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Structural Variations of the Genome
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Structural Variations of the Genome

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 7024

Special Issue Information

Dear Colleagues,

The genomes of eukaryotes are being understood in more and more detail due to DNA-directed studies at different levels of resolution. Already, with the help of cytogenetics, first insights into structural genomic variants, such as chromosomal heteromorphims, can be obtained. The underlying copy number variants can be further elucidated by means of molecular cytogenetics, molecular karyotyping, and/or sequencing approaches. Further, epigenetics may play a role in both the structural and flexible adaptations of genomes under specific evolutionary pressures. In the best-studied eukaryotic genome so far, that is, the human one, copy number variants as well as three-dimensional networking of the genome in “topologically associated domains” (TADs) are recognized to be important. Even when it comes to the origins of genetic disorders, underlying point mutations are not so much the only causes to be considered anymore.

For this Special Issue, we look forward to receiving original research manuscripts, as well as methodological and review articles, with a special focus on the structural variability and flexibility of the genome, which can be observable at various levels in different species (e.g., copy number variants of heterochromatic and euchromatic material, mechanisms of genetic silencing, position effects, 3D structure of the nucleus, epigenetic mechanisms). We are confident that the compiling of different aspects of eukaryote genome complexity in one volume will provide an important contribution to molecular genetics and genomics.

Dr. Thomas Liehr
Dr. Martina Rincic
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • copy number variants
  • gene silencing
  • position effects
  • topologically associated domains (TADs)
  • epigenetics
  • fragile sites
  • chromosomal evolution
  • repetitive elements
  • chromosomal rearrangements

Published Papers (3 papers)

