X Chromsome Silencing
2
0
Entering edit mode
7.8 years ago
BioICoder ▴ 40

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.

RNA-Seq next-gen sequencing gene • 1.5k views
ADD COMMENT
0
Entering edit mode

Hi,

are you working on human samples?

ADD REPLY
0
Entering edit mode

Hello there, yes I am!

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
7.8 years ago
Satyajeet Khare ★ 1.6k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode
7.8 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 3667 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6