To date, cross-species comparisons of genetic interactomes have been restricted to small or functionally related gene sets, limiting our ability to infer evolutionary trends. To facilitate a more comprehensive analysis, we constructed a genome-scale epistasis map (E-MAP) for the fission yeast Schizosaccharomyces pombe, providing phenotypic signatures for ~60% of the non-essential genome. Using these signatures, we generated a catalogue of 297 functional modules, and assigned function to 144 previously uncharacterised genes, including mRNA splicing and DNA damage checkpoint factors. Comparison with an integrated genetic interactome from the budding yeast Saccharomyces cerevisiae revealed a hierarchical model for the evolution of genetic interactions, with conservation highest within protein complexes, lower within biological processes, and lowest between distinct biological processes. Despite the large evolutionary distance and extensive rewiring of individual interactions, both networks retain conserved features and display similar levels of functional cross-talk between biological processes, suggesting general design principles of genetic interactomes.

A study of gene silencing within the mating-type region of fission yeast defines two distinct pathways responsible for the establishment of heterochromatin assembly. One is RNA interference-dependent and acts on centromere-homologous repeats (cenH). The other is a stochastic Swi6 (the fission yeast HP1 homolog)-dependent mechanism that is not fully understood. Here we find that activating transcription factor (Atf1) and Pcr1, the fission yeast bZIP transcription factors homologous to human ATF-2, are crucial for proper histone deacetylation of both H3 and H4. This deacetylation is a prerequisite for subsequent H3 lysine 9 methylation and Swi6-dependent heterochromatin assembly across the rest of the silent mating-type (mat) region lacking the RNA interference-dependent cenH repeat. Moreover, Atf1 and Pcr1 can form complexes with both a histone deacetylase, Clr6, and Swi6, and clr6 mutations affected the H3/H4 acetylation patterns, similar to the atf1 and pcr1 deletion mutant phenotypes at the endogenous mat loci and at the ctt1 ؉ promoter region surrounding ATF/CREbinding site. These data suggest that Atf1 and Pcr1 participate in an early step essential for heterochromatin assembly at the mat locus and silencing of transcriptional targets of Atf1. Furthermore, a phosphorylation event catalyzed by the conserved mitogen-activated protein kinase pathway is important for regulation of heterochromatin silencing by Atf1 and Pcr1. These findings suggest a role for the mitogen-activated protein kinase pathway and histone deacetylase in Swi6-based heterochromatin assembly.Methylation of histone H3 lysine 9 (H3 Lys-9) by the conserved H3 Lys-9-specific methyltransferase, Su(var)3-9 in flies, SUV39H1 in human, and Clr4 in the fission yeast Schizosaccharomyces pombe (1-4) correlates with heterochromatin assembly. The methylated Lys-9 residue recruits another conserved heterochromatin protein, which is called Swi6 in S. pombe and HP1 (heterochromatin protein 1) in higher eukaryotes (5, 6), leading to regional silencing of chromatin. In the fission yeast, recent studies (6 -8) addressing the silencing of the mating-type region provide insights for understanding the regulation of heterochromatin assembly in eukaryotes. Of particular interest, previous work (9) has defined sequential requirements for the establishment and maintenance of regional heterochromatic domains.Heterochromatin assembly at the mating-type region containing the mat2 and mat3 silent donor loci and an 11-kb interval (K region) between them requires several cis-acting DNA sequences as well as trans-acting factors (8, 10 -13). Heterochromatin formation at the centromeres and within the silent mat2/3 interval requires many of the same silencing factors, including Clr3 and Clr6 (H3/H4-specific histone deacetylases), the Clr4-Rik1 complexes, and Swi6 (2, 14 -19). The DNA elements involved in silencing within the entire 20 kb of the mat2/3 silent mating-type interval include REII (20), the mat3-M element including putative ATF 1 /CREB-binding sites (21), and the ...

