Mapping 3D Genome to go Beyond Sequencing


So far, 3D genomics has dealt with the regulation of specific genes, working with cells grown in a lab. However, this is on a road to change with a 3D map created by scientists from St. Jude Research Hospital. It shows insights into genomic organization and function when development happens. This will help in understanding how cells respond to factors like diseases and stress. The journal Neuron has published the report. The data is also available on St. Jude Cloud, the hospital’s data sharing resource platform.

The 3D genomic map of the mouse cerebellum focuses on how the 8000 plus genes switch on and off during retinal development. The scientists, therefore, directed attention to light-sensing rod cells. They are, now, studying neural circuits in the retina.

Scientists used data from a number of sources in an integrated manner, using machine learning. With that, they demonstrated that change in the genomic organization is not random. Instead, it is part of the overall development program. It is important to note here that changes are therefore different in different stages. They also used Hi-C analysis, also called ultra-deep chromosome conformation capture. The technology aided in figuring out interactions in these cells.

Understanding 3D Genome and Placing Mapping in the Process

3 billion chemical bases of human DNA encapsulate the human genome. Here it is important to note that DNA fits into the nucleus in loops. Due to this structural property, regions that are situated far in the 6 feet long DNA thread can come close, altering interaction dynamics.

The research under lens has sketched out long distance communication between enhancers and promoters. It has also tracked how organization alters in genome. Another parameter studied is the accessibility of genes for transcription purpose.

Moreover, the study highlights workings of super enhancers, which are significant as these can be captured in developmental cancers. Also, it was observed that if core regulatory circuit super enhancer for Vsx2 was removed, bipolar neurons were eliminated.



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