Fig. 7

Gene expression patterns around TAD boundaries are robust to local species-specific losses of individual CTCF sites. a We identified M. musculus castaneus (CAST)-specific CTCF site losses at TAD boundaries and estimated the gene expression patterns around them, by calculating the log₂(fold change) between the closest downstream to the closest upstream gene. b, c Comparisons of log₂(fold change) values of gene pairs flanking the CAST-specific losses of CTCF sites between C57BL/6J and CAST, with inconsistent CTCF binding, as well as between C57BL/6J and M. caroli, with consistent CTCF binding. Only genes that have a one-to-one orthologous relationship and similar gene lengths among C57BL/6J, CAST, and M. caroli were used. d M. caroli-specific CTCF site losses at TAD boundaries and estimated the gene expression patterns around them, with calculated log₂(fold change) between the closest downstream and the closest upstream gene. e, f Comparisons of log₂(fold change) values of gene pairs flanking the M. caroli-specific losses of CTCF sites between C57BL/6J and CAST, with consistent CTCF binding, as well as between C57BL/6J and M. caroli, with inconsistent CTCF binding. g For reference, Mus-conserved CTCF sites and calculated gene expression patterns around them with computed log₂(fold change) of the closest downstream to the closest upstream gene in each of the species. h, i Comparisons of log2(fold change) values of gene pairs flanking the examined Mus-conserved CTCF sites between C57BL/6J and CAST, as well as between C57BL/6J and M. caroli