I want to investigate that which part of a chromosome is more stable i-e means having lesser breakpoints and which is less stable having more breakpoints by using the Hi-C data. Is it possible? Please guide me. Thanks
I dont know if this is possible with Hi-C data. If I remember correct it gives you information on which regions of the genome are physically close to each other, right?
Why don't you use standard paired end reads over multipe experiments from eg. SRA to estimate that. I guess what you will find is that towards the end of the chromosomes there are more mutations compared to the middle or close to the centromere.
Plus what exactly do you mean with breakpoints? Inversions or translocations or general structural mutations?
Sir, you are absolutely right it gives information on which regions of the genome are physically close to each other. With reference to breakpoints, the regions on chromosome from where chromosome breaks, breakpoints of chromosome and its after story that after breakage causes chromosomal rearrangements like inversion or translocations etc.But my objective is to "Investigation of breakpoint regions and more stable regions of chromosomes in human by using Hi-C data".Thanks for your time.
I think you might want to explore other techniques to study this. It should be much easier with DNA-SEq reads and SV calling over several samples.Or you look at the results of the 1000 genome data. Again I think what you will find is that at the outer sides of chromosomes you will find more SVs whereas towards the centromere you will find less.
Thank you sir for your nice suggestions and also try your recommendations..Thanks.
That's an interesting research point.
Detection of chromosome breakpoints apart from subsequent inversions and translocations seems to be a risky task. Right after chromosome breakage, the chromosome parts might stay in their chromosome territory. In other words, interactions with other chromosomes might provide restrictions to the 3D positioning of the broken parts. Thus large-scale Hi-C changes might be not visible since the positioning is very similar. But the possibility that broken chromosomes diffuse to their non-typical chromosome territories after the breakage also seems to be a relevant idea. I will be happy if you could recommend some papers on this.
The other scenario is the detection of inversions, insertions, etc. with Hi-C. I think a lot of work has been done so far. There are examples of 4C implications for rearrangements detection, de novo genome assembly with Hi-C, haplotype detection and more (briefly reviewed in Fraser et al. 2015 [1]). A clear example of unannotated rearrangements detection as bright spots of intensive Hi-C signals located far off the diagonal could be found in Ulianov et al. 2016 [2]. Chromosome rearrangements could be detected even via single-cell Hi-C (see Stevens 2017 [3]).
In my opinion, some Hi-C-based measure of predisposition to chromosome breakage should be invented already. Could someone provide a link?
I find the problem of poorly annotated and assembled genomes related to your question. E.g. in Grob & Grossniklaus 2017 [4] I've found an idea that observed chromosome arms sub-compartmentalization and centromere insulation in some species such as Drosophila could be a result of poor genome assembly of the centromeric region. Is there any additional research on that?
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