scholarly journals X chromosome gene expression in human tissues: Male and female comparisons

Genomics ◽  
2006 ◽  
Vol 88 (6) ◽  
pp. 675-681 ◽  
Author(s):  
Zohreh Talebizadeh ◽  
Stephen D. Simon ◽  
Merlin G. Butler
Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1167-1181
Author(s):  
Pei-Wen Chiang ◽  
David M Kurnit

Abstract Using a sensitive RT-QPCR assay, we analyzed the regulatory effects of sex and different dosage compensation mutations in Drosophila. To validate the assay, we showed that regulation for several genes indeed varied with the number of functional copies of that gene. We then confirmed that dosage compensation occurred for most genes we examined in male and female flies. Finally, we examined the effects on regulation of several genes in the MSL pathway, presumed to be involved in sex-dependent determination of regulation. Rather than seeing global alterations of either X chromosomal or autosomal genes, regulation of genes on either the X chromosome or the autosomes could be elevated, depressed, or unaltered between sexes in unpredictable ways for the various MSL mutations. Relative dosage for a given gene between the sexes could vary at different developmental times. Autosomal genes often showed deranged regulatory levels, indicating they were in pathways perturbed by X chromosomal changes. As exemplified by the BR-C locus and its dependent Sgs genes, multiple genes in a given pathway could exhibit coordinate regulatory modulation. The variegated pattern shown for expression of both X chromosomal and autosomal loci underscores the complexity of gene expression so that the phenotype of MSL mutations does not reflect only simple perturbations of genes on the X chromosome.


Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1825-1832 ◽  
Author(s):  
Barbara P Rattner ◽  
Victoria H Meller

Abstract The MSL complex of Drosophila upregulates transcription of the male X chromosome, equalizing male and female X-linked gene expression. Five male-specific lethal proteins and at least one of the two noncoding roX RNAs are essential for this process. The roX RNAs are required for the localization of MSL complexes to the X chromosome. Although the mechanisms directing targeting remain speculative, the ratio of MSL protein to roX RNA influences localization of the complex. We examine the transcriptional regulation of the roX genes and show that MSL2 controls male-specific roX expression in the absence of any other MSL protein. We propose that this mechanism maintains a stable MSL/roX ratio that is favorable for localization of the complex to the X chromosome.


Nature ◽  
2017 ◽  
Vol 550 (7675) ◽  
pp. 244-248 ◽  
Author(s):  
Taru Tukiainen ◽  
◽  
Alexandra-Chloé Villani ◽  
Angela Yen ◽  
Manuel A. Rivas ◽  
...  

Abstract X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of ‘escape’ from inactivation varying between genes and individuals1,2. The extent to which XCI is shared between cells and tissues remains poorly characterized3,4, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression5 and phenotypic traits6. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity6,7. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.


2010 ◽  
Vol 107 (8) ◽  
pp. 3704-3709 ◽  
Author(s):  
Yukio Yasukochi ◽  
Osamu Maruyama ◽  
Milind C. Mahajan ◽  
Carolyn Padden ◽  
Ghia M. Euskirchen ◽  
...  

2020 ◽  
Vol 30 (6) ◽  
pp. 860-873 ◽  
Author(s):  
Alexander K. Godfrey ◽  
Sahin Naqvi ◽  
Lukáš Chmátal ◽  
Joel M. Chick ◽  
Richard N. Mitchell ◽  
...  

Genetics ◽  
2022 ◽  
Author(s):  
Barbara J Meyer

Abstract Abnormalities in chromosome number have the potential to disrupt the balance of gene expression and thereby decrease organismal fitness and viability. Such abnormalities occur in most solid tumors and also cause severe developmental defects and spontaneous abortions. In contrast to the imbalances in chromosome dose that cause pathologies, the difference in X-chromosome dose used to determine sexual fate across diverse species is well tolerated. Dosage compensation mechanisms have evolved in such species to balance X-chromosome gene expression between the sexes, allowing them to tolerate the difference in X-chromosome dose. This review analyzes the chromosome counting mechanism that tallies X-chromosome number to determine sex (XO male and XX hermaphrodite) in the nematode Caenorhabditis elegans and the associated dosage compensation mechanism that balances X-chromosome gene expression between the sexes. Dissecting the molecular mechanisms underlying X-chromosome counting has revealed how small quantitative differences in intracellular signals can be translated into dramatically different fates. Dissecting the process of X-chromosome dosage compensation has revealed the interplay between chromatin modification and chromosome structure in regulating gene expression over vast chromosomal territories.


