4C data set

Published: 27 April 2022| Version 1 | DOI: 10.17632/cz3thnr9kf.1
Vigneshwaran Venkatesan


We have identified putative repressor region (PRR) to exon-1 of β-globin (βE1) in the β-globin cluster as a core region in all the HPFH deletions that activate fetal hemoglobin and silences adult hemoglobin. To test the impact of PRR-βE1 gene editing in β-globin cluster configuration, we employed Circular chromosome conformation capture (4C) analysis to assess the LCR interaction to the -globin promoter. Using HBG2 promoter as viewpoint,4C analysis showed an increased interaction of HBG promoter to the hypersensitive (HS) sites of the LCR in HUDEP-2 clones harbouring PRR-βE1 biallelic deletions compared to control HUDEP-2 cells.


Steps to reproduce

HUDEP-2 control and PRR-βE1 clone were fixed with 1.5% formaldehyde and quenched with glycine (125 mM) and lysed using Dounce homogenizer . The 3C digestion was performed with Csp6I and ligation was performed by the T4 DNA ligase in 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer (500 mM Tris-HCl pH7.5, 100 mM MgCl2, 100 mM DTT), 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water).