The Eutherian Pseudoautosomal Region

Raudsepp, Terje; Chowdhary, Bhanu P.

doi:10.1159/000443157

Cited by 86 publications

(82 citation statements)

References 117 publications

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“…Enrichment with cell cycle-associated genes is characteristic for B chromosomes not only in A. flavicollis, but also in the gray brocket deer Receptor genes abundant in Bs of A. peninsulae were previously associated with evolutionary breakpoint regions of pig genome (Groenen et al 2012). X-chromosomal region of A. flavicollis encompassing Kdm6 gene is located close to the eutherian ancestral pseudoautosomal region (Raudsepp and Chowdhary 2015), indicating a potential functional connection between supernumerary and sex chromosomes. Taken together, these facts give evidence in favor of common mechanisms underlying various kinds of genomic instability.…”

Section: Comparison Of B Chromosomes In Two Apodemus Speciesmentioning

confidence: 97%

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

et al. 2018

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Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately 1 of 2000 postnatal cases. Due to low frequency in population, human sSMCs are not considered B chromosomes. Genetic content of both B-chromosomes and sSMCs in most cases remains understudied. Here, we apply microdissection of single chromosomes with subsequent low-pass sequencing on Ion Torrent PGM and Illumina MiSeq to identify unique and repetitive DNA sequences present in a single human sSMC and several B chromosomes in mice Apodemus flavicollis and Apodemus peninsulae. The pipeline for sequencing data analysis was made available in Galaxy interface as an addition to previously published command-line version. Human sSMC was attributed to the proximal part of chromosome 15 long arm, and breakpoints leading to its formation were located into satellite DNA arrays. Genetic content of Apodemus B chromosomes was species-specific, and minor alterations were observed in both species. Common features of Bs in these Apodemus species were satellite DNA and ERV enrichment, as well as the presence of the vaccinia-related kinase gene Vrk1. Understanding of the non-essential genome elements content provides important insights into genome evolution in general.

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Section: Comparison Of B Chromosomes In Two Apodemus Speciesmentioning

confidence: 97%

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

et al. 2018

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“…All these were confirmed by the GO approach. On the other hand, MOSPD2 remained a doubtful case because the DEF criteria suggested contradictory classifications (Disease: Development; Expression: did not pass Bgee filter; Function: ISRG but based on a single publication [36], i.e. not convincingly).…”

Section: Discussionmentioning

confidence: 99%

SeXY chromosomes and the immune system: reflections after a comparative study

et al. 2020

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Background: Sex bias in immune function has been contributed in part to a preponderance of immune systemrelated genes (ISRG) on the X-chromosome. We verified whether ISRG are more abundant on the X chromosome as compared to autosomal chromosomes and reflected on the impact of our findings. Methods: Consulting freely accessible databases, we performed a comparative study consisting of three complementary strategies. First, among coding X/Y-linked genes, the abundance of ISRG was compared to the abundance of genes dedicated to other systems. Genes were assigned considering three criteria: disease, tissue expression, and function (DEF approach). In addition, we carried out two genome-wide approaches to compare the contribution of sex and autosomal chromosomes to immune genes defined by an elevated expression in lymphatic tissues (LTEEG approach) or annotation to an immune system process, GO:0002376 (GO approach).Results: The X chromosome had less immune genes than the median of the autosomal chromosomes. Among Xlinked genes, ISRG ranked fourth after the reproductive and nervous systems and genes dedicated to development, proliferation and apoptosis. On the Y chromosome, ISRG ranked second, and at the pseudoautosomal region (PAR) first. According to studies on the expression of X-linked genes in a variety of (mostly non-lymphatic) tissues, almost two-thirds of ISRG are expressed without sex bias, and the remaining ISRG presented female and male bias with similar frequency. Various epigenetic controllers, X-linked MSL3 and Y-linked KDM5D and UTY, were preferentially expressed in leukocytes and deserve further attention for a possible role in sex biased expression or its neutralisation. Conclusions: The X chromosome is not enriched for ISRG, though particular X-linked genes may be responsible for sex differences in certain immune responses. So far, there is insufficient information on sex-biased expression of X/ Y-linked ISRG in leukocytes to draw general conclusions on the impact of X/Y-linked ISRG in immune function. More research on the regulation of the expression X-linked genes is required with attention to 1) female and male mechanisms that may either augment or diminish sex biased expression and 2) tissue-specific expression studies.

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“…Seven of the 14 human X-Y pair genes are not present on the mouse Y chromosome: five were lost and two were retrotransposed onto autosomes (Hughes, Skaletsky, Koutseva, Pyntikova, & Page, 2015; Soh et al, 2014). Additionally, almost all of the orthologs of the human PAR genes are found on mouse autosomes or are missing in the mouse genome (Table 1) (Raudsepp & Chowdhary, 2015). Moreover, sex chromosome gene dosage regulation differs between mice and humans; only 3–7% of X-linked genes are expressed from both X alleles in the mouse, compared to at least 23% in humans (Berletch et al, 2015; Tukiainen et al, 2017).…”

Section: Experimental Models For Identifying Phenotypes Mediated By Smentioning

confidence: 99%

A strategic research alliance: Turner syndrome and sex differences

Roman

Page

2019

American J of Med Genetics Pt C

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Sex chromosome constitution varies in the human population, both between the sexes (46,XX females and 46,XY males), and within the sexes (for example, 45,X and 46,XX females, and 47,XXY and 46,XY males). Coincident with this genetic variation are numerous phenotypic differences between males and females, and individuals with sex chromosome aneuploidy. However, the molecular mechanisms by which sex chromosome constitution impacts phenotypes at the cellular, tissue, and organismal levels remain largely unexplored. Thus emerges a fundamental question connecting the study of sex differences and sex chromosome aneuploidy syndromes: How does sex chromosome constitution influence phenotype? Here, we focus on Turner syndrome (TS), associated with the 45,X karyotype, and its synergies with the study of sex differences. We review findings from evolutionary studies of the sex chromosomes, which identified genes that are most likely to contribute to phenotypes as a result of variation in sex chromosome constitution. We then explore strategies for investigating the direct effects of the sex chromosomes, and the evidence for specific sex chromosome genes impacting phenotypes. In sum, we argue that integrating the study of TS with sex differences offers a mutually beneficial alliance to identify contributions of the sex chromosomes to human development, health, and disease.

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The Eutherian Pseudoautosomal Region

Cited by 86 publications

References 117 publications

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

SeXY chromosomes and the immune system: reflections after a comparative study

A strategic research alliance: Turner syndrome and sex differences

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