Clinical, cytogenetic and molecular study of a case of ring chromosome 10

Čiuladaitė, Živilė; Burnytė, Birutė; Vansevičiūtė, Danutė; Dagytė, Evelina; Kučinskas, Vaidutis; Utkus, Algirdas

doi:10.1186/s13039-015-0124-9

Cited by 9 publications

(6 citation statements)

References 32 publications

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“…We converted a linear synV to a ring by design, a process that could eventually enable more precise modeling of ring chromosome disorders if performed in mammalian cells. Circular "ring" chromosomes have been reported in a wide variety of human genetic disorders, including epilepsy (14,15), intellectual delay (15), various dysmorphic features (16), leukemia (17), and microcephaly (18,19). Further, therapies for genetic disorders based on chromosome circularization have been proposed (20).…”

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confidence: 99%

“Perfect” designer chromosome V and behavior of a ring derivative

Xie

Mitchell

et al. 2017

Science

200

151

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INTRODUCTION The Saccharomyces cerevisiae 2.0 project (Sc2.0) aims to modify the yeast genome with a series of densely spaced designer changes. Both a synthetic yeast chromosome arm (synIXR) and the entirely synthetic chromosome (synIII) function with high fitness in yeast. For designer genome synthesis projects, precise engineering of the physical sequence to match the specified design is important for the systematic evaluation of underlying design principles. Yeast can maintain nuclear chromosomes as rings, occurring by chance at repeated sequences, although the cyclized format is unfavorable in meiosis given the possibility of dicentric chromosome formation from meiotic recombination. Here, we describe the de novo synthesis of synthetic yeast chromosome V (synV) in the “Build-A-Genome China” course, perfectly matching the designer sequence and bearing loxPsym sites, distinguishable watermarks, and all the other features of the synthetic genome. We generated a ring synV derivative with user-specified cyclization coordinates and characterized its performance in mitosis and meiosis. RATIONALE Systematic evaluation of underlying Sc2.0 design principles requires that the final assembled synthetic genome perfectly match the designed sequence. Given the size of yeast chromosomes, synthetic chromosome construction is performed iteratively, and new mutations and unpredictable events may occur during synthesis; even a very small number of unintentional nucleotide changes across the genome could have substantial effects on phenotype. Therefore, precisely matching the physical sequence to the designed sequence is crucial for verification of the design principles in genome synthesis. Ring chromosomes can extend those design principles to provide a model for genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders. RESULTS We chemically synthesized, assembled, and incorporated designer chromosome synV (536,024 base pairs) of S. cerevisiae according to Sc2.0 principles, based on the complete nucleotide sequence of native yeast chromosome V (576,874 base pairs). This work was performed as part of the “Build-A-Genome China” course in Tianjin University. We corrected all mutations found—including duplications, substitutions, and indels—in the initial synV strain by using integrative cotransformation of the precise desired changes and by means of a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)–based method. Altogether, 3331 corrected base pairs were required to match to the designed sequence. We generated a strain that exactly matches all designer sequence changes that displays high fitness under a variety of culture conditions. All corrections were verified with whole-genome sequencing; RNA sequencing revealed only minor changes in gene expression—most notably, decreases in expression of genes relocated near synthetic telomeres as a result of design. We constructed a functional circular synV (ring_synV) derivative in yeast by precisely joining both chromosome ends (telomeres) at specified coordinates. The ring chromosome showed restoration of subtelomeric gene expression levels. The ring_synV strain exhibited fitness comparable with that of the linear synV strain, revealed no change in sporulation frequency, but notably reduced spore viability. In meiosis, heterozygous or homozygous diploid ring_wtV and ring_synV chromosomes behaved similarly, exhibiting substantially higher frequency of the formation of zero-spore tetrads, a type that was not seen in the rod chromosome diploids. Rod synV chromosomes went through meiosis with high spore viability, despite no effort having been made to preserve meiotic competency in the design of synV. CONCLUSION The perfect designer-matched synthetic chromosome V provides strategies to edit sequence variants and correct unpredictable events, such as off-target integration of extra copies of synthetic DNA elsewhere in the genome. We also constructed a ring synthetic chromosome derivative and evaluated its fitness and stability in yeast. Both synV and synVI can be circularized and can power yeast cell growth without affecting fitness when gene content is maintained. These fitness and stability phenotypes of the ring synthetic chromosome in yeast provide a model system with which to probe the mechanism of human ring chromosome disorders. Synthesis, cyclization, and characterization of synV . ( A ) Synthetic chromosome V (synV, 536,024 base pairs) was designed in silico from native chromosome V (wtV, 576,874 base pairs), with extensive genotype modification designed to be phenotypically neutral. ( B ) CRISPR/Cas9 strategy for multiplex repair. ( C ) Colonies of wtV, synV, and ring_synV strains.

