ∼50 nt,34 the clustering distance of 50 nt may be considered as optimal in this example. The cut-off threshold affects the number of nearest neighbours, but it retains the mode of correlations at a given clustering distance. These observations are in accordance with the data on the coordinate action of the E(Z), Pc-S2, and Psc proteins, and the H3me3K27 marks in the silencing mechanisms for D. melanogaster.29,30Figure 2.
Affiliation: Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia firstname.lastname@example.org.