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To understand mechanisms of epigenetic regulation, it is imperative to investigate the cooperative nature of chromatin modifications and genomic elements.
We then linked the CpG loci in the DNA methylation profile data with chromatin modifications and genomic elements using the CM measure.
The figure suggests that chromatin modifications and genomic features form a highly connected regulatory network, and that certain features co-function in concert with other specific features for activation or repression.
The potential for interaction between these factors is increasingly understood, however the relationship between specific epigenetic modifications and genomic features, whether independent or dependent, is poorly explained in the context of disease and phenotype.
The interactions among chromatin modifications and genomic elements characterized by a closeness measure help elucidate cooperative patterns of chromatin modification in transcriptional regulation and help decipher complex histone codes.
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Aberrant expression of APOBECs in the cell has been proposed to cause promiscuous nucleotide modification and genomic instability [26].
Using a high-quality set of transcriptional enhancers and associated histone marks, we demonstrate that SS-CoSBI outperforms its predecessor by finding histone modification and genomic locus biclusters with higher enrichment of enhancers.
Positioned nucleosomes are important for the hypothesis that nucleosomes constitute a signaling module, because gross movements of modified nucleosomes along the chromatin fibers may lead to a loss of coherence between the modifications and the genomic features and/or functions.
Sequenced RNAs associated with chromatin also were analyzed individually to reveal any potential link between the region of specific histone modifications and the genomic origin of the small RNAs.
The factors that determine the rate of Tax expression at a given proviral load remain unknown; possible factors include epigenetic modifications and the genomic integration site of HTLV-1 (Kiran N. Meekings, G.P.T., C.R.M.B., material submitted).
We assigned labels to each cluster based on the histone modification pattern and genomic localization.
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modifications and gene
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modifications and specific
modifications and procedural
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