Open Access
Frontiers in Genetics, volume 12
Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure
Publication type: Journal Article
Publication date: 2021-09-20
Journal:
Frontiers in Genetics
Quartile SCImago
Q2
Quartile WOS
Q2
Impact factor: 3.7
ISSN: 16648021
PubMed ID:
34616432
Genetics
Molecular Medicine
Genetics(clinical)
Abstract
A constellation of chromosome conformation capture methods (С-methods) are an important tool for biochemical analysis of the spatial interactions between DNA regions that are separated in the primary sequence. All these methods are based on the long sequence of basic steps of treating cells, nuclei, chromatin, and finally DNA, thus representing a significant technical challenge. Here, we present an in-depth study of the basic steps in the chromatin conformation capture procedure (3С), which was performed using Drosophila Schneider 2 cells as a model. We investigated the steps of cell lysis, nuclei washing, nucleoplasm extraction, chromatin treatment with SDS/Triton X-100, restriction enzyme digestion, chromatin ligation, reversion of cross-links, DNA extraction, treatment of a 3C library with RNases, and purification of the 3C library. Several options were studied, and optimal conditions were found. Our work contributes to the understanding of the 3C basic steps and provides a useful guide to the 3C procedure.
Citations by journals
|
1
|
|
|
Frontiers in Genetics
|
Frontiers in Genetics
1 publication, 33.33%
|
|
1
|
Citations by publishers
|
1
|
|
|
Frontiers Media S.A.
|
Frontiers Media S.A.
1 publication, 33.33%
|
|
1
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2022,2023,2024],"ids":[0,0,0],"codes":[0,0,0],"imageUrls":["","",""],"datasets":[{"label":"Citations number","data":[2,0,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6"],"percentage":["66.67",0,"33.33"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Frontiers in Genetics"],"ids":[13242],"codes":[0],"imageUrls":["\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp"],"datasets":[{"label":"","data":[1],"backgroundColor":["#3B82F6"],"percentage":[33.33],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Frontiers Media S.A."],"ids":[208],"codes":[0],"imageUrls":["\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp"],"datasets":[{"label":"","data":[1],"backgroundColor":["#3B82F6"],"percentage":[33.33],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex
Cite this
GOST
Copy
Bylino O. V. et al. Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure // Frontiers in Genetics. 2021. Vol. 12.
GOST all authors (up to 50)
Copy
Bylino O. V., Ibragimov A. N., Pravednikova A. E., Shidlovskii Y. V. Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure // Frontiers in Genetics. 2021. Vol. 12.
Cite this
RIS
Copy
TY - JOUR
DO - 10.3389/fgene.2021.733937
UR - https://doi.org/10.3389%2Ffgene.2021.733937
TI - Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure
T2 - Frontiers in Genetics
AU - Bylino, Oleg V
AU - Ibragimov, Airat N
AU - Pravednikova, Anna E
AU - Shidlovskii, Yulii V
PY - 2021
DA - 2021/09/20 00:00:00
PB - Frontiers Media S.A.
VL - 12
PMID - 34616432
SN - 1664-8021
ER -
Cite this
BibTex
Copy
@article{2021_Bylino,
author = {Oleg V Bylino and Airat N Ibragimov and Anna E Pravednikova and Yulii V Shidlovskii},
title = {Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure},
journal = {Frontiers in Genetics},
year = {2021},
volume = {12},
publisher = {Frontiers Media S.A.},
month = {sep},
url = {https://doi.org/10.3389%2Ffgene.2021.733937},
doi = {10.3389/fgene.2021.733937}
}
Profiles