H3K56 deacetylation and H2A.Z deposition are required for aberrant heterochromatin spreading. Neurospora crassa

The self-propagating nature of heterochromatin requires mechanisms to restrict heterochromatin spreading within defined boundaries to prevent euchromatic genes silencing. In the filamentous fungus Neurospora crassa, the JmjC domain protein DNA METHYLATION MODULATOR-1 (DMM-1) prevents aberrant spreading of heterochromatin but the molecular details remain unknown. Here, we revealed that DMM-1 is highly enriched at a well-defined 5-kb heterochromatin domain and constrained its aberrant spreading. Interestingly, the aberrant spreading of the 5-kb heterochromatin domain observed in dmm-1KO strain is accompanied by the sharp deposition of histone variant H2A.Z, and deletion of H2A.Z abolishes the encroachment of the 5-kb heterochromatin domain on adjacent euchromatin. Furthermore, lysine 56 of histone H3 is deacetylated at the expanded heterochromatin regions, and mimicking H3K56 acetylation with an H3K56Q mutation effectively blocks H2A.Z-mediated aberrant spreading of the 5-kb heterochromatin domain. More importantly, genome-wide analyses demonstrated the general roles of H3K56 deacetylation and H2A.Z deposition in the aberrant spreading of heterochromatin. Altogether, our results illustrate a previously unappreciated regulatory process that mediates the aberrant heterochromatin spreading.