Hi everybody, I was wondering if someone know a tool or program to analyze the specific direction of DNA replication, or in others words, to analyze if the replication is happening in the same direction as transcription.
Many thanks in advance!
In humans, the precise locations of replication origins are not known. There are protocols such as Repli-Seq (Pubmed ID: 19966280) that can be used to map replication origins and termination zones. Once you know the replication origins and replication termini, one can make the assumption that in the region between origin and termini the replication predominantly happens in a single direction (from origin to termination zone). For lymphoblastoid cell lines replication maps are available but there is of course tissue-specific variation in DNA replication time.
Thank you very much! As I can read for your comments is something difficult to address ...so I will work on it and if I found the way, I will let you know. Thank you very much again
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It is not clear where the bioinformatics relevance of this question is. What type of data are you analyzing?
If this is a purely biology question then other forums should be used to have it answered. Even in that case it is not clear what you mean: DNA is always synthesized in the 5' to 3' direction. Both strands get replicated, to get a 5'-3' replication on a lagging strand a complex phenomena takes place: see Okazaki fragments. As explained in DNA replication on Wikipedia,
Sorry for the explanation, what I want to know is if there is a way to say that the replication is happening in the same direction as transcription, not the direction perse of the strand (I know that). But for example if I have RNAseq, I can say that I have some transcript in one direction and in another direction, so how can I say which ones are transcribed in which "replication strand"? Not sure if is clear enough
Your explanation is still lacking important details. Which organismen are you dealing with? Do you know the genomic sequence of the particular isolate you have RNAseqed?
I would deduce from your avatar that you are dealing with bacteria. Most eubacteria have circular chromosomes and the location of the origin of DNA replication (ORI) is usually easy to deduce. Except for E.coli, most people who care about this, do linerarize their chromosomes at the origin of replication. DNA replication runs from ORI to a locus called TER, the terminus of DNA replication. This locus is not so easy to identify and it it is not annoted in most genomes. A rough guess is that it is located opposite of ORI, at about 180 degree in the circular chromosome. A better method is to use a GC skewness plot to find it. If you have located ORI and TER in your chromosomal sequence, than you will be able to determine for a given gene whether it is oriented towards ORI or towards TER. The algorithm to calculate this is pretty simple. I am not aware of a program that does this kind of calculation out of the box.
since both processes have a directionality and even on the lagging strand the replication still takes place in the 5' - 3' direction via the mentioned Okazaki fragments. The DNA gets "spooled ahead" as small fragments then is read backwards. So it does not matter what strand to you look at both will be "read" in the same direction. The transcription also has a directionality 3' to 5' on the template strand (5' to 3' on the coding strand). Hence there you might have your answer.
But perhaps what you are trying to ask is whether the leading and lagging strands of a DNA replication process are always the same for a given organism, and whether these correspond to the forward/reverse strands. I don't know the answer to that question. piet has posted more details on how this might work.
The replication complex is a huge protein machinery. It moves from ORI to TER. During its move, both strands are replicated. This is complicated since the mechanisms for the leading and the lagging strand are totally different. However, the overall move of the whole replication apparatus (sometimes also called the move of the replication fork) is from ORI to TER. And only this overall move is compared with the direction of transcription.
I haven't checked this in depth since I'm not really an expert on this matter but I thought this recent report was interesting.
So is there any way to identify if the okazafi fragments are in the + or - strand in the human genome from bam files (ChIPseq or RNAseq)? I know that there are some studies that analyzed that in human genome (https://www.nature.com/articles/ncomms10208), but they use other NGS methodology. many thanks