Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants

Abstract

Nucleosome structural integrity underlies the regulation of DNA metabolism and transcription. Using a synthetic approach, a versatile library of 486 systematic histone H3 and H4 substitution and deletion mutants that probes the contribution of each residue to nucleosome function was generated in Saccharomyces cerevisiae. We probed fitness contributions of each residue to perturbations of chromosome integrity and transcription, mapping global patterns of chemical sensitivities and requirements for transcriptional silencing onto the nucleosome surface. Each histone mutant was tagged with unique molecular barcodes, facilitating identification of histone mutant pools through barcode amplification, labeling, and TAG microarray hybridization. Barcodes were used to score complex phenotypes such as competitive fitness in a chemostat, DNA repair proficiency, and synthetic genetic interactions, revealing new functions for distinct histone residues and new interdependencies among nucleosome components and their modifiers.

Fig. 1

Features of synthetic histone cassette. A. Schematic representation of histone H3/H4 cassette in pRS414. The two selectable markers, TRP1 and URA3, can be ued to select an episomal copy or an integrated cassette respectively. B. Cassettes contain synthetic H3 and H4 genes (HHTS and HHFS) flanking a central native HHT2/HHF2 promoter region (P_HHT2-HHF2). Mutations are engineered into either HHTS or HHFS and tagged with molecular barcodes (TAGs, labeled *). Upper cassette indicated is used as base construct for HHTS (H3) mutants; lower one is used as base construct for HHFS (H4) mutagenesis. C. The mutant library consists of an alanine scan with other systematic residue swaps and systematic tail deletions, totaling 486 mutants.

Fig. 2

Analysis of lethal histone alleles. A. Substitution mutations above the sequence are lethal in the S288C strain background (blue); those below are lethal in GRF167 (green). Arrows indicate substitution mutations with strain-specific lethality. Clusters of amino acids at crucial nucleosomal locations are boxed. B. Nucleosome view indicating lethal substitutions tracking DNA binding surface at nucleosome dyad. Only lethal mutants common to both genetic backgrounds are shown. C. Correlation between lethal point mutants and evolutionary conservation. Evolutionary conservation scores for each histone residue were calculated using Consurf. D. Distinct sets of lethal tail deletions in two strain backgrounds. Gray boxes, deleted amino acids in viable mutants; red boxes, deletions lethal in both genetic backgrounds; Blue box, lethal in S288C strain only. E. Protein stability of episome-remedial lethal mutants was monitored by immunoblotting. JDY strains expressing indicated lethal mutations were transformed with FLAG-His tagged WT histone (FH-WT) blotted for either anti-histone H3 or anti-histone H4, and anti-tubulin as a loading control. Arrows indicate position of the mutated histone protein (MUT) and tagged WT histone protein. See also Fig. S2.

Fig. 3

High-throughput phenotypic analysis. A. Pie chart shows % of mutants with pleiotropy values of 0−5, defined as the number of phenotype classes with at least one non-wild-type phenotype. B. Distinct but overlapping substitution mutations affect transcriptional silencing. Red, mutations losing rDNA or telomeric silencing; or aqua, mutations enhancing silencing. Individual residues can be identified by mousing over a region(s) of interest on www.histonehits.org. C. Evolutionary conservation scores for each residue, calculated using Consurf, are averaged for mutants binned by pleiotropy. D. Average pleiotropy values are shown for mutants binned into four geographical nucleosome domains: tail, disk surface, lateral surface or buried (Supplementary methods). E. Average pleiotropy values are shown for mutants binned by ΔpK_a. Acidic-to-neutral and basic-to-neutral changes are significantly more pleiotropic than basic-to-basic (see text). F. Average deletion lengths are shown for tail deletion mutants binned by pleiotropy. For C−F, vertical bars indicate the standard errors of the binned means.

Fig. 4

Tail deletions affect K79 methylation. A. Immunoblots of extracts of cells expressing wild-type or indicated H4 tail-deletion mutants using antibodies against dimethylated K79 (diMeK79). Antibodies against histone H3 and H4 were used as loading controls; dot1Δ strain is the negative control. B. Immunoblot analysis as in Fig. 4A but with H4 point mutant extracts.

Fig. 5

Chemostat growth profiles reveal subset of mutants that outgrow wild-type. Cells were cultured in a glucose-limited chemostat at 30°C and sampled as indicated. A. Microarray ratio images. Red features represent mutants depleted after chemostat. B. Reproducibility of chemostat growth profiles. Two independent chemostat cultures were grown in parallel to day 10. The log₂ ratios express relative enrichment of mutants. C. Chemostat population profile at day 10. Scatter plot depicts log₂ signal intensity associated with each mutant before (x-axis) and after (y-axis) growth; colors stratify mutant population by relative abundance. D. Population profile at day 20; color assignments as in C. E. Chemostat growth of over-represented mutants. Mutants from the top strata of C were cocultured as above for 10 days in competition with a matched WT strain. Changes in log₂ signal intensity are depicted as in C. Yellow triangle, WT. Small open squares, mutants not present in this experiment.

Fig. 6

Assaying complex phenotypes using TAG arrays. A. Double mutant analysis of histone library with ubp8Δ. Scatter plot depicting log₂ ratio of abundance of each mutant in a ubp8Δ strain. Gray vertical lines (alleles 235−288 and 461−488) separate allelic classes (left to right: H3 substitutions, H3 deletions, H4 substitutions, H4 deletions). Red squares identify substitution mutants verified individually for synthetic interactions. B. Tetrad analysis to determine viability. Haploid strains carrying ubp8Δ or the indicated histone mutation were mated for 4 hours, and then diploids were purified and sporulated. Tetrads were dissected on YPD medium to score fitness defects. Relevant genotypes are indicated. C. Double mutant analysis of histone library with set2Δ. Scatter plot as in A, depicting log₂ ratios in a set2Δ strain. D. Analysis of NHEJ phenotypes. Scatter plot indicating the log₂ ratio of signal intensities of cut/uncut plasmid transformations for each mutant; annotations as in A. E. Individual quantification of transformant recovery of indicated strains transformed with digested plasmid relative to a non-digested control; lig4Δ strain serves as a negative control.