Sperm-inherited H3K27me3 epialleles are transmitted transgenerationally in cis

The role that gamete-inherited chromatin states serve in regulating gene expression across generations is poorly understood. To interrogate how histone marks inherited on parental genomes influence gene expression in offspring, we profiled different tissue contexts in worms that inherited the sperm genome lacking the repressive mark H3K27me3. We found that worms that inherited the sperm genome lacking H3K27me3 upregulated genes in all tissues profiled, which included hermaphrodite and male germlines and mixed soma. We found that most upregulated genes were upregulated specifically from sperm alleles and in a tissue-specific manner, highlighting the importance of cellular context in determining which genes are sensitive to upregulation when H3K27me3 repression is absent. To determine whether chromatin states can impact gene expression transgenerationally, i.e. across 3 generations, we profiled gene expression and chromatin states in the germlines of worms that inherited the sperm genome lacking H3K27me3 (F1 generation) and in the germlines of their offspring (F2 generation). We found that genes upregulated in F1 germlines maintained the H3K27me3(-) state of sperm alleles and that the upregulated and H3K27me3(-) state of sperm alleles was maintained in the germlines of their offspring (F2 generation). These findings demonstrate that histone marks can serve as a transgenerational carrier. Overall design: We generated genetically identical worms that inherited the sperm genome with H3K27me3 (K27me3 M+P+) or without H3K27me3 (K27me3 M+P-) by mating wild-type females with males heterozygous or homozygous mutant for the PRC2 component MES-3, respectively. We used single nucleotide polymorphisms (SNPs) between the oocyte-inherited (Hawaii/CB4856 genetic background) and sperm-inherited (Bristol/N2 genetic background) genomes to distinguish from which parental genome RNA-sequencing and CUT&RUN (H3K27me3 and H3K36me3) sequencing reads came. We profiled transcripts from 3 tissues in K27me3 M+P- and K27me3 M+P+ worms: hermaphrodite and male germlines and mixed soma. To assess chromatin and gene expression patterns in germlines across 3 generations, we profiled transcripts and the chromatin marks H3K27me3 and H3K36me3 via CUT&RUN (Skene and Henikoff 2017; Skene et al. 2018) in him-8 males (a surrogate for wild-type fathers), K27me3 M+P- and K27me3 M+P+ offspring (F1 generation) hermaphrodites, and their genetically identical hermaphrodite grandoffspring, K27me3 GM+GP- & K27me3 GM+GP+ (F2 generation). All germline analysis was performed from distal halves of germlines from day 1 adults. Mixed soma samples were prepared from newly hatched, never starved L1 larvae. For transcript analysis, libraries were prepared from polyA-selected RNA and sequenced to acquire paired-end 50 bp or 75 bp reads on NovaSeq or NextSeq Illumina sequencing platforms. 50 bp reads were mapped (75 bp reads were trimmed to 50 bp) to the ce10 genome in 2 ways: single-end for SNP analysis and paired-end for differential gene expression analysis. For chromatin analysis, libraries were prepared from DNA associated with H3K27me3 and H3K36me3 collected using the CUT&RUN method and sequenced to acquire paired-end 50 bp or 75 bp reads on NovaSeq or NextSeq Illumina sequencing platforms. 50 bp reads were mapped (75 bp reads were trimmed to 50 bp) to the ce10 genome.