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confidence: 99%

“Perfect” designer chromosome V and behavior of a ring derivative

Xie

Mitchell

et al. 2017

Science

200

151

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“…No other major specific focal neurologic deficit has been described to date. Nonetheless, our patient presents body rocking-and severe hair picking-like stereotypes; remarkably, case n • 19 presented stereotyped repetitive hand movements, pressing her palms in the midline, and stroking her thumbs [17]. Concerning psychopathological and psychiatric comorbidities, hyperactivity and mood disorders have been sporadically associated.…”

Section: Discussionmentioning

confidence: 70%

“…Our patient presents an approximately 4.1 Mb deletion in 10p and 8.2 Mb deletion in 10q, affecting several protein-coding genes. A number of these genes have been previously associated with DD/ID, such as ZMYND11, EBF3, DIP2C, PRR26, and IDI2 [16,17].…”

Section: Discussionmentioning

confidence: 99%

“…Only papers published in English were reviewed. Nineteen previously published cases were identified in the literature [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17].…”

Section: Search Strategy and Analysis Of Literaturementioning

confidence: 99%

“…It is currently reported in 19 unrelated patients in the medical literature, but most patients were described before the introduction of chromosomal microarray technology, and the precise definition of deleted regions and encompassed genes is lacking. Typical clinical features include intellectual disability and/or developmental delay (ID/DD), microcephaly, short stature, facial dysmorphisms, ophthalmologic abnormalities and genitourinary malformations [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]. In constitutional ring chromosomes, the regions involved by the breakage, the amount of lost information, and the level of mosaicism resulting from the unstable nature of the ring upon cell division may vary each time, causing patients with a seemingly analogous ring chromosome to display diverse clinical pictures [18].…”

Section: Introductionmentioning

confidence: 99%

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Expanding the Neurological Phenotype of Ring Chromosome 10 Syndrome: A Case Report and Review of the Literature

Pruccoli

Graziano

Locatelli

et al. 2021

Genes

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Ring chromosome 10 [r(10)] syndrome is a rare genetic condition, currently described in the medical literature in a small number of case report studies. Typical clinical features include microcephaly, short stature, facial dysmorphisms, ophthalmologic abnormalities and genitourinary malformations. We report a novel case of r(10) syndrome and review the neurological and neuroradiological phenotypes of the previously described cases. Our patient, a 3 year old Italian girl, represents the 20th case of r(10) syndrome described to date. Intellectual disability/developmental delay (ID/DD), microcephaly, strabismus, hypotonia, stereotyped/aggressive behaviors and electroencephalographic abnormalities were identified in our patient, and in a series of previous cases. A brain MRI disclosed a complex malformation involving both the vermis and cerebellar hemispheres; in the literature, posterior cranial fossa abnormalities were documented by CT scan in another case. Two genes deleted in our case (ZMYND11 in 10p and EBF3 in 10q) are involved in autosomal dominant neurodevelopmental disorders, characterized by different expressions of brain and posterior cranial fossa abnormalities, ID/DD, hypotonia and behavioral problems. Our case expands the neurological and neuroradiological phenotype of r(10) syndrome. Although r(10) syndrome represents an extremely rare condition, with a clinical characterization limited to case reports, the recurrence of specific neurological and neuroradiological features suggests the need for specific genotype-phenotype studies.

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