• Title/Summary/Keyword: X chromosome

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X-Chromosome Inactivation: A Complex Circuits regulated by Non-coding RNAs and Pluripotent Factors

  • Hwang, Jae Yeon;Lee, Chang-Kyu
    • Reproductive and Developmental Biology
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    • v.41 no.2
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    • pp.33-40
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    • 2017
  • X-chromosome inactivation is one of the most complex events observed in early embryo developments. The epigenetic changes occurred in female X-chromosome is essential to compensate dosages of X-linked genes between males and females. Because of the relevance of the epigenetic process to the normal embryo developments and stem cell studies, X-chromosome inactivation has been focused intensively for last 10 years. Initiation and regulation of the process is managed by diverse factors. Especially, proteins and non-coding RNAs encoded in X-chromosome inactivation center, and a couple of transcription factors have been reported to regulate the event. In this review, we introduce the reported factors, and how they regulate epigenetic inactivation of X-chromosomes.

Reanalysis of Ohno's hypothesis on conservation of the size of the X chromosome in mammals

  • Kim, Hyeongmin;Lee, Taeheon;Sung, Samsun;Lee, Changkyu;Kim, Heebal
    • Animal cells and systems
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    • v.16 no.6
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    • pp.438-446
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    • 2012
  • In 1964, Susumu Ohno, an evolutionary biologist, hypothesized that the size of X chromosome was conserved in mammalian evolution, and that this was based on chromosomal length. Today, unlike Ohno's method which was based on estimated lengths, we know the exact lengths of some mammalian sequences. The aim of this study was to reanalyze Ohno's hypothesis. In mammalian species, variation in the length of the X chromosome is greater than in the autosomes; however, this variation is not statistically significant. This means that differences in chromosomal length occur equally in the X chromosome and in the autosomes. Interspersed nuclear elements and genetic rearrangements were analyzed to maintain the same variance between the length of the X chromosome and the autosomes. The X chromosome contained fewer short interspersed elements (SINEs) (0.90 on average); however, it did contain more long interspersed elements (LINEs) than did autosomes (1.56 on average). An overall correlation of LINEs and SINEs with genetic rearrangements was observed; however, synteny breaks were more closely associated with LINEs in the autosomes, and with SINEs in the X chromosome. These results suggest that the chromosome-specific activities of LINEs and SINEs result in the same variance between the lengths of the X chromosome and the autosomes. This is based on the function of interspersed nuclear elements, such as LINEs, which can inactivate the X chromosome and the reliance of non-autonomous SINEs on LINEs for transposition.

Change of X Chromosome Status during Development and Reprogramming

  • Jung, Yong-Wook;Park, In-Hyun
    • Development and Reproduction
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    • v.15 no.3
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    • pp.187-195
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    • 2011
  • X chromosome inactivation (XCI) is a process that enables mammalian females to ensure the dosage compensation for X-linked genes. Investigating the mechanism of XCI might provide deeper understandings of chromosomal silencing, epigenetic regulation of gene expressions, and even the course of evolution. Studies on mammalian XCI conducted with mice have revealed many fundamental findings on XCI. However, difference of murine and human XCI necessitates the further investigation in human XCI. Recent success in reprogramming of differentiated cells into pluripotent stem cells showed the reversibility of XCI in vitro, X chromosome reactivation (XCR), which provides another tool to study the change in X chromosome status. This review summarizes the current knowledge of XCI during early embryonic development and describes recent achievements in studies of XCI in reprogramming process.