SummaryHistone variant H2A.Z has a conserved role in genome stability, although it remains unclear how this is mediated. Here we demonstrate in fission yeast that the Swr1 ATPase inserts H2A.Z (Pht1) into chromatin and Kat5 acetyltransferase (Mst1) acetylates it. Deletion or unacetylatable mutation of Pht1 leads to genome instability, primarily caused by chromosome entanglement/breakage at anaphase. This leads to the loss of telomere-proximal markers, though telomere protection and repeat length are unaffected by the absence of Pht1. Strikingly the chromosome entanglement in pht1Δ anaphase cells can be rescued by forcing chromosome condensation prior to anaphase onset. We show that the condensin complex, required for the maintenance of anaphase chromosome condensation, prematurely dissociates from chromatin in the absence of Pht1. This and other findings suggest an important role for H2A.Z in the architecture of anaphase chromosomes.

The assembly of prespliceosomes is responsible for selection of intron sites for splicing. U1 and U2 snRNPs recognize 5= splice sites and branch sites, respectively; although there is information regarding the composition of these complexes, little is known about interaction among the components or between the two snRNPs. Here we describe the protein network of interactions linking U1 and U2 snRNPs with the ATPase Prp5, important for branch site recognition and fidelity during the first steps of the reaction, using fission yeast Schizosaccharomyces pombe. The U1 snRNP core protein U1A binds to a novel SR-like protein, Rsd1, which has homologs implicated in transcription. Rsd1 also contacts S. pombe Prp5 (SpPrp5), mediated by SR-like domains in both proteins. SpPrp5 then contacts U2 snRNP through SF3b, mediated by a conserved DPLD motif in Prp5. We show that mutations in this motif have consequences not only in vitro (defects in prespliceosome formation) but also in vivo, yielding intron retention and exon skipping defects in fission yeast and altered intron recognition in budding yeast Saccharomyces cerevisiae, indicating that the U1-U2 network provides critical, evolutionarily conserved contacts during intron definition. Intron removal from new transcripts by pre-mRNA splicing is a fundamental feature of all eukaryotes. Such splicing is catalyzed by the spliceosome, a dynamic RNA-protein complex containing Ͼ150 proteins and five snRNAs. The assembly of the spliceosome is considered to be a dynamic process with a large number of RNA-RNA and RNA-protein rearrangements (31, 35). In the canonical pathway, U1 snRNP recognizes the pre-mRNA at the 5= splice site (5=SS); then, U2 snRNP stably binds the branch site (BS) region to form a prespliceosome. U4/5/6 tri-snRNP then joins, after rearrangements, U1 and U4 snRNPs are released, and the remaining U2/5/6 core forms the catalytic spliceosome. Both the early recognition of pre-mRNA and the rearrangements of snRNP structures to form an active conformation are facilitated by DExD/H ATPases, which couple ATP binding/hydrolysis with structural alterations (33,35).Two modes for early exon and intron specification have been described: exon definition for short exons flanked by long introns, which mostly appear in vertebrates, and intron definition for short introns, which are often present in lower eukaryotes (5). Interactions between U1 and U2 snRNPs are critical to both exonand intron-defined phases of spliceosome assembly. In the formation of commitment complexes in budding yeast Saccharomyces cerevisiae, or E complexes in mammals, cross-intron bridging interactions are proposed to connect from Prp40 in U1 snRNP at the 5=SS to SF1/BBP at the branch site or to U2AF at the polypyrimidine tract (PPT), respectively (1, 24). However, in prespliceosome formation, the first ATP-dependent transition, the BS-SF1/BBP interaction (or the PPT-U2AF interaction) is disrupted and replaced by BS-U2 snRNP interactions (28,33). This exchange of interactions is facilitated by the ATPase Prp...

Background: Transcription is disruptive to chromatin structure and can expose cryptic promoters. Results: We identify those factors that might regulate cryptic transcription from within inactive and transcribed locations. Conclusion: Nucleosome shielding prevents cryptic transcription, and replication-independent histone replacement is co-operatively mediated by three H3-H4 chaperones. Significance: Understanding how cryptic transcription is regulated and lost histones replaced is of fundamental importance.