scholarly journals Diverse developmental strategies of X chromosome dosage compensation in eutherian mammals

2019 ◽  
Vol 63 (3-4-5) ◽  
pp. 223-233 ◽  
Author(s):  
Alexander I. Shevchenko ◽  
Elena V. Dementyeva ◽  
Irina S. Zakharova ◽  
Suren M. Zakian
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Mammalian Species ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Autosomal Gene ◽  
Mammalian Development ◽  
Compensation Mechanisms ◽  
Early Mammalian Development

In eutherian mammals, dosage compensation arose to balance X-linked gene expression between sexes and relatively to autosomal gene expression in the evolution of sex chromosomes. Dosage compensation occurs in early mammalian development and comprises X chromosome upregulation and inactivation that are tightly coordinated epigenetic processes. Despite a uniform principle of dosage compensation, mechanisms of X chromosome inactivation and upregulation demonstrate a significant variability depending on sex, developmental stage, cell type, individual, and mammalian species. The review focuses on relationships between X chromosome inactivation and upregulation in mammalian early development.

scholarly journals Diversity of X-chromosome inactivation patterns during early mammalian development

2009 ◽  
Vol 331 (2) ◽  
pp. 392-393
Author(s):  
Ikuhiro Okamoto ◽  
Veronique Duranthon ◽  
Dominique Thepot ◽  
Nathalie Peynot ◽  
Jean Paul Renard ◽  
...  
Keyword(s):  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Mammalian Development ◽  
Early Mammalian Development

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 Landscape of X chromosome inactivation across human tissues

Nature ◽  
2017 ◽  
Vol 550 (7675) ◽  
pp. 244-248 ◽  
Author(s):  
Taru Tukiainen ◽  
◽  
Alexandra-Chloé Villani ◽  
Angela Yen ◽  
Manuel A. Rivas ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Mammalian Cells ◽  
Phenotypic Diversity ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Phenotypic Traits ◽  
Human Tissues ◽  
X Chromosomes ◽  
Chromosomal Genes

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.

139 SEX-SPECIFIC GENE EXPRESSION IN PORCINE PRE-IMPLANTATION EMBRYOS

2016 ◽  
Vol 28 (2) ◽  
pp. 199
Author(s):  
D. Kradolfer ◽  
J. Knubben ◽  
V. Flöter ◽  
J. Bick ◽  
S. Bauersachs ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Current Knowledge ◽  
Critical Time ◽  
Blastocyst Stage ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Specific Gene ◽  
Embryo Survival ◽  
Specific Gene Expression

X-Chromosome inactivation in female mammals starts during early blastocyst stage with expression of the X-inactive specific transcript (XIST), which coats and silences the inactive X chromosome. However, this compensation is not complete in blastocysts, as a large number of X-linked transcripts are more highly expressed in female embryos than in males. Furthermore, the process of X chromosome inactivation is altered in IVF and cloned porcine embryos, possibly explaining problems of embryo survival with these techniques. The aim of this study was to gain more insights into the transcriptional dynamics of the porcine pre-implantation embryo, with a particular focus on sex-specific differences. RNA sequencing (RNA-Seq) was performed for individual blastocysts at 8, 10, and 12 days after ovulation, and the temporal development of sex-specific transcripts was analysed. German Landrace sows were cycle synchronized and inseminated with sperm of the same Pietrain boar. On Days 8, 10, and 12 post-insemination, sows were slaughtered and embryos were removed from the uterus using 10 mL of PBS (pH 7.4) per horn. Single embryos were shock frozen in liquid nitrogen and stored at –80°C until the extraction of RNA and DNA (AllPrep DNA/RNA Micro Kit, Qiagen, Valencia, CA, USA). Using the isolated DNA, the sex of the embryos was determined and 5 female and male embryos, respectively, were analysed per stage. Illumina TruSeq Stranded mRNA libraries (Illumina Inc., San Diego, CA, USA) were sequenced on a HiSEqn 2500 (Illumina Inc.), and 15 to 25 million 100-bp single-end reads were generated per sample. Reads were filtered and processed using Trimmomatic and mapped to the porcine genome assembly Sscrofa10.2 with TopHat2. Mapped reads were counted by the use of QuasR qCount based on the current National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) GFF3 annotation file. Statistical analysis of count data was performed with the BioConductor R (https://www.bioconductor.org/) package DESEqn 2. At all 3 stages, we found 7 Y-linked transcripts that were highly expressed in male embryos (EIF2S3, EIF1AY, LOC100624590, LOC100625207, LOC100624329, LOC102162178, LOC100624937). On the other hand, 47 X-linked transcripts showed increased expression in female blastocysts, most of them at all 3 time points. However, a small number of genes (DDX3X, LAMP2, and RPS6KA3) were more highly expressed in females at Days 8 and 10 but more highly expressed in males at Day 12. Three X-linked genes (OFD1, KAL1, and LOC100525092) were more highly expressed in male embryos, although only at a low fold change of 1.2 to 1.4. Furthermore, expression of 8 transcripts located on autosomes was higher in females. In conclusion, our study expands the current knowledge of sex-specific gene expression in 8- to 12-day-old porcine blastocysts, a critical time period during pre-implantation embryo development.

