X Chromsome Silencing

Question

[BioICoder]

Hi all,

I was wondering if there is some tool that can somehow tell you if a raw data of RNA-seq has regions in which X-chromosome silencing occurred? or can someone tell me how that can be done theoretically?

Thanks a lot in advance.

[Farbod]

Hi,

are you working on human samples?

[BioICoder]

Hello there, yes I am!

[Farbod]

Dear friend,

It is a fascinating course in Coursera about epigenetics and in the course she has mentioned many genes same as Xist and other X-iactivation related genes. maybe some DEG analysis on these genes culd help you and you can ask some of your questions from the Coursera mentors.

I think it is chance for you to check that course and personally I do not think that RNA-seq could clearly shows the X-inactivation except many bio-replications and very well designed approaches.

Answer 1

[Satyajeet Khare]

Can be done if you have following samples for comparison...

1. A control female sample in which both X-chromosomes are active. The locus of your interest should show half the expression as compared to this control if the one X-chromosome in your sample is inactive.
2. A control male sample or a female sample with only one X-chromosome active. The locus of interest should show equal expression to this control if one X-chromosome is inactive.

Or in absence of any control for comparison, if you know the sequence of both X-chromosomes in your sample you might be able to use SNPs in the locus of your interest to tell which locus on chromosome is active and which one is inactive.

[BioICoder]

Hi Satya,

Thanks for the nice explanation. My question is how to know if the x-chr of raw sequence is active or inactive?

Thanks

[Satyajeet Khare]

Hi Saudi,

Can you provide some more information? Are you interested in a specific locus on the X-chromosome? Do you already know if this locus is present in a region of X-chromosome that gets inactivated? Do you need allele specific information, as in, if the locus of your interest is present on active or inactive X-chromosome?

If you just wanted to know the procedure for my previous post, then you need to perform alignment of your RNA-Seq reads to the genome using tool such as Tophat or HISAT etc. If you want allele specific information, then as I mentioned earlier, you need to know SNPs of the two X-chromosomes. In such case, you may need to generate a hybrid genome first, followed by the RNA-Seq alignment.

Answer 2

[WouterDeCoster]

I think this is biologically not possible, given that in each cell a random X chromosome (theoretically, can be skewed) will be inactivated. Since you sequence RNA from millions of cells you will get a mixture of both. Unless you do single cell RNA-seq you will have expression from both chromosomes.