Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.

ABSTRACT: While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a "cytological ruler" for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription "hot zones." Transcription h

SUBMITTER: Chen Y 

PROVIDER: S-EPMC6219710 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature