HACking centrochromatin: on the relationship between centromeres and repressive chromatin

The centromere is a chromosomal locus required for accurate segregation of sister chromatids during cell division. They are maintained epigenetically in most eukaryotes, by incorporating the H3 variant CENP-A, and can, in rare instances, change location on the chromosome throughout generations. Centromeres are transcribed, and an active transcription chromatin signature is required for centromere maintenance. For this reason, insight into the nature of this so-called “centrochromatin” is essential for understanding a centromere’s place in the chromosome. The body of work contained in this thesis shows my efforts to understand the centromere in the context of chromatin, revealing interactions and new evidence for repressive chromatin domains with centromere activity, in two different vertebrate models: chicken DT40 cells and human HeLa cells. Centromeres are generally embedded within large domains of heterochromatic repetitive sequences in most eukaryotes, and mapping “centrochromatin” to high-resolution has proven difficult. However, chromosomes 5, 27 and Z of Gallus gallus are not located within repeat arrays, and are fully sequenced. CENP-A distribution on these centromeres has been mapped by ChIP-seq, and I have performed ChIP against selected histone modifications as part of a collaboration. While levels of heterochromatin are naturally quite low in these centromeres, I have shown that repressive polycomb chromatin instead is enriched in these non-repetitive centromeres, suggesting a replacement of one silenced chromatin state with another. Additional mapping of these centromeres showed a pattern of active chromatin marks distinct from that reported for human cells, which exhibited dynamic distribution throughout the cell cycle. Furthermore, conditionally generated neocentromeres in DT40 cells revealed that centrochromatin formation lowers, but does not eliminate, active transcription. To directly study the interaction of polycomb and heterochromatin with centrochromatin, I used a synthetic Human Artificial Chromosome (HAC), which allows for specific conditional targeting of chromatin modification enzymes, allowing manipulation of the underlying chromatin. Enrichment of the polycomb chromatin state on the HAC centromere, by EZH2 tethering, reduced its active transcriptional chromatin signature, but did not impair its actual transcription or mitotic activity. However, direct tethering of polycomb secondary silencing effector PRC1 caused centromere loss, and this effect was mimicked with homologous heterochromatin factors, indicating that centromeres can subsist within repressive chromatin domains, but are lost when direct repression is applied. To understand the contribution of the local repressive heterochromatin to centromere stability, I erased heterochromatin marks from the HAC centromere by tethering JMJD2D (an H3K9me3 demethylase): long-term (but not short-term) heterochromatin loss impaired CENP-A assembly, perturbed mitotic behaviour, and resulted in significant HAC mis-segregation. These results strongly suggest that local heterochromatin is essential to maintain normal CENP-A dynamics and centromere function. Together with previous observations, these data suggest that a repressive chromatin environment contributes to centromere stability, and that centromeres likely have natural mechanisms to maintain their transcriptional activity within such domains