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Research

15 pages, 4852 KiB  
Article
Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts
by Alejandra Damián, Raluca Oancea Ionescu, Marta Rodríguez de Alba, Alejandra Tamayo, María José Trujillo-Tiebas, María Carmen Cotarelo-Pérez, Olga Pérez Rodríguez, Cristina Villaverde, Lorena de la Fuente, Raquel Romero, Gonzalo Núñez-Moreno, Pablo Mínguez, Carmen Ayuso and Marta Cortón
Int. J. Mol. Sci. 2021, 22(23), 12713; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222312713 - 24 Nov 2021
Cited by 2 | Viewed by 2155
Abstract
Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed [...] Read more.
Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects. Full article
(This article belongs to the Special Issue Structural Variations of the Genome)
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15 pages, 2309 KiB  
Article
Telomere Length in Chromosomally Normal and Abnormal Miscarriages and Ongoing Pregnancies and Its Association with 5-hydroxymethylcytosine Patterns
by Mikhail I. Krapivin, Andrei V. Tikhonov, Olga A. Efimova, Anna A. Pendina, Anna A. Smirnova, Olga G. Chiryaeva, Olga E. Talantova, Lubov’ I. Petrova, Vera S. Dudkina and Vladislav S. Baranov
Int. J. Mol. Sci. 2021, 22(12), 6622; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126622 - 21 Jun 2021
Cited by 4 | Viewed by 1915
Abstract
The present study investigates telomere length (TL) in dividing chorionic cytotrophoblast cells from karyotypically normal and abnormal first trimester miscarriages and ongoing pregnancies. Using Q-FISH, we measured relative TLs in the metaphase chromosomes of 61 chorionic villous samples. Relative TLs did not differ [...] Read more.
The present study investigates telomere length (TL) in dividing chorionic cytotrophoblast cells from karyotypically normal and abnormal first trimester miscarriages and ongoing pregnancies. Using Q-FISH, we measured relative TLs in the metaphase chromosomes of 61 chorionic villous samples. Relative TLs did not differ between karyotypically normal samples from miscarriages and those from ongoing pregnancies (p = 0.3739). However, among the karyotypically abnormal samples, relative TLs were significantly higher in ongoing pregnancies than in miscarriages (p < 0.0001). Relative TLs were also significantly higher in chorion samples from karyotypically abnormal ongoing pregnancies than in those from karyotypically normal ones (p = 0.0018) in contrast to miscarriages, where relative TL values were higher in the karyotypically normal samples (p = 0.002). In the karyotypically abnormal chorionic cytotrophoblast, the TL variance was significantly lower than in any other group (p < 0.05). Assessed by TL ratios between sister chromatids, interchromatid TL asymmetry demonstrated similar patterns across all of the chorion samples (p = 0.22) but significantly exceeded that in PHA-stimulated lymphocytes (p < 0.0001, p = 0.0003). The longer telomere was predominantly present in the hydroxymethylated sister chromatid in chromosomes featuring hemihydroxymethylation (containing 5-hydroxymethylcytosine in only one sister chromatid)—a typical sign of chorionic cytotrophoblast cells. Our results suggest that the phenomena of interchromatid TL asymmetry and its association to 5hmC patterns in chorionic cytotrophoblast, which are potentially linked to telomere lengthening through recombination, are inherent to the development programme. The TL differences in chorionic cytotrophoblast that are associated with karyotype and embryo viability seem to be determined by heredity rather than telomere elongation mechanisms. The inheritance of long telomeres by a karyotypically abnormal embryo promotes his development, whereas TL in karyotypically normal first-trimester embryos does not seem to have a considerable impact on developmental capacity. Full article
(This article belongs to the Special Issue Structural Variations of the Genome)
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18 pages, 3169 KiB  
Article
Telomere Length in Metaphase Chromosomes of Human Triploid Zygotes
by Anna A. Pendina, Mikhail I. Krapivin, Olga A. Efimova, Andrei V. Tikhonov, Irina D. Mekina, Evgeniia M. Komarova, Alla S. Koltsova, Alexander M. Gzgzyan, Igor Yu. Kogan, Olga G. Chiryaeva and Vladislav S. Baranov
Int. J. Mol. Sci. 2021, 22(11), 5579; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115579 - 25 May 2021
Cited by 5 | Viewed by 2227
Abstract
The human lifespan is strongly influenced by telomere length (TL) which is defined in a zygote—when two highly specialised haploid cells form a new diploid organism. Although TL is a variable parameter, it fluctuates in a limited range. We aimed to establish the [...] Read more.
The human lifespan is strongly influenced by telomere length (TL) which is defined in a zygote—when two highly specialised haploid cells form a new diploid organism. Although TL is a variable parameter, it fluctuates in a limited range. We aimed to establish the determining factors of TL in chromosomes of maternal and paternal origin in human triploid zygotes. Using Q-FISH, we examined TL in the metaphase chromosomes of 28 human triploid zygotes obtained from 22 couples. The chromosomes’ parental origin was identified immunocytochemically through weak DNA methylation and strong hydroxymethylation in the sperm-derived (paternal) chromosomes versus strong DNA methylation and weak hydroxymethylation in the oocyte-derived (maternal) ones. In 24 zygotes, one maternal and two paternal chromosome sets were identified, while the four remaining zygotes contained one paternal and two maternal sets. For each zygote, we compared mean relative TLs between parental chromosomes, identifying a significant difference in favour of the paternal chromosomes, which attests to a certain “imprinting” of these regions. Mean relative TLs in paternal or maternal chromosomes did not correlate with the respective parent’s age. Similarly, no correlation was observed between the mean relative TL and sperm quality parameters: concentration, progressive motility and normal morphology. Based on the comparison of TLs in chromosomes inherited from a single individual’s gametes with those in chromosomes inherited from different individuals’ gametes, we compared intraindividual (intercellular) and interindividual variability, obtaining significance in favour of the latter and thus validating the role of heredity in determining TL in zygotes. A comparison of the interchromatid TL differences across the chromosomes from sets of different parental origin with those from PHA-stimulated lymphocytes showed an absence of a significant difference between the maternal and paternal sets but a significant excess over the lymphocytes. Therefore, interchromatid TL differences are more pronounced in zygotes than in lymphocytes. To summarise, TL in human zygotes is determined both by heredity and parental origin; the input of other factors is possible within the individual’s reaction norm. Full article
(This article belongs to the Special Issue Structural Variations of the Genome)
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