gravatar for robert.mclaughlin

2 hours ago by

Question:

Is it possible to take two (inter-) chromosomal coordinates, and estimate the distance between points in 3D? Starting with a collection of 3D coordinates of sampled genomic loci across all chromosomes would be sufficient. 🙂

Distance in 3D is what I am after, not genomic coordinate distance. I do not necessarily need nanometer values.

I realize chromatin is highly dynamic and the chromosomal and domain organization may vary highly from cell to cell. For this reason, it would be ideal to have a database of samples, but i understand such a thing is likely not available in 2021.

Some of my attempts:

Some recently compiled intrachromosomal contacts can be found here: 3dgnome.cent.uw.edu.pl/browser/ but this is not exactly what i am after. It looks like there are a few other biostars posts with links to databases like this.

This shiny app from the Science paper "In situ genome sequencing resolves DNA sequence and structure in intact biological samples" plots coordinates of chromosomes in 3D for a mouse embryo.
buenrostrolab.shinyapps.io/insituseq/. It would be amazing to download these collections of 3D coordinates, especially for the human genome.

Thanks for reading. I have been looking forward to such a resource for a while, so if you have any suggestions, that would really make my day.



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