Limits...
Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI - DNA Res. (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia jiri@eimb.ru.

Show MeSH
(a) The binding profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks over chromosome 3R of Drosophila melanogaster. For the study of correlations, these profiles were preliminary filtered by the cut-off threshold mean + 2 SD and clustered with distance of 50 nt [Preprocessing of input genetic data and Equation (12)]. The input data after preprocessing are shown below initial profiles. (b) z-ratios [Equation (23)] characterizing pairwise positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for the H3me3K27 mark in the different chromosomes of D. melanogaster. The input data were preprocessed as described above. The numbers below the chromosome nomenclature correspond to that of the nearest neighbours. The horizontal broken lines for z-ratios correspond to 5% (/z/ = 1.96) and 1% (/z/ = 2.58) significance thresholds for random correlations. (c) Ratios characterizing positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks in the chromosome 2R of D. melanogaster at the different clustering lengths. The profiles were preliminary filtered by the cut-off threshold mean + 2 SD. The positive values of zcorr reflect a trend towards shorter distances between profiles relative to the reference model (or correlations), whereas the negative values of zcorr reflect a trend towards longer distances between profiles (or anticorrelations).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4379982&req=5

DSU044F2: (a) The binding profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks over chromosome 3R of Drosophila melanogaster. For the study of correlations, these profiles were preliminary filtered by the cut-off threshold mean + 2 SD and clustered with distance of 50 nt [Preprocessing of input genetic data and Equation (12)]. The input data after preprocessing are shown below initial profiles. (b) z-ratios [Equation (23)] characterizing pairwise positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for the H3me3K27 mark in the different chromosomes of D. melanogaster. The input data were preprocessed as described above. The numbers below the chromosome nomenclature correspond to that of the nearest neighbours. The horizontal broken lines for z-ratios correspond to 5% (/z/ = 1.96) and 1% (/z/ = 2.58) significance thresholds for random correlations. (c) Ratios characterizing positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks in the chromosome 2R of D. melanogaster at the different clustering lengths. The profiles were preliminary filtered by the cut-off threshold mean + 2 SD. The positive values of zcorr reflect a trend towards shorter distances between profiles relative to the reference model (or correlations), whereas the negative values of zcorr reflect a trend towards longer distances between profiles (or anticorrelations).

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.


Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI - DNA Res. (2015)

(a) The binding profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks over chromosome 3R of Drosophila melanogaster. For the study of correlations, these profiles were preliminary filtered by the cut-off threshold mean + 2 SD and clustered with distance of 50 nt [Preprocessing of input genetic data and Equation (12)]. The input data after preprocessing are shown below initial profiles. (b) z-ratios [Equation (23)] characterizing pairwise positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for the H3me3K27 mark in the different chromosomes of D. melanogaster. The input data were preprocessed as described above. The numbers below the chromosome nomenclature correspond to that of the nearest neighbours. The horizontal broken lines for z-ratios correspond to 5% (/z/ = 1.96) and 1% (/z/ = 2.58) significance thresholds for random correlations. (c) Ratios characterizing positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks in the chromosome 2R of D. melanogaster at the different clustering lengths. The profiles were preliminary filtered by the cut-off threshold mean + 2 SD. The positive values of zcorr reflect a trend towards shorter distances between profiles relative to the reference model (or correlations), whereas the negative values of zcorr reflect a trend towards longer distances between profiles (or anticorrelations).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379982&req=5

DSU044F2: (a) The binding profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks over chromosome 3R of Drosophila melanogaster. For the study of correlations, these profiles were preliminary filtered by the cut-off threshold mean + 2 SD and clustered with distance of 50 nt [Preprocessing of input genetic data and Equation (12)]. The input data after preprocessing are shown below initial profiles. (b) z-ratios [Equation (23)] characterizing pairwise positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for the H3me3K27 mark in the different chromosomes of D. melanogaster. The input data were preprocessed as described above. The numbers below the chromosome nomenclature correspond to that of the nearest neighbours. The horizontal broken lines for z-ratios correspond to 5% (/z/ = 1.96) and 1% (/z/ = 2.58) significance thresholds for random correlations. (c) Ratios characterizing positional correlations between profiles for proteins E(Z), Pc-S2, and Psc, and for H3me3K27 histone marks in the chromosome 2R of D. melanogaster at the different clustering lengths. The profiles were preliminary filtered by the cut-off threshold mean + 2 SD. The positive values of zcorr reflect a trend towards shorter distances between profiles relative to the reference model (or correlations), whereas the negative values of zcorr reflect a trend towards longer distances between profiles (or anticorrelations).
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia jiri@eimb.ru.

Show MeSH