Genome-wide changes in gene expression caused by the disruption of dosage compensation.
Genes were separated into different gene sets based on their length, origin, and chromosome (X vs autosome) to compare GRO-seq gene expression between the sdc-2 mutant and control RNAi embryos. Shown are the total number of genes, the median sdc-2 mutant/control RNAi expression ratio, the average sdc-2 mutant/control RNAi expression ratio together with the standard error of the mean, and the number of genes in each set that are more highly expressed in each condition. Across numerous protein-coding gene sets, the X chromosome is more highly expressed and the autosomes are slightly less expressed in the sdc-2 mutant. Furthermore, when X-linked genes are significantly changed in expression, they are almost exclusively increased in expression. Each gene set is separated into two sets, one containing all genes and the other containing genes that are significantly changed in expression as determined by analysis with DESeq (p<0.05) (Anders and Huber, 2010). For the first two lists (labeled with ‘≥250 bp’), average GRO-seq gene expression was calculated from the beginning to the end of either the WormBase (WB) model or the newly annotated transcription start site (TSS) gene model. WB genes had to be expressed at greater than 1 RPKM (reads per kilobase per million), and have at least 250 uniquely mappable bases in both sets. For the next set (labeled with ‘WormBase WS230 Genes ≥1.1 kb’), average GRO-seq expression was calculated for genes greater than 1.1 kb, with the first and last 300 bp of the gene excluded. The level of expression had to be ≥1 RPKM for WB genes, and have at least 250 uniquely mappable bases for a gene to be included. For the final two sets of genes (labeled with ‘≥1.1 kb’ and ‘≥1.5 kb’), expression was calculated for genes of the indicated length that have a newly annotated TSS, with the first and last 300 bp of the gene excluded. A gene had to have at least 250 uniquely mappable bases for it to be included. RNA polymerase II transcribed microRNAs are controlled by dosage compensation, while RNA polymerase III transcribed tRNAs are not. Average GRO-seq gene expression from sdc-2 mutant and control RNAi embryos was compared across ncRNAs. For microRNAs, expression values were calculated from the full length of the WB ‘primary transcript’ or re-annotated TSS gene models. For tRNAs, expression values were calculated from the beginning of the ‘mature transcript’ to 50 bp downstream of the stop. Because tRNAs are highly repetitive and transcription of highly transcribed tRNAs continues downstream of the stop, the extra 50 bp was included to increase the unique mappability of each tRNA. For a gene to be considered for analysis, it had to have at least 25 bp of uniquely mappable DNA, and to have an average expression of at least 1 RPKM in both control RNAi and sdc-2 mutant embryos. The median and mean sdc-2/control expression levels show that X-linked microRNAs are more susceptible to dosage compensation than autosomal microRNAs. X-linked tRNAs are decreased slightly in expression in the sdc-2 mutant, suggesting that its expression is not controlled by dosage compensation.