X chromosome

About: X chromosome is a research topic. Over the lifetime, 9862 publications have been published within this topic receiving 407354 citations. The topic is also known as: GO:0000805 & chrX.

Derivation of consensus inactivation status for X-linked genes from genome-wide studies

Abstract: X chromosome inactivation is the epigenetic silencing of the majority of the genes on one of the X chromosomes in XX therian mammals. In humans, approximately 15 % of genes consistently escape from this inactivation and another 15 % of genes vary between individuals or tissues in whether they are subject to, or escape from, inactivation. Multiple studies have provided inactivation status calls for a large subset of the genes on the X chromosome; however, these studies vary in which genes they were able to make calls for and in some cases which call they give a specific gene. This analysis aggregated three published studies that have examined X chromosome inactivation status of genes across the X chromosome, generating consensus calls and identifying discordancies. The impact of expression level and chromosomal location on X chromosome inactivation status was also assessed. Overall, we assigned a consensus XCI status 639 genes, including 78 % of protein-coding genes expressed outside of the testes, with a lower frequency for non-coding RNA and testis-specific genes. Study-specific discordancies suggest that there may be instability of XCI during cell culture and also highlight study-specific variations in call type. We observe an enrichment of discordant genes at boundaries between genes subject to and escaping from inactivation. This study has compiled a comprehensive list of X-chromosome inactivation statuses for genes and also discovered some biases which will help guide future studies examining X-chromosome inactivation.

Expression in aneuploid Drosophila S2 cells.

Abstract: Extensive departures from balanced gene dose in aneuploids are highly deleterious However, we know very little about the relationship between gene copy number and expression in aneuploid cells We determined copy number and transcript abundance (expression) genome-wide in Drosophila S2 cells by DNA-Seq and RNA-Seq We found that S2 cells are aneuploid for >43 Mb of the genome, primarily in the range of one to five copies, and show a male genotype (∼ two X chromosomes and four sets of autosomes, or 2X;4A) Both X chromosomes and autosomes showed expression dosage compensation X chromosome expression was elevated in a fixed-fold manner regardless of actual gene dose In engineering terms, the system “anticipates” the perturbation caused by X dose, rather than responding to an error caused by the perturbation This feed-forward regulation resulted in precise dosage compensation only when X dose was half of the autosome dose Insufficient compensation occurred at lower X chromosome dose and excessive expression occurred at higher doses RNAi knockdown of the Male Specific Lethal complex abolished feed-forward regulation Both autosome and X chromosome genes show Male Specific Lethal–independent compensation that fits a first order dose-response curve Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide For the X chromosome, compensation includes fixed and dose-dependent components

DNA methylation stabilizes X chromosome inactivation in eutherians but not in marsupials: evidence for multistep maintenance of mammalian X dosage compensation

Abstract: In marsupials and eutherian mammals, X chromosome dosage compensation is achieved by inactivating one X chromosome in female cells; however, in marsupials, the inactive X chromosomes is always paternal, and some genes on the chromosome are partially expressed. To define the role of DNA methylation in maintenance of X chromosome inactivity, we examined loci for glucose-6-phosphate dehydrogenase and hypoxanthine phosphoribosyltransferase in a North American marsupial, the opossum Didelphis virginiana, by using genomic hybridization probes cloned from this species. We find that these marsupial genes are like their eutherian counterparts, with respect to sex differences in methylation of nuclease-insensitive (nonregulatory) chromatin. However, with respect to methylation of the nuclease-hypersensitive (regulatory) chromatin of the glucose-6-phosphate dehydrogenase locus, the opossum gene differs from those of eutherians, as the 5' cluster of CpG dinucleotides is hypomethylated in the paternal as well as the maternal gene. Despite hypomethylation of the 5' CpG cluster, the paternal allele, identified by an enzyme variant, is at best partially expressed; therefore, factors other than methylation are responsible for repression. In light of these results, it seems that the role of DNA methylation in eutherian X dosage compensation is to "lock in" the process initiated by such factors. Because of similarities between dosage compensation in marsupials and trophectoderm derivatives of eutherians, we propose that differences in timing of developmental events--rather than differences in the basic mechanisms of X inactivation--account for features of dosage compensation that differ among mammals.

Dosage Compensation in Drosophila

Abstract: Dosage compensation in Drosophila increases the transcription of genes on the single X chromosome in males to equal that of both X chromosomes in females. Site-specific histone acetylation by the male-specific lethal (MSL) complex is thought to play a fundamental role in the increased transcriptional output of the male X. Nucleation and sequence-independent spreading of the complex to active genes serves as a model for understanding the targeting and function of epigenetic chromatin-modifying complexes. Interestingly, two noncoding RNAs are key for MSL assembly and spreading to active genes along the length of the X chromosome.

Familial X-linked mental retardation with an X chromosome abnormality.

Abstract: An X-linked pattern of transmission observed in four families with familial mental retardation in several generations was associated with a probable secondary constriction at the distal end of the q arms of the X chromosome. Twenty retarded males and no retarded females were observed. All available live retarded males and most of their normal mothers were found to have the abnormal X chromosome. The marker chromosome was shown to be the X chromosome in each case by Giemsa banding. In affected male and female carriers the marker chromosome varied in appearance and was not present in all metaphases. The significance of this study in relation to previously reported pedigrees showing non-specific X-linked mental retardation is discussed.