Navigating the Xenopus tropicalis Genome

2012 ◽  
pp. 43-65 ◽  
Author(s):  
Ira L. Blitz
Keyword(s):  
Xenopus Tropicalis ◽  
Tropicalis Genome

scholarly journals Identification of REST targets in the Xenopus tropicalis genome

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Banu Saritas-Yildirim ◽  
Christopher P Childers ◽  
Christine G Elsik ◽  
Elena M Silva
Keyword(s):  
Xenopus Tropicalis ◽  
Tropicalis Genome

The Xenopus Tropicalis Genome Project

2003 ◽  
Vol 4 (8) ◽  
pp. 645-652 ◽  
Author(s):  
Paul Richardson ◽  
Jarrod Chapman
Keyword(s):  
Genome Project ◽  
Xenopus Tropicalis ◽  
Tropicalis Genome

scholarly journals Three-dimensional folding dynamics of the Xenopus tropicalis genome

2021 ◽  
Author(s):  
Longjian Niu ◽  
Wei Shen ◽  
Zhaoying Shi ◽  
Yongjun Tan ◽  
Na He ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
De Novo ◽  
Three Dimensional ◽  
Xenopus Tropicalis ◽  
Chromosome Conformation ◽  
Chromosome Architecture ◽  
Tropicalis Genome ◽  
Architectural Proteins ◽  
Folding Dynamics

AbstractAnimal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.

scholarly journals Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0137526 ◽  
Author(s):  
Nicolas Buisine ◽  
Xiaoan Ruan ◽  
Patrice Bilesimo ◽  
Alexis Grimaldi ◽  
Gladys Alfama ◽  
...  
Keyword(s):  
Xenopus Tropicalis ◽  
Tropicalis Genome

Generation and Characterization of Developmental Mutations in Xenopus tropicalis

2003 ◽  
Vol 4 (8) ◽  
pp. 673-685 ◽  
Author(s):  
Takuya Nakayama ◽  
Robert Grainger
Keyword(s):  
Xenopus Tropicalis

scholarly journals Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
William L. Macken ◽  
Annie Godwin ◽  
Gabrielle Wheway ◽  
Karen Stals ◽  
Liliya Nazlamova ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Donor Site ◽  
Xenopus Tropicalis ◽  
Splice Donor Site ◽  
Homologous Region ◽  
Disease Genes ◽  
Coat Proteins ◽  
Splice Donor ◽  
Severe Intellectual Disability

Abstract Background Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as “coatopathies”. Methods Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1’s splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2’s missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2’s mutation. Results We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β’-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. Conclusions This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.

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