@ Institute for Information Transmission Problems, Russia
Three-dimensional structure and functional state of chromatin: who is the driver?
Recent advances in large-scale experimental techniques, such as RNA-Seq, ChIP-Seq, HiC and others, provide data for integrated analysis of chromatin 3D state, epigenetic markers, and gene expression. Not surprisingly, these turned out to be highly interlinked. Contacting chromatin regions tend to carry similar histone modifications and gene expression in such regions tends to be correlated. On a finer scale, topologically associating domains (TADs) also seem to depend on histone modifications and transcription. Indeed, TADs are enriched in repressive chromatin markers, wheres inter-TAD regions are enriched in active markers and highly transcribed genes. Moreover, differences in TAD structure between cell lines are accompanied by corresponding differences in transcription. These observations seem to indicate that gene active expression is the driving force behind formation of the TAD structure. Finally, there are preliminary indications that regions forming many distant contacts are also enriched in active markers and actively transcribed genes.