Monoallelic Methylation of the Human Androgen Receptor Gene as Detected by the HUMARA Clonality Assay Does Not Consistently Reflect X-Chromosome Inactivation and Is Therefore Unreliable for Assessment of Clonal Hematopoiesis.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4566-4566
Author(s):  
Sabina Swierczek ◽  
Jaroslav Jelinek ◽  
Neeraj Agarwal ◽  
Andrew Wilson ◽  
Kimberly Hickman ◽  
...  
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
X Inactivation ◽  
Chromosome Inactivation ◽  
Cag Repeats ◽  
Clonal Hematopoiesis ◽  
Healthy Elderly ◽  
Polymorphic Genes ◽  
Exon 1

Abstract Abstract 4566 Even in the absence of a disease specific chromosomal marker, clonality can be assessed in somatic tissues of female origin by using assays based on the pattern of X-chromosome inactivation. The most widely used technique for quantifying X-chromosome inactivation is the HUMARA method that is based on the putative role of DNA methylation at CpG sites close to trinucleotide repeats in exon 1 in silencing of the AR locus. However, using the HUMARA method, we and others have observed that approximately 30% of healthy elderly volunteers appear to have clonal hematopoiesis. This observation is at odds with the concept that normal hematopoiesis is a polyclonal process, suggesting that the finding of monoclonality or oligoclonality in a high percentage of healthy volunteers by using the HUMARA method, is a technical artifact. To address this issue, we developed a clonality assay based on gene expression of five X-linked polymorphic genes and found no evidence of clonal hematopoiesis in healthy elderly volunteers, although we confirmed extreme skewing of X inactivation (consistent with monoallelic methylation of AR) in 30% of the study subject when analyzed by HUMARA (Swierczek et al., Blood 2008). In the present studies, we have validated the accuracy and reproducibility of our quantitative transcription-based clonality assay (qTCA) using two different methods for quantifying gene expression and compared the results with those obtained using the HUMARA method. DNA and RNA were extracted from peripheral blood samples from 31 healthy female volunteers (age in years as follows: range, 22-55; mean, 35; median, 34). RNA was reverse transcribed (RT) and analyzed by using our qTCA in which expression of three polymorphic genes (MPP1, IDS and FHL1), that are subject to X inactivation, is quantified by allele-specific, real-time RT-PCR. Based on DNA analysis, 25 of the 31 (80%) volunteers were polymorphic for at least one of the test genes. Results are reported as the percentage of each of the two single nucleotide polymorphisms (SNPs) that is present in the sample (e. g., 60% A; 40% G). PCR primers are designed to provide maximum discrimination between SNPs with >13 PCR cycles (i. e., 13 log2) separating true-positive from false-positive amplification. Aliquots of the isolated RNA from the test samples were sent to an independent investigator (JJ), at a separate institution, who was blinded to the results of our qTCA, and the allele ratio was determined by using a different technique (quantitative pyrosequencing). Comparison of the results, confirmed the accuracy and reproducibility of the two methods with coefficients of correlation for each gene as follows: (MPP1, r=0.9385; IDS, r=0.8565; FHL1, r=0.8657). One of the 25 informative females (4%) showed extreme skewing (SNP ratio >75%:25%) of X inactivation by both methods. Based on allelic differences in the number of CAG repeats, 29/31 participants were informative in the HUMARA. Among most of the samples, a good correlation was observed between the pattern of X chromosome inactivation as determined by HUMARA and that determined by both qTCA and quantitative pyrosequencing, however, 8/29 (27%) samples analyzed by the HUMARA showed extreme skewing of allele methylation (ratio >75%:25%). Of the 8 subjects with extreme skewing, 3 were homozygous (i. e., non-informative) for all of the X-chromosome polymorphic genes used in the qTCA. Samples from the 5 informative participants were analyzed by using the qTCA, and, in contrast to the HUMARA results, only one subject showed extreme skewing of the SNP ratio (the same subject as identified in the original qTCA). We also quantified HUMARA gene expression using the difference in the number of exon 1 CAG repeats between the two AR alleles as the polymorphic marker. These experiments showed that, of the 8 volunteers with skewing of X inactivation based on HUMARA, 5 had skewing of AR allele expression and 3 had expression of both AR alleles, indicating that the correlation between DNA methylation at the AR locus and AR mRNA transcription is inconsistent. In conclusion, we found a good correlation between the HUMARA and qTCA in some females; however, this was not the case in many healthy females both elderly and young. These experiments demonstrate the accuracy and reproducibility of the qTCA and confirmed that this technique is not subject to the artifact of aberrant skewing of X-inactivation due to monoallelic methylation of AR that limits the applicability and value of the HUMARA. Disclosures: No relevant conflicts of interest to declare.

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