3D Chromatin Structure’s Special Effects on Transcription

January 25, 2012 Judging from showbiz ad campaigns, their latest motto seems to be “Everything is better in 3D!” Maybe that thought inspired this new study that uncovered how the 3-dimensional structure of chromatin has some very special effects on the regulation of gene transcription.

Researchers from the Genome Institute of Singapore (GIS) decided to take a look at chromatin interactions based on their real world configurations, instead of the more 2D analysis that researchers have previously been limited to, so they broke out their Chromatin Interaction Analysis with Paired-End-Tag (ChIA-PET) sequencing method to map out genome-wide, long range chromatin interactions associated with RNA pol II. Here are some of the things that grew out of the ChIA-PET data:

• Many promoter-promoter interactions were found that spanned 150-200 kb and sometimes even megabases of genomic distance.
• They categorized RNAPII associated chromatin structures into different bins: Basal promoters, Single gene interactions (longer, found in regions of lower gene density, higher inron/exon ratios) and Multi-gene interactions (shorter, high GC content and gene density, found in highly transcribed open-chromatin regions.)
• Multi-gene complexes seemed to organize expression for genes with similar functions, and may coordinate activation of groups of genes in response to stimulus.
• Interacting promoter regions may also function as enhancers for other genes. This is analogous to bacterial operons, so they dubbed them chromatin operon, or “chroperons”
• ChIA-PET analysis also found interactions with other elements, like enhancer RNA transcripts and SNPs, that could explain misunderstood gene regulation in disease, which is why the team thinks it is so important to continue to investigate the role of structure in transcriptional regulation.

Get a 3D view of the all their data at Cell, January 2012.