Acceleration of X-chromosome gene order evolution in the cattle lineage

  • Park, Woncheoul;Oh, Hee-Seok;Kim, Heebal
    • BMB Reports
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    • v.46 no.6
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    • pp.310-315
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    • 2013
  • The gene order on the X chromosome of eutherians is generally highly conserved, although an increase in the rate of rearrangement has been reported in the rodent lineage. Conservation of the X chromosome is thought to be caused by selection related to maintenance of dosage compensation. However, we herein reveal that the cattle (Btau4.0) lineage has experienced a strong increase in the rate of X-chromosome rearrangement, much stronger than that previously reported for rodents. We also show that this increase is not matched by a similar increase on the autosomes and cannot be explained by assembly errors. Furthermore, we compared the difference in two cattle genome assemblies: Btau4.0 and Btau6.0 (Bos taurus UMD3.1). The results showed a discrepancy between Btau4.0 and Btau6.0 cattle assembly version data, and we believe that Btau6.0 cattle assembly version data are not more reliable than Btau4.0.

Characterization of X-linked RNA Transcripts in Matured Bovine Spermatozoa

  • Jeon, Byeong-Gyun;Kumar, B. Mohana;Rho, Gyu-Jin
    • Reproductive and Developmental Biology
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    • v.35 no.3
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    • pp.209-214
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    • 2011
  • Although the function and utility of RNA transcripts derived from matured spermatozoa remains unclear, they might play important roles in the establishment of a paternal genome and subsequently embryo development. Herein, we investigated the expression of X-chromosome linked RNA transcripts in matured bovine spermatozoa. The total RNA was extracted from the matured spermatozoa, and then converted to cDNA. Autosomal genes (ACT-${\beta}$ and H-2A) and X-chromosome linked genes (ANT3, HPRT, MeCP2, RPS4X, XIAP, XIST and ZFX) were analyzed for the characterization of X-chromosome linked RNA transcripts and compared to female fibroblasts by RT-PCR. The transcripts of autosomal genes (ACT-${\beta}$ and H2A) and X-chromosome linked genes (ANT3, HPRT, MeCP2, RPS4X and ZFX) were not detected in spermatozoa. However, XIAP (X-linked inhibitor of apoptosis protein) and XIST (X-chromosome inactive-specific transcript, a kind of paternal imprinted gene) transcripts were detected in spermatozoa, and relative levels of XIAP and XIST transcripts were similar and 0.5-fold lower when compared to female fibroblasts, respectively. Based on the findings, it is summarized that the presence of RNA transcripts of XIAP and XIST in the isolated spermatozoa may imply their role in inhibition of apoptosis and induction of X-chromosome inactivation in embryo development.

A Screen for Genetic Loci on the X Chromosome Required for Body-Wall Muscle Development during Embryogenesis in Caenorhabditis elegans

  • Lee, Deok-Gyu;Sin, Ji-Yeon;An, Ju-Hong
    • Animal cells and systems
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    • v.1 no.2
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    • pp.355-361
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    • 1997
  • We have screened available chromosomal deficiencies on the X chromosome for genetic loci whose zygotic expression is required for body-wall muscle development during embryogenesis in Caenorhabditis elegans. Previously, it had been reported that no sign of muscle development was detected in nullo-X embryos arrested at an early stage of embryogenesis. Based on this observation, it has been suggested that genetic loci exist on the X chromosome whose zygotic expression is essential for body-wall muscle formation. In order to identify such myogenic loci, 9 chromosomal deficiencies covering approximately 45% of the X chromosome have been tested. Homozygous embryos from these deficiency strains were collected and terminal phenotypes of arrested embryos were observed by Nomarski microscopy. As a secondary assay, monoclonal antibodies against two myosin heavy chain (MHC) isoforms, the products of the myo-3 and unc-54 genes, were used to detect body-wall muscle differentiation. All the homozygous deficiency embryos were positively stained with both MHC antibodies and muscle twitching movement was observed in most cases. Combined with previously analyzed deficiencies, our deficiency screen has covered approximately 70% of the X chromosome. We conclude that the regions covered by the available deficiencies on the X chromosome do not include any myogenic locus required for body-wall muscle formation. Alternatively, the possibility that nullo-X embryo may not form body-wall muscle due to a general failure to differentiate during embryogenesis remains to be tested.

