E-GEOD-12690 - Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa

Status
Submitted on 4 September 2008, released on 15 May 2010, last updated on 1 May 2014
Organism
Neurospora crassa
Samples (26)
Array (1)
Protocols (13)
Description
Both RNAi-dependent and -independent mechanisms have been implicated in the establishment of heterochromatin domains, which may be stabilized by feedback loops involving chromatin proteins and modifications of histones and DNA. Neurospora crassa sports features of heterochromatin found in higher eukaryotes, namely cytosine methylation (5mC), methylation of histone H3 lysine9 (H3K9me) and HETEROCHROMATIN PROTEIN-1 (HP1), and provides a model to investigate heterochromatin establishment and maintenance. We mapped the distribution of HP1, 5mC, H3K9me3 and H3K4me2 at 100bp-resolution and explored their interplay. HP1, H3K9me3 and DNA methylation were extensively colocalized and defined 44 heterochromatic domains on linkage group VII, all relics of repeat-induced point mutation (RIP). Interestingly, the centromere was found in a striking ~350kb heterochromatic domain with no detectable H3K4me2. 5mC was not found in genes, in contrast to the situation in plants and animals. H3K9me3 is required for HP1 localization and DNA methylation. Here, we show that localization of H3K9me3 is independent of 5mC or HP1 at virtually all heterochromatin regions. In addition, we observed complete restoration of DNA methylation patterns after depletion and reintroduction of the H3K9 methylation machinery, indicating that the signals for de novo heterochromatin formation lie upstream of H3K9 methylation. These data show that A:T rich RIP’d DNA efficently directs methylation of H3K9, which in turn, directs methylation of associated cytosines. Immunoprecipitation experiments using antibodies to 5mC, H3K9me3, epitope-tagged HP1, and H3K4me2 were performed. The immunoprecipitate fraction was labeled with Cy5 and the total input was labeled with Cy3. Samples were hybridized to a N. crassa LGVII tiling path microarray.
Experiment types
ChIP-chip by tiling array, methylation profiling by array 
Contacts
Zachary A Lewis <zlewis@uoregon.edu>, Dirk Schubeler, Eric U Selker, Fabio Mohn, Jennifer K Jeffress, Michael Freitag, Shinji Honda, Tamir K Khlafallah
Citation
Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, Schübeler D, Selker EU.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-12690.idf.txt
Sample and data relationshipE-GEOD-12690.sdrf.txt
Raw data (1)E-GEOD-12690.raw.1.zip
Processed data (1)E-GEOD-12690.processed.1.zip
Array designA-GEOD-7253.adf.txt
R ExpressionSetE-GEOD-12690.eSet.r
Links