Thus, the cluster of modifications around ubiquitinated Lys-127 in HIST1H2BN (Figure 3), found only due to the application of ETD, may have similar regulatory functions.
This clustering yields patterns of modifications that can be correlated to the function of the chromatin, such as transcriptional start sites and enhancers, or to the underlying process, such as transcriptional elongation by RNA polymerase II.
Additional file 1: Figure S8 shows the clustering of the histone modifications employed by the medicinals composing the 200 formulas.
However, with the development of genome-wide assays, recent studies have revealed marked clustering of particular histone modifications over relatively large genomic regions; e.g. LOCKs and BLOCs (broad local enrichments) enriched with the histone marks H3K9me2 and H3K27me3, respectively.
For a fixed clustering, the optimal number of modifications can be computed in linear time by counting the edges between clusters and computing for each cluster a solution for SPLIT EDITING in linear time [ 14].
However, within each cluster, highly correlated pairs of modifications associated with transcriptional activity or silencing were detected (H3K4me2 and H3K4me3; H3K9me3 and H4K20me3).
We focused on Auts2, a gene linked to human evolution and cognitive disorders, which displays strong clustering of cocaine-induced chromatin modifications in this brain region.
Figure 1 and Additional file 1 Figure S1 show the hierarchical clustering of t-values (histone modification activities) at ORF (total 21 TFs) and promoter (total 12 TFs), respectively.
The analysis of genes involved in this clustering reveals modification of microarray expression in genes involved in cardiac muscle structure and organization and in inflammatory processes.
The filtered 3' ESTs were also assembled using PTA but with the sequence-clipping option disabled and annotation of LCRs and repeats enabled in order to prevent spurious clustering and modification of the input sequences and to facilitate subsequent identification of alternative polyadenylation.
