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Computational Molecular Biology 2014, Vol. 4, No. 10, 1-17
http://cmb.biopublisher.ca
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Figure 3 Characterization of co-localized peaks. (A) Venn diagram visualizing the targeting GO terms shared by me1me2,
me1me2me3, me1me3 and me2me3 co-localization. (B) Sequence patterns for all types of localized peaks in gene context. Except
me1me2me3, all are associated with CA or GT repeat, which is considered to have biological regulatory function
Though mono-, di- and tri-methylation of H3K4 were
generally considered to be co-localized in the same
regions, the GO term enrichment suggested that the
H3K4me triplet type had only three distinct GO terms.
The mark was related with signal transduction, cell
component, and transcription repression. Contrary to
the expectation, 12 out of 332 genes were annotated
with transcription repressor activity. We visualized
some of them to make a conclusion that several peaks
were co-localized in intronic regions, suggesting the
regulatory role in intronic regions. Besides introns,
other co-localized peaks for these 12 genes were
located in TSS upstream regions. Actually, the
observation of gene repression by H3K4me mediation
was supported by literature. For example, the ING PHD
domains provided robust binding modules for H3K4me
. In addition,
PEX14
is one of the 12
genes (see Figure 4 for visualization in UCSC Genome
Browser),
PEX14
encoded protein which could
function as a transcriptional corepressor and interact
with a histone deacetylase
.
GO terms associated with me2me3 were diverse,
which can be interpreted by the fact that me2me3 was
a common yet robust signal. We noted a GO term:
nucleosome is associated with me2me3 for 13 genes
(Supplementary Table 4), implying that me2me3 was
a potential signal for activating histone subunits
variants and might also be a robust and housekeeping
signal for promoters.
Table 4 Nucleotide composition in gene context for different types of localized peaks
Localization
type
A
T
G
C
G+C
CpG
TpG
CpG o/e
TpG o/e
me1me2
0.239±0.055 0.241±0.058 0.255±0.061 0.257±0.060 0.514±0.053 0.085±0.032 0.133±0.054 0.670±0.201 1.090±0.300
me1me2me3 0.226±0.050 0.221±0.047 0.272±0.058 0.276±0.058 0.552±0.057 0.103±0.040 0.121±0.051 0.741±0.181 1.022±0.263
me1me3
0.214±0.061 0.216±0.062 0.284±0.070 0.281±0.068 0.563±0.072 0.106±0.053 0.127±0.062 0.749±0.222 1.083±0.304
me2me3
0.229±0.054 0.227±0.054 0.267±0.058 0.267±0.059 0.536±0.064 0.102±0.042 0.116±0.044 0.761±0.207 0.972±0.236
Single
0.205±0.065 0.204±0.065 0.290±0.076 0.289±0.075 0.581±0.095 0.120±0.069 0.114±0.050 0.782±0.229 1.002±0.284