Dataset Information

Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation of EYA3/EFCAB4b.

ABSTRACT:

Introduction

The accurate detection of breakpoint regions of disease-associated chromosomal rearrangements helps understand the molecular mechanisms and identify the risks involved with disrupted genes.

Methods

In this study, a girl with growth retardation is characterized using positional cloning and genome sequencing. The techniques include fluorescence in situ hybridization (FISH) with paint (WCP) and bacterial-artificial chromosomes (BAC) probes, PCR, real-time PCR, and short and long-read sequencing.

Results

The translocation was identified by GTG banding and confirmed by WCP FISH. Microarray ruled out the involvement of other copy number variations except for 6 homozygous regions which are not disease-causing variants. Fine mapping with FISH showed split signals with BAC clone RP11-312A3. Genome sequencing of short-read with an average 30× depth and long-read sequencing technology with a 3.8× coverage identified both breakpoints, confirmed by Sanger sequencing, that showed microhomology. The breakpoint at 1p and 12p regions disrupted EYA3 and EFCAB4B genes. Expression analysis of EYA3 showed a 7-fold increase, suggesting the formation of a fusion gene with EFCAB4B. EYA3 is involved in skeleton development, and EFCAB4B plays a role in calcium metabolism, which may be relevant for the patient's phenotype.

Conclusion

The systematic application of genome techniques to translocations and their advantages is discussed.

SUBMITTER: Dutta UR

PROVIDER: S-EPMC9801327 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation of <i>EYA3/EFCAB4b</i>.

Dutta Usha R UR Bhattacherjee Amrita A Bahal Ashish A Posanapally Laxmi P LP Lone Kaisar A KA Bathula Siddardha S Dalal Ashwin A

Molecular syndromology 20220316 5

<h4>Introduction</h4>The accurate detection of breakpoint regions of disease-associated chromosomal rearrangements helps understand the molecular mechanisms and identify the risks involved with disrupted genes.<h4>Methods</h4>In this study, a girl with growth retardation is characterized using positional cloning and genome sequencing. The techniques include fluorescence in situ hybridization (FISH) with paint (WCP) and bacterial-artificial chromosomes (BAC) probes, PCR, real-time PCR, and short ...[more]

PMID: 36588754

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Project description:Balanced constitutional reciprocal translocations are the most common structural chromosomal rearrangements identiï¬ed in man and pigs. Carriers are generally phenotypically normal, but such rearrangements frequently lead to reproductive disorders. In reciprocal translocation heterozygotes, the homologous regions of the normal and derivative chromosomes involved in the rearrangement pair during the prophase of the first meiotic division, thanks to the synaptonemal complex (SC), and form a particular structure called quadrivalent. In some cases, chromosomal regions (within the quadrivalent) remain unsynapsed, especially around the breakpoints, which may trigger meiosis checkpoints leading to spermatogenesis arrest at the pachytene stage. Several hypotheses have been proposed to explain such effects of pairing failure on gametogenesis. The first one is an altered transcription of the genes located on the unpaired segments. Indeed, studies conducted in mice revealed a transcriptional repression of unpaired regions by a specific mechanism called âMeiotic Silencing of Unsynapsed Chromatinâ (MSUC) in individuals with a partial or total spermatogenesis arrest (Turner et al., 2005). If some genes necessary for the proper course of meiosis are located in such unsynapsed genomic regions, MSUC may result in an arrest of the meiotic division. Secondly, associations between the âquadrivalentâ and the XY bivalent which is transcriptionally silenced by a phenomenon known as meiotic sex chromosome inactivation (MSCI, (Turner, 2007) were also observed in individuals with altered semen parameters (azoospermic or oligospemic) (Oliver-Bonet et al., 2005; Sciurano et al., 2007a, 2012). Such an association could result in a partial reactivation of the XY body (XYB) leading to the expression of some genes located on the X chromosome (Lifschytz and Lindsley, 1972), or result in the spreading of the XYB inactivation towards the autosomal segments attached to the XYB, without reactivation of the latter (Jaafar et al., 1993). Beyond the potential spermatogenesis failure mentioned above, reciprocal translocations are systematically responsible for the production of genetically unbalanced gametes. Here we report the detailed analysis of the whole meiotic process (from spermatocytes to spermatozoa) in the case of a constitutional balanced reciprocal translocation responsible for severe oligoasthenoteratospermia. Total RNA was extracted in 3 replicates from testicular biopsies control animals, from testicular biopsy of an oligospermic boar and from testicular biopsy of a severe oligo-astheno-teratospermic boar carrier of the trcp(1;14) reciprocal translocation.

Project description:Balanced constitutional reciprocal translocations are the most common structural chromosomal rearrangements identiﬁed in man and pigs. Carriers are generally phenotypically normal, but such rearrangements frequently lead to reproductive disorders. In reciprocal translocation heterozygotes, the homologous regions of the normal and derivative chromosomes involved in the rearrangement pair during the prophase of the first meiotic division, thanks to the synaptonemal complex (SC), and form a particular structure called quadrivalent. In some cases, chromosomal regions (within the quadrivalent) remain unsynapsed, especially around the breakpoints, which may trigger meiosis checkpoints leading to spermatogenesis arrest at the pachytene stage. Several hypotheses have been proposed to explain such effects of pairing failure on gametogenesis. The first one is an altered transcription of the genes located on the unpaired segments. Indeed, studies conducted in mice revealed a transcriptional repression of unpaired regions by a specific mechanism called “Meiotic Silencing of Unsynapsed Chromatin” (MSUC) in individuals with a partial or total spermatogenesis arrest (Turner et al., 2005). If some genes necessary for the proper course of meiosis are located in such unsynapsed genomic regions, MSUC may result in an arrest of the meiotic division. Secondly, associations between the “quadrivalent” and the XY bivalent which is transcriptionally silenced by a phenomenon known as meiotic sex chromosome inactivation (MSCI, (Turner, 2007) were also observed in individuals with altered semen parameters (azoospermic or oligospemic) (Oliver-Bonet et al., 2005; Sciurano et al., 2007a, 2012). Such an association could result in a partial reactivation of the XY body (XYB) leading to the expression of some genes located on the X chromosome (Lifschytz and Lindsley, 1972), or result in the spreading of the XYB inactivation towards the autosomal segments attached to the XYB, without reactivation of the latter (Jaafar et al., 1993). Beyond the potential spermatogenesis failure mentioned above, reciprocal translocations are systematically responsible for the production of genetically unbalanced gametes. Here we report the detailed analysis of the whole meiotic process (from spermatocytes to spermatozoa) in the case of a constitutional balanced reciprocal translocation responsible for severe oligoasthenoteratospermia.