Genetics ◽  
1987 ◽  
Vol 117 (4) ◽  
pp. 657-670
Author(s):  
Leslie DeLong ◽  
Lawrence P Casson ◽  
Barbara J Meyer

ABSTRACT Caenorhabditis elegans compensates for the difference in X chromosome gene dose between males (XO) and hermaphrodites (XX) through a mechanism that equalizes the levels of X-specific mRNA transcripts between the two sexes. We have devised a sensitive and quantitative genetic assay to measure perturbations in X chromosome gene expression caused by mutations that affect this process of dosage compensation. The assay is based on quantitating the precocious alae phenotype caused by a mutation that reduces but does not eliminate the function of the X-linked gene lin-14. We demonstrate that in diploid animals the lin-14 gene is dosage compensated between XO and XX animals. In XXX diploid animals, however, lin-14 expression is not compensated, implying that the normal dosage compensation mechanism in C. elegans lacks the capacity to compensate completely for the additional X chromosome in triplex animals. Using the lin-14 assay we compare the effects of mutations in the genes dpy-21, dpy-26, dpy-27, dpy-28, and dpy-22 on X-linked gene expression. Additionally, in the case of dpy-21 we correlate the change in phenotypic expression of lin-14 with a corresponding change in the lin-14 mRNA transcript level.


2018 ◽  
Vol 28 (12) ◽  
pp. 1987-1992.e3 ◽  
Author(s):  
Rebecca J. Davis ◽  
Esther J. Belikoff ◽  
Elizabeth H. Scholl ◽  
Fang Li ◽  
Maxwell J. Scott

2011 ◽  
Vol 23 (1) ◽  
pp. 155
Author(s):  
Y. Gao ◽  
V. Hall ◽  
P. Hyttel

During embryonic development in mammals, the first cell fate decision occurs at the morula stage, which leads to the establishment of the inner cell mass (ICM) and trophectoderm (TE). At this point of development, differential patterns of gene expression and epigenetic marks are observed within these two lineages. The ICM later differentiates to form the epiblast. Previous reports suggest that the distinct patterns of expression might be substantially regulated by epigenetic marks such as DNA methylation and post-transcriptional modifications. In this study, we examined the global H3K27me3 distribution, as well as the expression levels of H3K27me3 specific methyltransferases and XIST in the epiblast and TE of Day 10 in vivo porcine embryos. A total of 33 embryos were collected by non-surgical flushing from inseminated, and later, culled sows. The embryos were sexed by PCR (sequences of ZFX (X chromosome) and SRY (Y chromosome) genes were amplified by PCR using primers) because the H3K27me3 has been associated with X chromosome inactivation. For immunocytochemistry, a small piece of TE was removed before fixation and analysed for sexing by PCR. For comparative RT-PCR studies, embryos were mechanically separated, sexed, and then later pooled as male or female epiblast and TE (male = 6, female = 8). Global H3K27me3 was analysed by immunocytochemistry in 11 male and 8 female Day 10 embryos. Expression of methylases (EZH2, EED and SUZ12, three core components of PRC2), demethylases (JMJD3 and UTX) of H3K27me3, and XIST was performed on the pooled epiblasts and pooled TE. Expression levels were normalized to the reference gene, GAPDH, and was further normalized to Day 9 embryos. Our results show that high nuclear expression of H3K27me3 was observed in both male and female TE cells, with little to no observable expression in the epiblast. However, a single, small, punctate spot could be detected within the nuclei of the female epiblast and TE. XIST, a non-coding RNA associated with the initiation of X chromosome inactivation (XCI), was observed to be highly expressed in the female epiblast and TE, which suggests H3K27me3 punctate spots that presented in female epiblast or TE are potentially expressed on the inactive X chromosomes. We also detected higher expression of the H3K27me3 methylase (EZH2) and the methylase cofactors (EED, SUZ12) in both male and female TE. Of interest, EED expression was higher in the female epiblast and TE compared to the male epiblast and TE. This suggests that EED may play an important role in the initiation of XCI. The expression of H3K27me3 demethylases JMJD3 and UTX, were also higher in the TE compared to the epiblast, which indicates the trimethylation of H3K27 in the embryos is a dynamic process. We suggest that no, or extremely low, H3K27me3 in the porcine epiblast might be required for the cells to program gene expression towards different cell fates upon differentiation and the enrichment of H3K27me3 in the TE of Day 10 porcine embryos might reinforce the commitment towards the TE lineage.


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