I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between the two types of data such as the level of expression of gene segment and the interaction of the gene segment, since it seems that they are correlated. Thanks

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    $\begingroup$ Maybe start with some tutorials? This one looks interesting: jove.com/video/1869/… Also, you haven't done any background work for your question, so don't expect substantial answer $\endgroup$ – aaaaa says reinstate Monica Apr 8 '15 at 9:19
  • $\begingroup$ You need to be more clear than this. There are many things that you can do with the data. An experiment is performed to test some kind of hypothesis. With just the data and no underlying question you can calculate any thing. It can be even comparison of sequencing fidelities between two kinds of methods. The main point is what are you interested in finding? $\endgroup$ – WYSIWYG Apr 8 '15 at 10:41

This seems to me to be two independent pieces of data. mRNA seq allows one (in case of linear amplification) to quantify message RNA transcripts of genes of interest. that is, how many copies of mRNA for given gene are in the cell at the moment. It is ultimately, how active this gene is. In neurons different genes will be more active, than in epithelial cells, and vice versa. Genetic expression pattern provides identity of the cell.

Hi-C method, closely related to chromosome conformation capture answers question: what genes are physically interact in the nucleus via stabilizing proteins (e.g. enhcancers). There is more in the video, but general idea is that it allows you to see how genes positioned inside intricate chromatin. Since many genetic elements might physically interact via, for example, enhancers, 3C/Hi-C allows detection of such interactions. Or, at least, quantification of correlation between physical positions of two genes.

Now, the only direct connection between mRNA seq and Hi-C that I can draw is following logic: actively transcribed genes are located in expanded, less tense regions of chromatin. Hence, it will be hard to crosslink genes in such regions and correlation going to be low. Silent genes, if they are located closely in nucleus will be cross-linked with high probability, because chromatin is denser around non-transcribed genes.

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  • $\begingroup$ HiC and 3C (chromosome conformation capture) do not idenify which genes are located nearby in chromosome. These techniques capture long range DNA-DNA interactions such as that between enhancers and promoters. Basically it captures stable DNA loops. $\endgroup$ – WYSIWYG Apr 8 '15 at 10:38
  • $\begingroup$ would it be fair to say that such techniques detect physical proximity in chromatin? I understand, that they are not about position along the chromosome $\endgroup$ – aaaaa says reinstate Monica Apr 8 '15 at 15:43
  • $\begingroup$ yes they do. In fact trans-DNA regulation has also been studied but these interactions have to be stabilized by some factor which is usually a protein $\endgroup$ – WYSIWYG Apr 8 '15 at 16:38
  • $\begingroup$ RNA-Seq lets you measure the steady-state levels of a transcript in a cell or tissue at a specific time-point (averaged over all of the cells that were harvested and lysed). $\endgroup$ – mdperry Apr 9 '15 at 1:17

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