Cellular and genomic approaches for exploring structural chromosomal rearrangements

Hu, Qing; Maurais, Elizabeth G; Ly, Peter

doi:10.1007/s10577-020-09626-1

Cited by 23 publications

(13 citation statements)

References 93 publications

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“…With the advent of DNA sequencing and DNA cloning technologies, methods of classical comparative cytogenetics have changed (for a recent review, see Hu et al. 2020 ), enabling researchers to target and compare DNA sequences of individual chromosomes.…”

Section: Methodological Approaches To Analyze Chromosome-number Variamentioning

confidence: 99%

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Mayrose

Lysak

2020

Genome Biology and Evolution

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Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. While providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.

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Section: Methodological Approaches To Analyze Chromosome-number Variamentioning

confidence: 99%

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Mayrose

Lysak

2020

Genome Biology and Evolution

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“…Numerical and structure changes to the genome are associated with birth defects, reproductive abnormalities, and cancer. The article by Hu et al (2020) describes approaches ranging from classical cytogenetics to sequencing-based technologies used to identify structural chromosome rearrangements and to understand the molecular mechanisms that lead to genome rearrangements. The authors present a historical timeline of microscopy-based approaches, from early light microscopy of chromosome banding using synthetic dyes to higher resolution fluorescence microscopy approaches that use designer oligonucleotide Oligopaint probes to identify regions of chromosomes or illuminate entire chromosomes.…”

Section: Rna-seqmentioning

confidence: 99%

A sampling of methods to study chromosome and genome structure and function

Sullivan

2020

Chromosome Res

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“…Genome architecture at the DNA sequence level has long been recognized to play a key role in formation of structural genome variations [13,14]. A large series of studies using a panel of molecular, cytogenomic and bioinformatic techniques have shown that structural genomic variants (chromosomal rearrangements and CNV) frequently occur through mechanisms involving repeat sequences at the breakpoints as well as DNA recombination-based and replication-based processes [15][16][17][18][19]. At the chromosomal/subchromosomal levels, related phenomena have not been systematically addressed.…”

Section: Introductionmentioning

confidence: 99%

The Cytogenomic “Theory of Everything”: Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging

Iourov¹,

Vorsanova²,

Yurov³

et al. 2020

Preprint

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Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are incompletely understood. During SNP-array molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n=612), we observed colocalizaion of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n=47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either to partial/whole chromosome loss (e.g. aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g. prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything” like the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.

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Cellular and genomic approaches for exploring structural chromosomal rearrangements

Cited by 23 publications

References 93 publications

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

A sampling of methods to study chromosome and genome structure and function

The Cytogenomic “Theory of Everything”: Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging

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