Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster

Abstract The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand, testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.

x 392F mt R2 and 808M x 208F mt R2 are removed due to low quality, and not used in any analysis. The last two columns (chr and start) are the chromosome and position of the gene.
The dataset corresponds to Dataset S1 in this link: https://doi.org/10.15479/AT:ISTA:12933 Dataset S2. Overall TPM data in parentals and hybrids estimated using Kallisto. Each column contains TPM gene expression for a particular sample. Each sample is labeled as follows: 1 2 3. 1 indicates the maternal (F) and paternal (M) lines of the hybrid cross. 2 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes). 3 is the replicate: R1 or R2. Expression data for samples 392F x 757M mh R2, 392M x 392F mt R2 and 808M x 208F mt R2 are removed due to low quality, and not used in any analysis. The last two columns (chr and start) are the chromosome and position of the gene.
This dataset is used for the inheritance patterns classification.
The dataset corresponds to Dataset S2 in this link: https://doi.org/10.15479/AT:ISTA:12933 Dataset S3. Overall parental and allele-specific hybrid count expression estimated using ASETigar. Each column contains count gene expression for a particular sample.
Parental overall expression data has been estimated using the ASETigar pipeline (see Methods) so that the estimates are comparable to the allelic expression in the hybrids.
Expression for each specific pairwise comparison is labeled as 1_2_34_5. 1 and 2 are the two lines being compared, 3 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes), 4 is the replicate: R1 or R2. 5 is the line (corresponding with 1 or 2) for which expression is estimated. Hybrid allele-specific expression estimates are labeled as 1Fx2M_3_4_5. 1 and 2 indicate the maternal and paternal lines of the hybrid cross, respectively. 3 is the tissue and sex, 4 the replicate and 5 the line (corresponding with 1 or 2) for which allele-specific expression is estimated. Expression data for samples 392F x 392M mt R2, 208Fx808M_mt_R2 and 392Fx757M_mh_R2 are removed due to low quality and not used in the analysis. The last two columns (chr and start) are the chromosome and position of the gene. This dataset is used to estimate cis regulatory effects via the two 1 described methods: only hybrid allele-specific expression was used for CR, PO and MG estimates following Takada  Parental overall expression data has been estimated using the ASETigar pipeline (see Methods) so that the estimates are comparable to the allelic expression in the hybrids.
Expression for each specific pairwise comparison is labeled as 1_2_34_5. 1 and 2 are the two lines being compared, 3 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes), 4 is the replicate: R1 or R2. 5 is the line (corresponding with 1 or 2) for which expression is estimated. Hybrid allele-specific expression estimates are labeled as 1Fx2M_3_4_5. 1 and 2 indicate the maternal and paternal lines of the hybrid cross, respectively. 3 is the tissue and sex, 4 the replicate and 5 the line (corresponding with 1 or 2) for which allele-specific expression is estimated. Expression data for samples 392F x    Figure S7. Inheritance patterns inferred using statistical tests. Instead of fold differences, the classification into the various inheritance patterns was done via statistical testing for differences in expression between parentals and hybrid crosses (pooling the reciprocals together) using DEseq2 at FDR<0.05. A) Scatter plots of the relative overall expression between hybrids (H) and parentals (P) in each sex, tissue and cross. Each dot is a gene and is color-coded according to the inferred inheritance pattern, according to the legend in B). B) Proportion of genes with each inferred inheritance mechanism per sample.
Significance groups revealing differences in the proportion of genes displaying additive and dominant -in both directions combined-(in white and black respectively) across samples (two-proportions z-test at p-value <0.05) are denoted by different letters (a-b and a-c).