Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq

Seo, Minseok; Caetano-Anollés, Kelsey; Rodriguez-Zas, Sandra L.; Ka, Sojeong; Jeong, Jin Young; Park, Sungkwon; Kim, Min Ji; Nho, Whan Gook; Cho, Seoae; Kim, Heebal; Lee, Hyun Jeong

doi:10.1186/s12864-016-2400-4

Cited by 20 publications

(25 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Since sexually dimorphic genes have been shown to have tissue-specific patterns [20–22], it is possible that we may observe differences in the genetic control of gene expression across sexes if expression intensities are measured in other tissues. For example, if we measure gene expression in brain tissue, we may observe more cases where the genetic control of the expression of genes related to neurological and psychiatric disorders differs across the sexes.…”

Section: Discussionmentioning

confidence: 99%

“…Overall, there has been weak evidence for sex-specific eQTLs, which range from claims that 15% of detected cis -eQTLs show sex-specific effects in lymphoblastoid cell lines [17], to six autosomal and X chromosome genes showing sex-specific eQTLs in whole blood [19], to zero detected sex-specific eQTLs in cerebellar and frontal cortex brain tissue [18]. Potential reasons for these observations are: (1) the contribution of genotype-by-sex interactions to variation in gene expression may be tissue-specific, since sexually dimorphic genes have shown tissue-specific patterns [20–22]; (2) without sufficiently large sample sizes, the power to detect sex-specific eQTLs can be low, since there would need to be a correction to the significance threshold to account for both the number of genetic variants and the number of genes tested; or (3) the contribution of genotype-by-sex interactions to variation in gene expression occurs in a small number of genes, and, on average, males and females share the same common genetic control of gene expression.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Autosomal genetic control of human gene expression does not differ across the sexes

et al. 2016

View full text Add to dashboard Cite

BackgroundDespite their nearly identical genomes, males and females differ in risk, incidence, prevalence, severity and age-at-onset of many diseases. Sexual dimorphism is also seen in human autosomal gene expression, and has largely been explored by examining the contribution of genotype-by-sex interactions to variation in gene expression.ResultsIn this study, we use data from a mixture of pedigree and unrelated individuals with verified European ancestry to investigate the sex-specific genetic architecture of gene expression measured in whole blood across n=1048 males and n=1005 females by treating gene expression intensities in the sexes as two distinct traits and estimating the genetic correlation (r G) between them. These correlations measure the similarity of the combined additive genetic effects of all single-nucleotide polymorphisms across the autosomal chromosomes, and thus the level of common genetic control of gene expression across the sexes. Genetic correlations are estimated across the sexes for the expression levels of 12,528 autosomal gene expression probes using bivariate GREML, and tested for differences in autosomal genetic control of gene expression across the sexes. Overall, no deviation of the distribution of test statistics is observed from that expected under the null hypothesis of a common autosomal genetic architecture for gene expression across the sexes.ConclusionsThese results suggest that males and females share the same common genetic control of gene expression.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1111-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Autosomal genetic control of human gene expression does not differ across the sexes

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Instead, we applied genome annotation of BosTau7 to the expression data, and checked differential expression of XIST between sexes. XIST appeared as one of the most differentially expressed genes in all of the examined tissues (Seo et al 2016). …”

Section: Identification Of Sexually Dimorphic Gene Expressionmentioning

confidence: 96%

“…There are two approaches for identification of sexual dimorphic genes using RNA-seq data composed of two factors, gender and tissues (Seo et al 2016). The simplest approach for analysis of this data is to perform a two group test between data from female and males in each tissue, separately, as has been performed in previous studies (Yang et al 2006) using microarray data.…”

Section: Identification Of Sexually Dimorphic Gene Expressionmentioning

confidence: 99%

Status of dosage compensation of X chromosome in bovine genome

Seo

Kim

et al. 2016

Genetica

Self Cite

View full text Add to dashboard Cite

Dosage compensation system with X chromosome upregulation and inactivation have evolved to overcome the genetic imbalance between sex chromosomes in both male and female of mammals. Although recent development of chromosome-wide technologies has allowed us to test X upregulation, discrete data processing and analysis methods draw disparate conclusions. A series of expression studies revealed status of dosage compensation in some species belonging to monotremes, marsupials, rodents and primates. However, X upregulation in the Artiodactyla order including cattle have not been studied yet. In this study, we surveyed the genome-wide transcriptional upregulation in X chromosome in cattle RNA-seq data using different gene filtration methods. Overall examination of RNA-seq data revealed that X chromosome in the pituitary gland expressed more genes than in other peripheral tissues, which was consistent with the previous results observed in human and mouse. When analyzed with globally expressed genes, a median X:A expression ratio was 0.94. The ratio of 1-to-1 ortholog genes between chicken and mammals, however, showed considerable reduction to 0.68. These results indicate that status of dosage compensation for cattle is not deviated from those found in rodents and primate, and this is consistent with the evolutionary history of cattle.

show abstract

“…In these studies, gene expression is tested for mean differences between the sexes to identify sets of sex-differentially expressed genes within each tissue. These sets of genes are then compared across tissues, where genes that are not found at the intersection are deemed TSSD (14)(15)(16)(17)(18)(19). This analytical approach is limited in that first, there is no formal statistical testing when comparing sex-differentially expressed genes across tissues; second, there is no consideration for differences in the direction and magnitude of sex-differentiated expression across tissue-types; and finally, failure to account for repeated observations from the same individual increases the rates of false-positive and falsenegative associations.…”

Section: Introductionmentioning

confidence: 99%

Tissue-specific sex differences in human gene expression

Kassam

Yang

et al. 2019

Human Molecular Genetics

View full text Add to dashboard Cite

Despite extensive sex differences in human complex traits and disease, the male and female genomes differ only in the sex chromosomes. This implies that most sex-differentiated traits are the result of differences in the expression of genes that are common to both sexes. While sex differences in gene expression have been observed in a range of different tissues, the biological mechanisms for tissue-specific sex differences (TSSDs) in gene expression are not well understood. A total of 30 640 autosomal and 1021 X-linked transcripts were tested for heterogeneity in sex difference effect sizes in n = 617 individuals across 40 tissue types in Genotype–Tissue Expression (GTEx). This identified 65 autosomal and 66 X-linked TSSD transcripts (corresponding to unique genes) at a stringent significance threshold. Results for X-linked TSSD transcripts showed mainly concordant direction of sex differences across tissues and replicate previous findings. Autosomal TSSD transcripts had mainly discordant direction of sex differences across tissues. The top cis-expression quantitative trait loci (eQTLs) across tissues for autosomal TSSD transcripts are located a similar distance away from the nearest androgen and estrogen binding motifs and the nearest enhancer, as compared to cis-eQTLs for transcripts with stable sex differences in gene expression across tissue types. Enhancer regions that overlap top cis-eQTLs for TSSD transcripts, however, were found to be more dispersed across tissues. These observations suggest that androgen and estrogen regulatory elements in a cis region may play a common role in sex differences in gene expression, but TSSD in gene expression may additionally be due to causal variants located in tissue-specific enhancer regions.

show abstract

Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq

Cited by 20 publications

References 57 publications

Autosomal genetic control of human gene expression does not differ across the sexes

Autosomal genetic control of human gene expression does not differ across the sexes

Status of dosage compensation of X chromosome in bovine genome

Tissue-specific sex differences in human gene expression

Contact Info

Product

Resources

About