Student Wiki on methodology

This Wiki is intended to collectively make the point on methodologies employed in research papers we analyze during the course. "Writers" are students who wish to contribute to a specific subject. Before contributing, please add your name in the "Writers group choice". When initiating a contribution, please indicate your name in brackets.


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Please do not make extensive cut-and-paste: it s useless, anybody can go to the source you use and read it.  Read the texts, digest, and make a short résumé. If you wih you can include link(s) to the source(s).

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Epigenomics: ChIP-Seq, DNase-Seq, FAIRE, ATAC-Seq, Nucleosome positioning

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Modified: 19 March 2019, 2:42 PM   User: Audrey Champier  → 

index

[Audrey CHAMPIER]


                                                                ChIP-Seq 

Methode used to analyse the interactions between proteins and DNA.

The technique consists in a chromatin  immunoprecipitation followed by a parallel DNA  sequencing in order to identify the binding sites of one protein on DNA. ( Before it, scientists used Chip on Chip : Chromatin immunoprecipitation + sequencing with  DNA -microarray technique )


Chromatin immunoprecipitation :   ( for more details see  : " Wet-Lab portion of the workflow in the following link" :  https://en.wikipedia.org/wiki/ChIP-on-chip#Workflow_of_a_ChIP-on-chip_experiment)

The protein of interest is first cross-linked with the  DNA site it binds,  thanks to formaldehyde for example.

Then the cells are lysed and the DNA , thanks to sonication, becomes small fragments.

After this , we introduce an antibody specific of  the protein that interests us.  This antibodies are bound to a surface and so we obtain,on this surface, all the sequence of DNA that bind the protein. In order to obtain only the DNA sequence, we reverse the cross-linking of DNA and proteins,  thanks to heat.

Sequencing:  

We use Parallel DNA sequencing method in order to obtain the sequence of all the fragments of DNA we just obtained with immunoprecipitation. 


For more informations see: 

https://en.wikipedia.org/wiki/ChIP-sequencing#ChIP