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TurretLauncher OP t1_j3k41kp wrote

Abstract

Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challenging due to the lack of high-throughput experimental methods. Here we present a comprehensive characterization of the mechanical code. Utilizing high-throughput measurements of DNA bendability via loop-seq, we quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. We used our measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. We validated the model by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. We applied our model to test the predictions of all-atom molecular dynamics simulations and to demonstrate that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts.

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foodfood321 t1_j3kbpwe wrote

This is unbelievable to live at this period of science! This is incredible, intricate scientific knowledge. Amazing. What will we learn in the coming years?

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TitillatingTrilobite t1_j3khj64 wrote

Wow this is really cool. The influence of simple mechanical forces in biology is incredible. Also cool to see a real science paper get posted!

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FellowConspirator t1_j3m81j2 wrote

The title’s a bit misleading. It was known the sequence affected the bendability, here they quantify the impact of DNA methylation on that.

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MrHanoixan t1_j3m00tm wrote

So it’s not junk DNA, it’s origami?

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zenzukai t1_j3m3fzc wrote

There still is 'junk' DNA, but large sections of a chromosome is structural. Allows for histone binding and conformational changes. This isn't new or groundbreaking. This paper is defining properties for classifying and labeling functional regions that will predict these changes.

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MrHanoixan t1_j3mo1kf wrote

My comment was a lazy joke, but I appreciate your earnest response!

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