Satellite DNA evolution: old ideas, new approaches

Lower, Sarah Sander; McGurk, Michael P; Clark, Andrew G.; Barbash, Daniel A.

doi:10.1016/j.gde.2018.03.003

Cited by 147 publications

(136 citation statements)

References 65 publications

(74 reference statements)

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“…Historically, many methods not evaluated here have been used to quantify rDNA copy number, including 1) quantitative rRNA hybridization to total DNA (Schmickel 1973), to microarrays (Robyr et al 2002;Carter 2007), or in situ to chromosomes (Henderson et al 1972); 2) quantitative Southern blot (Kobayashi et al 1998;Kwan et al 2013); and 3) cytogenetic observations (Verma et al 1977). Similarly, we did not discuss or explore more recent methods such as optical mapping (Lower et al 2018). However, much of recent reporting of rDNA copy number variation has relied on estimation from short-read whole genome sequencing (Thompson et al 2013;Gibbons et al 2014Gibbons et al , 2015Xu et al 2017;Wang and Lemos 2017;Parks et al 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Ultimately, however, full understanding of any relationship between rDNA copy number and health and phenotype is hostage to our ability to accurately quantify that copy number. Herein, we compare major copy number estimation methods available for rDNA as an example for other tandemly repeated loci of large (kilobase-scale) units such as satellite DNA (Lower et al 2018). These approaches include pulsed-field gel electrophoresis, droplet digital PCR (ddPCR), and whole genome sequencing (WGS).…”

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confidence: 99%

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Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

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Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Challenges and Approaches to Genotyping Repetitive DNA

Morton¹,

Hall

Kwan³

et al. 2020

G3 Genes|Genomes|Genetics

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“…Assembling ETRs is important since variations in ETR have been linked to cancer and infertility (Barra and Fachinetti, 2018;Black and Giunta, 2018;Ferreira et al, 2015;Giunta and Funabiki, 2017;Miga et al, 2019;Smurova and De Wulf, 2018;Zhu et al, 2018) . ETR sequencing is also important for addressing open problems about centromere evolution (Alkan et al, 2007;Lower et al, 2018;Shepelev et al, 2009, Henikoff et al, 2015 .…”

Section: Introductionmentioning

confidence: 99%

The String Decomposition Problem and its Applications to Centromere Assembly

Dvorkina

Bzikadze²,

Pevzner

2019

Preprint

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Recent attempts to assemble long tandem repeats (such as multi-megabase long centromeres) faced the challenge of accurate translation of long error-prone reads from the nucleotide alphabet into the alphabet of repeat units . Centromeres represent a particularly complex type of nested tandem repeats , where each unit is itself a repeat formed by chromosome-specific monomers (a repeat within repeat). Given a set of monomers forming a specific centromere, translation of a read into monomers is modeled as the String Decomposition Problem, finding a concatenate of monomers with the highest-scoring sequence alignment to a given read. We developed a StringDecomposer algorithm for solving this problem, benchmarked it on the set of reads generated by the Telomere-to-Telomere consortium, and identified a novel (rare) monomer that extends the set of twelve X-chromosome specific monomers identified more than three decades ago. The accurate translation of each read into a monomer alphabet turns centromere assembly into a more tractable problem than the notoriously difficult problem of assembling centromeres in the nucleotide alphabet. Our identification of a novel monomer emphasizes the importance of careful identification of all (even rare) monomers for follow-up centromere assembly efforts.

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“…To our knowledge, no tool currently exists to identify TR arrays in long, error-prone sequencing reads. Tools solving similar problems, primarily developed to work with short reads or assembled genomes, have limitations when applied to this use case (Lower et al , 2018) . Some of them fail to model asymmetric rates of insertions vs. deletions (e.g.…”

Section: Introductionmentioning

confidence: 99%

Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

Harris

Čechová

Makova

2018

Preprint

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Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG) n repeat involved in heat shock stress response. Availability and implementationNCRF is implemented in C, supported by several python scripts. Source code, under the MIT open source license, and simulation data are available at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder , and also in bioconda. Contact

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Satellite DNA evolution: old ideas, new approaches

Cited by 147 publications

References 65 publications

Challenges and Approaches to Genotyping Repetitive DNA

Challenges and Approaches to Genotyping Repetitive DNA

The String Decomposition Problem and its Applications to Centromere Assembly

Noise-Cancelling Repeat Finder: Uncovering tandem repeats in error-prone long-read sequencing data

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