Expression quantitative trait loci: replication, tissue- and sex-specificity in mice

Abstract

By treating the transcript abundance as a quantitative trait, gene expression can be mapped to local or distant genomic regions relative to the gene encoding the transcript. Local expression quantitative trait loci (eQTL) generally act in cis (that is, control the expression of only the contiguous structural gene), whereas distal eQTL act in trans. Distal eQTL are more difficult to identify with certainty due to the fact that significant thresholds are very high since all regions of the genome must be tested, and confounding factors such as batch effects can produce false positives. Here, we compare findings from two large genetic crosses between mouse strains C3H/HeJ and C57BL/6J to evaluate the reliability of distal eQTL detection, including "hotspots" influencing the expression of multiple genes in trans. We found that >63% of local eQTL and >18% of distal eQTL were replicable at a threshold of LOD > 4.3 between crosses and 76% of local and >24% of distal eQTL at a threshold of LOD > 6. Additionally, at LOD > 4.3 four tissues studied (adipose, brain, liver, and muscle) exhibited >50% preservation of local eQTL and >17% preservation of distal eQTL. We observed replicated distal eQTL hotspots between the crosses on chromosomes 9 and 17. Finally, >69% of local eQTL and >10% of distal eQTL were preserved in most tissues between sexes. We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability.

Figure 1.—

Replication of local (a) and distal (b) eQTL between crosses. The percentage of eQTL that replicated between crosses at various LOD thresholds is depicted in adipose, brain, liver, and muscle tissue. The eQTL at LOD > 2.7, 4.3, and 6 of the mouse crosses were screened for detection at LOD > 2.7 in their respective comparison crosses. The percentage indicates the degree of replication of eQTL at LOD > 4.3 in cross I that overlap in cross II at LOD > 2.7 over the total number of eQTL at LOD > 4.3 detected in cross I and vice versa. For example, at LOD > 6, >80% of the local eQTL in cross I were preserved in cross II of the adipose tissue.

Figure 2.—

Preservation of local (a) and distal (b) eQTL across tissues. The percentage of eQTL that were preserved across tissues at various LOD thresholds is depicted in adipose, brain, liver, and muscle tissue. The eQTL at LOD > 2.7, 4.3, and 6 of a tissue were screened for detection at LOD > 2.7 in their respective comparison tissues (sex and mouse crosses were combined). The percentage indicates the degree of replication of eQTL at LOD > 4.3 in one tissue that overlap in its comparison tissue at LOD > 2.7 over the total number of eQTL at LOD > 4.3 detected in the first tissue and vice versa. For example, for the local eQTL in cross I, ∼70% of the local eQTL found in adipose at LOD > 6 were detected in brain at LOD > 2.7. The bar graph reflects the eQTL at LOD > 4.3 of the adipose tissue as compared to the eQTL at LOD > 2.7 of the brain, liver, and muscle (brain compared to adipose, liver, and muscle; liver compared to adipose, brain, and muscle; and muscle compared to adipose, brain, and liver).

Figure 3.—

Preservation of local (a) and distal (b) eQTL between females and males. The percentage of eQTL that replicated between sexes at various LOD thresholds is depicted in adipose, brain, liver, and muscle tissue. The eQTL at LOD > 2.7, 4.3, and 6 of one sex were screened for detection at LOD > 2.7 in the opposite sex. The percentage indicates the degree of replication of eQTL at LOD > 4.3 in females that overlap in males at LOD > 2.7 over the total number of eQTL at LOD > 4.3 detected in females and vice versa. For example, at LOD > 6, female adipose in cross I shows >80% of the local eQTL preserved in the male adipose cross I group.

Figure 4.—

Replication of distal eQTL between crosses at different significance thresholds. The percentage of eQTL that replicated between crosses at various LOD thresholds is depicted in (a) adipose, (b) brain, (c) liver, and (d) muscle tissue. The eQTL at LOD > 2.7–10 of the mouse crosses were screened for detection at LOD > 2.7–10 in their respective comparison crosses. The heat map reflects the degree of replication as the percentage of eQTL at various LOD thresholds in cross I that overlap in cross II at various LOD thresholds and vice versa. For example, in adipose tissue (a), ∼80% of eQTL at LOD > 2.7 in cross II were detected in cross I (bottom right corner).

Figure 5.—

Replication of eQTL hotspots between crosses. The chromosomes were screened for the highest relative frequency of distal eQTL at LOD > 5.7 of the crosses (cross I vs. cross II). The detection of loci with eQTL greater than or equal to three standard deviations above the average frequency of distal eQTL in one tissue alluded to the presence of an eQTL hotspot. (a) Adipose; (b) brain; (c) liver; (d) muscle.

Figure 5.—

Replication of eQTL hotspots between crosses. The chromosomes were screened for the highest relative frequency of distal eQTL at LOD > 5.7 of the crosses (cross I vs. cross II). The detection of loci with eQTL greater than or equal to three standard deviations above the average frequency of distal eQTL in one tissue alluded to the presence of an eQTL hotspot. (a) Adipose; (b) brain; (c) liver; (d) muscle.