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X-linked Gene Expression Profiles by RNAi-Mediated BRCA1 Knockdown in MCF7 Cells

  • Song, Min-Ae;Park, Jung-Hoon;Ahn, Hee-Jeong;Ko, Jung-Jae;Lee, Su-Man
    • Genomics & Informatics
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    • v.3 no.4
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    • pp.154-158
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    • 2005
  • Germ-line mutations of the BRCA1 gene confer an increased risk for breast and ovarian cancers. BRCA1 in female cells is directly related with the maintenance of the inactive X chromosome (Xi). The effect by the loss of the BRCA1 function on the X chromosome gene expression remains unclear in cancer cells. We attempted to investigate the expression pattern of the X-linked genes by performing BRCA1 knockdown via RNA interference in the MCF7 breast cancer cell line. The transcriptional and translational levels of BRCA1 were decreased over 95% in the MCF7 cells after BRCA1 knockdown. The expression patterns of one hundred ninety X-linked genes were profiled by the X chromosome-specific cDNA arrays. A total of seven percent of the X-linked genes (14/190) were aberrantly expressed by over 2-fold in the MCF7-BRCA1 knockdown cells, which contained two up-regulated genes (2/190, 1 %) and 12 down-regulated genes (12/190, 6.3%). It is interesting that 72% of the aberrantly expressed X-linked genes were located on the Xq (10/14,) region. Our data suggests that BRCA1 may not be important to maintain X chromosome inactivation in cancer because the BRCA1 knockdown did increase the expression of the only one percent of X-linked genes in the human breast cancer cells.

Second locus for late-onset familial Amyotrophic Lateral Sclerosis (가족성 근위축성측삭경화증을 유발시키는 두 번째 유전자 위치)

  • 홍성출
    • Journal of Life Science
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    • v.11 no.3
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    • pp.279-283
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    • 2001
  • Amyotrophic lateral sclerosis(ALS) is a progressive neurologic disorder resulting from the degeneration of upper and lower motor neurons, and is inherited in 10% of cases. About 20% of familial ALS, clinically indistinguishable from sporadic ALS, is caused by mutations of Cu/Zn superoxide dismutase on chromosome 21q22.21 inherited as an autosomal dominant trait. We now report a new locus in the non-SOD1 dominantly inherited ALS. We screened a large ALS family with 11 affected individuals and one obligate gene carrier with genome-wide ABI polymorphic markers using the ABI 377 automated system. No evidence of linkage was obtained with the autosomal markers. We next screened this family with X chromosome markers as there was no evidence of male-to-male tran-smission of the disease. Linkage was established with several X chromosome markers with a lod score up to 3.8; almost the maximum possible score in this family. Our finding imply that a gene for the dominant expression of a neuronal degeneration is coded on X chromosome and raise the question of the role of X-linked genes that escape inactivation in this pathogenesis. More importantly, our finding that a gene causing ALS is localized on X-chromosome has direct investigational relevance to sporadic ALS, where epidemiological studies show male gender predominance(1.3:1) and earlier onset in men by 5-10 years.

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Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail

  • Zhu, Caiye;Li, Mingna;Qin, Shizhen;Zhao, Fuping;Fang, Suli
    • Asian-Australasian Journal of Animal Sciences
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    • v.33 no.9
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    • pp.1378-1386
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    • 2020
  • Objective: Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. Methods: In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. Results: In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. Conclusion: The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.

Beyond X-Chromosome Inactivation: The Oncogenic Facet of XIST in Human Cancers

  • Madhi, Hamadi;Kim, Myoung Hee
    • Biomedical Science Letters
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    • v.25 no.2
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    • pp.113-122
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    • 2019
  • Long-non coding RNAs (LncRNAs) constitute a wide and extremely diverse family of RNA transcripts that are greater than 200 base pairs in length and are not translated into proteins. X-inactive specific transcript (XIST) was the first long non-coding RNA to be discovered, back in 1991. Its function in X-chromosome inactivation has been extensively studied for three decades, though other functional roles of XIST that involve a variety of fascinating mechanisms remain to be elucidated. Here, we review the emerging oncogenic role of XIST in various human cancers.