Use of a Sibling Subtraction Method (SSM) for Identifying Causal Mutations in<i>C. elegans</i>by Whole-Genome Sequencing

Joseph, Braveen B; Blouin, Nicolas A.; Fay, David S.

doi:10.1101/166355

Cited by 4 publications

(6 citation statements)

References 52 publications

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“…Complementation analysis indicated that mib41 and mib42 affect two independent loci. We determined the genomic regions of interest by single nucleotide polymorphism (SNP) mapping (Davis et al, 2005), and identified candidate causative mutations using the sibling subtraction method for mapping by whole-genome sequencing (Joseph et al, 2018). We obtained a single cluster of candidate mutations for each mutant allele on opposite arms of the X chromosome, consistent with the SNP mapping data.…”

Section: Resultsmentioning

confidence: 99%

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BBLN-1 is essential for intermediate filament organization and apical membrane morphology

Remmelzwaal

Geisler

Stucchi

et al. 2020

Preprint

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Epithelial tubes are essential components of metazoan organ systems that control the flow of fluids and the exchange of materials between body compartments and the outside environment. The size and shape of the central lumen confer important characteristics to tubular organs and need to be carefully controlled. Here, we identify the small coiled-coil protein BBLN-1 as a regulator of lumen morphology in the C. elegans intestine. Loss of BBLN-1 causes the formation of bubble-shaped invaginations of the apical membrane into the cytoplasm of intestinal cells, and abnormal aggregation of the subapical intermediate filament (IF) network. BBLN-1 interacts with IF proteins and localizes to the IF network in an IF-dependent manner. The appearance of invaginations is a result of the abnormal IF aggregation, indicating a direct role for the IF network in maintaining lumen homeostasis. Finally, we identify bublin (BBLN) as the mammalian ortholog of BBLN-1. When expressed in the C. elegans intestine, bublin recapitulates the localization pattern of BBLN-1 and can compensate for the loss of BBLN-1. In mouse intestinal organoids, bublin localizes subapically, together with the IF protein keratin 8. Our results therefore may have implications for understanding the role of IFs in regulating epithelial tube morphology in mammals.SummaryWe identify BBLN-1 as an evolutionary conserved regulator of lumen morphology in the C. elegans intestine. Loss of bbln-1 causes intermediate filament network reorganization that induces severe apical morphology defects. We also identify bublin (BBLN) as the mammalian ortholog, which can compensate for the loss of BBLN-1 in C. elegans.

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Section: Resultsmentioning

confidence: 99%

“…We used the sibling subtraction method to identify the causative mib41 and mib42 mutations by whole-genome sequencing (WGS) (Joseph et al, 2018). From heterozygous erm-1::GFP/+; mib41/+ or erm-1::GFP/+; mib42/+ hermaphrodites we isolated homozygous mib41 or mib42 mutant, homozygous nonmutant, or heterozygous F2 progeny.…”

Section: Methodsmentioning

confidence: 99%

BBLN-1 is essential for intermediate filament organization and apical membrane morphology

Remmelzwaal

Geisler

Stucchi

et al. 2020

Preprint

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“…Complementation analysis indicated that mib41 and mib42 affect different loci. Through single-nucleotide polymorphism mapping and whole-genome sequencing, 22,23 we identified a single cluster of candidate mutations for each allele.…”

Section: Loss Of Bbln-1 Causes Cytoplasmic Invaginations Of the Intestinal Apical Membranementioning

confidence: 99%

“…We used the sibling subtraction method to identify the causative mib41 and mib42 mutations by whole-genome sequencing (WGS). 23 From heterozygous erm-1::GFP/+; mib41/+ or erm-1::GFP/+; mib42/+ hermaphrodites we isolated homozygous mib41 or mib42 mutant, homozygous nonmutant, or heterozygous F2 progeny. Genomic DNA was then purified from pooled F3 progeny derived from 12-16 F2 animals and sequenced on an Illumina HiSeq X Ten platform.…”

Section: Identification Of Mib41 and Mib42 Mutationsmentioning

confidence: 99%

BBLN-1 is essential for intermediate filament organization and apical membrane morphology

et al. 2021

View full text Add to dashboard Cite

Epithelial tubes are essential components of metazoan organ systems that control the flow of fluids and the exchange of materials between body compartments and the outside environment. The size and shape of the central lumen confer important characteristics to tubular organs and need to be carefully controlled. Here, we identify the small coiled-coil protein BBLN-1 as a regulator of lumen morphology in the C. elegans intestine. Loss of BBLN-1 causes the formation of bubble-shaped invaginations of the apical membrane into the cytoplasm of intestinal cells and abnormal aggregation of the subapical intermediate filament (IF) network. BBLN-1 interacts with IF proteins and localizes to the IF network in an IF-dependent manner. The appearance of invaginations is a result of the abnormal IF aggregation, indicating a direct role for the IF network in maintaining lumen homeostasis. Finally, we identify bublin (BBLN) as the mammalian ortholog of BBLN-1. When expressed in the C. elegans intestine, BBLN recapitulates the localization pattern of BBLN-1 and can compensate for the loss of BBLN-1 in early larvae. In mouse intestinal organoids, BBLN localizes subapically, together with the IF protein keratin 8. Our results therefore may have implications for understanding the role of IFs in regulating epithelial tube morphology in mammals.

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“…147 148 Nonsense mutation in elpc-2 causes progressive loss of adult locomotor function in 149 ix243 worms 150 We used whole genome sequencing and a modified version of the sibling 151 subtraction method to identify the causative mutation site in the ix243 strain ( Fig. S5) 152 (Joseph et al, 2018). Mutations were evenly induced on all chromosomes in the ix243 153 mutant strain before backcrossing ( Fig.…”

Section: Introduction 31mentioning

confidence: 99%

Forward genetic screen forCaenorhabditis elegansmutants with a shortened locomotor healthspan

Kawamura

Maruyama

2018

Preprint

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Two people with the same lifespan do not necessarily have the same healthspan. One person may retain locomotor and cognitive functions until the end of life, while another person may lose them during adulthood. Unbiased searches for genes that are required to maintain locomotor capacities during adulthood may uncover key regulators of locomotor healthspan. Here, we take advantage of the relatively short lifespan of the nematodeCaenorhabditis elegansand develop a novel screening procedure to collect mutants with locomotor deficits that become apparent in adulthood. After ethyl methanesulfonate mutagenesis, we isolated fiveC. elegansmutant strains that progressively lose adult locomotor activity. In one of the mutant strains, a nonsense mutation in Elongator Complex Protein Component 2 (elpc-2)causes a progressive decline in locomotor function. Mutants and mutations identified in the present screen may provide insights into mechanisms of age-related locomotor impairment and the maintenance of locomotor healthspan.

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Use of a Sibling Subtraction Method (SSM) for Identifying Causal Mutations inC. elegansby Whole-Genome Sequencing

Cited by 4 publications

References 52 publications

BBLN-1 is essential for intermediate filament organization and apical membrane morphology

BBLN-1 is essential for intermediate filament organization and apical membrane morphology

BBLN-1 is essential for intermediate filament organization and apical membrane morphology

Forward genetic screen forCaenorhabditis elegansmutants with a shortened locomotor healthspan

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