In today’s world there’s not much you can be sure of, particularly when it comes to understanding the complexities of human cognition. Thankfully, the epigenome offers some much needed explanation, as demonstrated by the insight gained from DNA methylation maps of human neurodevelopment. However, genetic interactions created by 3-D chromosome structure have remained more of a mystery – one which is now beginning to unwind thanks to the Geschwind lab at UCLA.
In order to discover genome-wide chromosome contacts, the team used Hi-C. In Hi-C, chromatin interactions are captured regardless of physical distance. This is done by cross-linking chromatin with formaldehyde, restriction enzyme digesting, and then re-ligating the interacting DNA into a circle with biotin-labeled nucleotides, which allows for purification followed by sequencing. By using Hi-C, the talented team captured long-range chromosome contacts on a genome-wide scale in human fetal brain cerebral cortex during the peak of neurogenesis and cell migration. Here’s what went down:
- They validated their Hi-C system by examining for expected results:
- Promoters and enhancers with interactions identified by Hi-C show significantly higher correlations in chromatin accessibility than those that don’t. This was determined by comparing to the DNaseI hypersensitivity sites of fetal brains from the Roadmap Epigenomics dataset.
- Expression quantitative trait loci (eQTL), which represent gene regulatory elements such as enhancers, and associated genes, show a significantly higher chromatin contact frequency than background in a tissue specific manner.
- By integrating their results with FANTOM5 datasets, they found that expression of enhancer RNAs (eRNAs) and related genes showed a higher correlation for interacting enhancer/promoter pairs than for non-interacting pairs.
- Shedding light onto our evolutionary origins, they uncovered hundreds of enhancer interactions recently gained by humans, highlighting their role in cognition and related disorders.
- Since recent schizophrenia genome-wide association studies (GWAS) have identified a major role for non-coding regions, they integrated their Hi-C data with schizophrenia associated SNPs to identify genes interacting with these SNPs. These genes were enriched for neurodevelopmental functions including chromatin remodeling.
- Finally, they used CRISPR/Cas9 to confirm a novel 760 kb gene regulatory relationship between a non-coding SNP and a target gene (FOXG1) in human neural progenitor cells.
Overall, this paper presents an impressive Hi-C data set and analysis relevant to neurodevelopment, cognition, and related disorders. It also demonstrates the utility of an emerging approach: confirming (epi)genome-wide scans with CRISPR/Cas9.
Catch all the chromatin contacts critical to cortical development over at Nature, October 2016