1) We produced two new chromosome-length genome assemblies in Drosophila using Hi-C data and our new tool HiCAssembler:https://github.com/maxplanck-ie/HiCAssembler …
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Read the new @AsifaAkhtar1 Lab paper: #HiC guided #assemblies reveal conserved regulatory #topologies on #Xchromosome and autosomes despite extensive #genome shuffling in @GenesDev .
Description in the comments below
http://genesdev.cshlp.org/content/early/2019/10/09/gad.328971.119 …
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2) TADs shuffle in the
#genomes as cards in a deck: By comparing the newly assembled Drosophila busckii and Drosophila virilis genomes to Drosophila melanogaster, we find that active#TADs and A/B#compartments are conserved over 40 million years of#evolution.Prikaži ovu nit -
3) The clustering of High Affinity Sites (HAS) in the
#nucleus#3D space supporting#dosage#compensation is conserved over#Drosophila#evolution.Prikaži ovu nit -
4) The location of
#HAS is flexible: they cover the entire X chromosome and their vicinity is enriched in conserved genes, but they do not show particular enriched functions.Prikaži ovu nit
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This paper includes a visualization of Hi-C contact heatmaps inside a
#circos plot. An official support from circos for such contact matrices would be great@MKrzywinski, anything planned? (For the records, I had to use pyGenomeTracks,@ImageMagick and@inkscape).pic.twitter.com/SNleSptgX0
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Very interesting. Do you have any explanation why in D. busckii 2L and 2R interact more strongly with 3L and 3R (Fig1A), respectively compared to 2L with 2R?
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I am not sure. I would say that it might correspond to repetitive regions interactions that we assemble better in Dbus since we used PacBio reads compared to Dvir. It can also be how efficient was the Hi-C (fraction of cis vs trans contacts). I'm not sure that it's biological.
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