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The ENCODE Project publishes new genomic insights in special issue of Genome Research
Date:9/5/2012

ped a new tool called the Clustered Aggregation Tool (CAGT). The method was applied to datasets of chromatin marks and transcription factor binding to generate an extensive catalog of histone modifications and nucleosome positioning around bound transcription factors. The analysis indicated that both histone modifications and the positions of nucleosomes around transcription factor binding sites are highly heterogeneous, a surprising finding that suggests the features of many regulatory elements are asymmetrical.

References:

  • Cheng et al., Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res doi: 10.1101/gr.136838.111
  • Wang et al., Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res doi: 10.1101/gr.136101.111
  • Kundaje et al., Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res doi: 10.1101/gr.136366.111

4. Regulatory variation and the genetic basis of disease

The data and analyses of The ENCODE Project will help the research community to not only understand genome function, but also disease, with the aim of designing new strategies of treatment and prevention. Much effort in the last decade to understand the genetic basis of disease has been through genome-wide association studies. Many genetic variants found to associate with disease lie in non-coding regions and are relatively common in the population. This challenge in interpreting the data has highlighted the need to understand the influence of genetic variation on the function of genes and regulatory regions.

Two studies in this special ENCODE issue take a step forward in this effort, analyzing the potential functional consequences of individual genetic variants. In a paper from Vernot and colleagues, the most comprehensive assessment of human regulatory vari
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Contact: Peggy Calicchia
calicchi@cshl.edu
516-422-4012
Cold Spring Harbor Laboratory
Source:Eurekalert

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