Fig. 1: The human genome is globally accessible in living MCF7 cells.
From: Nucleosome dynamics render heterochromatin accessible in living human cells
a Schematic of adenovirus transduction and time course experiment to express Dam methylase in live cells. b Anti-HA immunoblot to detect Dam-3HA-eGFP expression in MCF7 cells. c Agarose gel electrophoresis of DpnI-digested genomic DNA purified from MCF7 cells as a function of time of adenovirus treatment. ‘un’, undigested genomic DNA; ‘MboI’, DNA from non-transduced cells digested with MboI as a marker for complete digestion at GATC sites; M, DNA size marker. d Almost complete methylation of GATC sites in MCF7 cells after transduction. Red line and shading: median GATC site methylation with data range indicated. e, f Nucleosome phasing with respect to the TSS for active and inactive genes, as defined by ATAC-seq34. Grey profile: nucleosome dyad distribution in nuclei (MNase-seq data for MCF7 cells arbitrarily normalised to 30%). g The effect of transcriptional activity on methylation rate. Active genes were divided into quintiles Q1 to Q5 based on increasing transcriptional activity (Q5 is the highest) using RNA-seq data from ref. 34; methylation of the median GATC site in each quintile is shown. Inactive genes are treated as a single separate group (‘NoTrans’). h Median GATC methylation for various genomic regions. i Nucleosome phasing around CTCF motifs using the motif shown.
