During chromosome segregation in mammals, spindle fibers connect to each chromosome on a region called the primary constriction, which consists of a central core called the centromere and flanking regions called the pericentromeres. Both centromere and pericentric regions comprise several megabase long highly repetitive DNA arrays referred to as “satellites” that constitute up to ~10% of the genome. Centromeric satellites assemble specialized nucleosomes in which canonical histone H3 is replaced by a variant, Centromere Protein A (CENP-A). CENP-A chromatin serves as the foundation for kinetochore - a multiprotein complex that binds to spindle microtubules. Pericentric satellites assemble highly compact heterochromatin characterized by the methylation of Lysine-9 of H3 (H3K9me3) and is bound to cohesin that holds sister chromatids together to prevent their premature separation. Defects in chromatin underlying CEN and/or periCEN lead to chromosome mis-segregation, which gives rise to aneuploidy and genomic instability. Nucleosomes assembled on both centromere and pericentric satellites are considered to be epigenetic, in that they are maintained indefinitely through cell division over the lifetime of an organism. Our goal is to understand nature of these epigenetic processes in mammalian species.

We are also interested in understanding the structural organization of distinct chromatin domains in the nucleus. Besides chromatin modifying proteins, chromatin is also associated with a significant fraction of mature transcripts, mostly long non-coding RNAs (lncRNAs). The ability of RNA to form multivalent interactions via its sequence and extensive secondary structures makes it an excellent modifier of chromatin structure. Emerging evidence suggests that chromatin-associated RNA is indeed involved in chromatin organization. To understand how lncRNAs modify chromatin structure, we are investigating chromatin-RNA interactions using the latest chromatin profiling techniques combined with cytological visualization. Using in situ chromatin profiling method CUT&RUN that preserves the native chromatin conformation combined with RNA depletion, we have found that the direct interactions with RNA are required for the “compaction” of global heterochromatin, including that of surrounding centromeres (pericentric) and the inactive X-chromosome.