scholarly journals Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex

2021 ◽  
Author(s):  
Richard P Meisel ◽  
Danial Asgari ◽  
Florencia Schlamp ◽  
Robert L Unckless
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Reproductive Tract ◽  
Sex Chromosome ◽  
Accessory Gland ◽  
Gene Content ◽  
Dosage Compensation Complex ◽  
Specific Expression ◽  
Chromosome Gene

Sex chromosome gene content frequently differs from that of the autosomes, a phenomenon that can be informative of the effects of chromatin environment, sex-specific selection, recombination, and ploidy on genome evolution. For example, the Drosophila X chromosome is depauperate in genes with male-biased expression or limited expression in specific tissues—in particular those expressed in the accessory gland of the male reproductive tract. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex (DCC) on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments known to have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (up-regulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (down-regulated) following treatment. We further show that whether a gene is bound by the DCC in males can largely explain the paucity of both up- and down-regulated genes on the X chromosome. Specifically, genes that are bound by the DCC are unlikely to be up- or down-regulated after treatment. Moreover, genes that are closer to a high-affinity site where the DCC is thought to initiate binding to the X chromosome experience a smaller change in expression following treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that DCC binding, or the associated chromatin modifications, inhibit both up- and down-regulation of X chromosome gene expression within specific contexts. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific expression, in addition to the paucity of X-linked genes differentially expressed after biotic or abiotic treatments. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first (Mof), a component of the DCC, as a dampener of gene expression variance in both males and females.

scholarly journals Chromosome-wide mechanisms to decouple gene expression from gene dose during sex-chromosome evolution

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Bayly S Wheeler ◽  
Erika Anderson ◽  
Christian Frøkjær-Jensen ◽  
Qian Bian ◽  
Erik Jorgensen ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Nuclear Periphery ◽  
Single Copy ◽  
Dosage Compensation Complex ◽  
Gene Dose ◽  
Caenorhabditis Elegans Genome

Changes in chromosome number impair fitness by disrupting the balance of gene expression. Here we analyze mechanisms to compensate for changes in gene dose that accompanied the evolution of sex chromosomes from autosomes. Using single-copy transgenes integrated throughout the Caenorhabditis elegans genome, we show that expression of all X-linked transgenes is balanced between XX hermaphrodites and XO males. However, proximity of a dosage compensation complex (DCC) binding site (rex site) is neither necessary to repress X-linked transgenes nor sufficient to repress transgenes on autosomes. Thus, X is broadly permissive for dosage compensation, and the DCC acts via a chromosome-wide mechanism to balance transcription between sexes. In contrast, no analogous X-chromosome-wide mechanism balances transcription between X and autosomes: expression of compensated hermaphrodite X-linked transgenes is half that of autosomal transgenes. Furthermore, our results argue against an X-chromosome dosage compensation model contingent upon rex-directed positioning of X relative to the nuclear periphery.

scholarly journals GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation

2018 ◽  
Author(s):  
Edridge D’Souza ◽  
Elizaveta Hosage ◽  
Kathryn Weinand ◽  
Steve Gisselbrecht ◽  
Vicky Markstein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Binding Sites ◽  
Convergent Evolution ◽  
Fruit Fly ◽  
Dosage Compensation Complex ◽  
X Chromosomes ◽  
Repeat Sequences

ABSTRACTOver 50 years ago, Susumo Ohno proposed that dosage compensation in mammals would require upregulation of gene expression on the single active X chromosome, a mechanism which to date is best understood in the fruit fly Drosophila melanogaster. Here, we report that the GA-repeat sequences that recruit the conserved MSL dosage compensation complex to the Drosophila X chromosome are also enriched across mammalian X chromosomes, providing genomic support for the Ohno hypothesis. We show that mammalian GA-repeats derive in part from transposable elements, suggesting a mechanism whereby unrelated X chromosomes from dipterans to mammals accumulate binding sites for the MSL dosage compensation complex through convergent evolution, driven by their propensity to accumulate transposable elements.

scholarly journals Mechanisms of sex determination and X-chromosome dosage compensation

Genetics ◽  
2022 ◽  
Author(s):  
Barbara J Meyer
Keyword(s):  
Gene Expression ◽  
Chromosome Number ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Molecular Mechanisms ◽  
Chromosome Counting ◽  
Developmental Defects ◽  
Chromosome Gene ◽  
Compensation Mechanisms ◽  
The Difference

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.

scholarly journals Assessment of X Chromosome Dosage Compensation in Caenorhabditis elegans by Phenotypic Analysis of lin-14

Genetics ◽  
1987 ◽  
Vol 117 (4) ◽  
pp. 657-670
Author(s):  
Leslie DeLong ◽  
Lawrence P Casson ◽  
Barbara J Meyer
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Phenotypic Expression ◽  
Transcript Level ◽  
Phenotypic Analysis ◽  
Linked Gene ◽  
Chromosome Gene ◽  
The Difference

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.

scholarly journals Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

2019 ◽  
Author(s):  
Ava C. Carter ◽  
Jin Xu ◽  
Meagan Y. Nakamoto ◽  
Yuning Wei ◽  
Quanming Shi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosome ◽  
Embryonic Stem ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Rna Domains ◽  
In Cis

Dosage compensation between the sexes has emerged independently multiple times during evolution, often harnessing long noncoding RNAs (lncRNAs) to alter gene expression on the sex chromosomes. In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNA Xist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expression in cis1,2. How Xist evolved new functional RNA domains to recruit ancient, pleiotropic protein partners is of great interest. Here we show that Spen, an Xist-binding repressor protein essential for XCI3-7, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de-repression of a subset of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing8-9. ERV RNA and Xist A-repeat bind the RRM3 domain of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in local gene silencing in cis. These results suggest that insertion of an ERV element into proto-Xist may have been a critical evolutionary event, which allowed Xist to coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.

scholarly journals Dosage Compensation Systems

2021 ◽  
pp. 67-89
Author(s):  
Renato Paro ◽  
Ueli Grossniklaus ◽  
Raffaella Santoro ◽  
Anton Wutz
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Molecular Mechanisms ◽  
Sex Chromosome ◽  
Fruit Fly ◽  
X Chromosomes ◽  
Compensation Systems ◽  
A Cell ◽  
Males And Females

AbstractThis chapter provides an introduction to chromosome-wide dosage compensation systems. We will examine the evolution of dosage compensation, which is thought to be driven by the appearance of differentiated sex chromosomes. In a subset of species with X chromosomal sex determination or XY sex chromosome systems, expression of X-linked genes is regulated by chromosome-wide modifications that equalize gene expression differences between males and females. The molecular mechanisms of X chromosome-wide dosage compensation have been studied in flies, worms, and mammals. Each of these species uses a distinct dosage compensation strategy with a different molecular mechanism. In the wormCaenorhabditis elegans, gene expression on the two X chromosomes of hermaphrodites is reduced to a level that approximates a single X chromosome in males. The fruit flyDrosophila melanogasterachieves dosage compensation by increased transcription of the single X chromosome in males to a level that is similar to the two X chromosomes in females. Lastly, in mammals, one of the two X chromosomes in female cells is transcriptionally inactive and a single X chromosome is transcribed in both sexes. Studies of dosage compensation systems provide insights into how epigenetic regulation controls gene expression and chromatin organization differentially within a cell.

scholarly journals A gene-by-gene mosaic of dosage compensation strategies on the human X chromosome

2021 ◽  
Author(s):  
Adrianna K. San Roman ◽  
Alexander K. Godfrey ◽  
Helen Skaletsky ◽  
Daniel W Bellott ◽  
Abigail F Groff ◽  
...  
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
Sex Chromosome ◽  
Loss Of Function ◽  
Specific Expression ◽  
X Chromosomes ◽  
Mediated Effects ◽  
Multiple Dimensions ◽  
Allele Specific ◽  
Health And Disease

Dosage compensation in humans - ensuring the viability and fitness of females, with two X chromosomes, and males, with one - is thought to be achieved chromosome-wide by heterochromatinization of one X chromosome during female development. We reassessed this through quantitative gene-by-gene analyses of expression in individuals with one to four X chromosomes, tolerance for loss-of-function mutations, regulation by miRNAs, allele-specific expression, and the presence of homologous genes on the Y chromosome. We found a mosaic of dosage compensation strategies on the human X chromosome reflecting gene-by-gene differences in multiple dimensions, including sensitivity to under- or over-expression. These insights enrich our understanding of Turner, Klinefelter, and other sex chromosome aneuploidy syndromes, and of sex-chromosome-mediated effects on health and disease in euploid males and females.

Study of Dosage Compensation in Drosophila

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1167-1181
Author(s):  
Pei-Wen Chiang ◽  
David M Kurnit
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Qpcr Assay ◽  
Male And Female ◽  
Multiple Genes ◽  
Chromosomal Changes ◽  
Regulatory Effects

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.

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