The recent advances and future perspectives of genetic compensation studies in the zebrafish model

Rouf, Muhammad Abdul; Wen, Lin; Mahendra, Yoga; Wang, Jinxuan; Zhang, Kun; Liang, Shuang; Wang, Yuming; Li, Zhenggong; Wang, Yeqi; Wang, Guixue

doi:10.1016/j.gendis.2021.12.003

Cited by 21 publications

(13 citation statements)

References 75 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Section: Discussionmentioning

confidence: 97%

“…This autoregulation mechanism compensates for the loss of one allele in BRN3a heterozygotes by increasing transcription of the remaining allele, thereby suppressing haploinsufficiency (Trieu et al, 2003). There have also been recent reports of transcriptional adaptation mechanisms observed in model organisms including Caenorhabditis elegans and zebrafish mutants, with chromatin remodeling or expression modulation by long noncoding RNAs as stated potential mechanisms at play (El‐Brolosy & Stainier, 2017; Jakutis & Stainier, 2021; Rouf et al, 2022; Sztal & Stainier, 2020; Zundo, 2021). While the precise mechanism of genetic compensation in individual XGS28‐P‐R is not known, the full elucidation of the molecular mechanisms involved will add to the growing understanding of genotype‐phenotype relationships in the context of transcriptional adaptation in human disease, particularly the role of copy number alterations in cancer and genomic disorders (Bhattacharya et al, 2020; Carelle‐Calmels et al, 2009; Lupski, 2022).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Chander

Mahmoud

et al. 2022

Human Mutation

View full text Add to dashboard Cite

Xia-Gibbs syndrome is a rare mendelian disorder characterized by Development Delay (DD), intellectual disability (ID), and hypotonia. Individuals with XGS typically harbor de novo protein-truncating mutations in the AT-Hook DNA binding motif containing 1 (AHDC1) gene, although some missense mutations can also cause XGS.Large de novo heterozygous deletions that encompass the AHDC1 gene have also been ascribed as diagnostic for the disorder, without substantial evidence to support their pathogenicity. We analyzed 19 individuals with large contiguous deletions involving AHDC1, along with other genes. One individual bore the smallest known contiguous AHDC1 deletion (∼350 Kb), encompassing eight other genes within chr1p36.11 (Feline Gardner-Rasheed, IFI6, FAM76A, STX12, PPP1R8, THEMIS2, RPA2, SMPDL3B) and terminating within the first intron of AHDC1. The breakpoint junctions and phase of the deletion were identified using both short and long read sequencing (Oxford Nanopore). Quantification of RNA expression patterns in whole blood revealed that AHDC1 exhibited a mono-allelic expression pattern with no deficiency in overall AHDC1 expression levels, in contrast to the other deleted genes, which exhibited a 50% reduction in mRNA expression. These results suggest that

show abstract

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Chander

Mahmoud

et al. 2022

Human Mutation

View full text Add to dashboard Cite

show abstract

“…In both developmental and genetic investigations, zebrafish are recognized as a very useful model organism to study vertebrate biology. [14][15][16] In vitro fertilization, high fecundity, rapid embryonic growth, and optical transparency are just a few of the benefits of zebrafish as model organisms. [17][18][19] These characteristics make it possible to study developmental processes and morphological endpoints during the early stages of life.…”

Section: Evaluatedmentioning

confidence: 99%

“…In both developmental and genetic investigations, zebrafish are recognized as a very useful model organism to study vertebrate biology 14–16 . In vitro fertilization, high fecundity, rapid embryonic growth, and optical transparency are just a few of the benefits of zebrafish as model organisms 17–19 .…”

Section: Introductionmentioning

confidence: 99%

Intergenerational toxic effects of parental exposure to [C_nmim]NO₃ (n = 2,4,6) on nervous and skeletal development in zebrafish offspring

Liu

et al. 2023

Environmental Toxicology

View full text Add to dashboard Cite

Ionic liquids (ILs) are thought to have negative effects on human health. Researchers have explored the effects of ILs on zebrafish development during the early stages, but the intergenerational toxicity of ILs on zebrafish development has rarely been reported. Herein, parental zebrafish were exposed to different concentrations (0, 12.5, 25, and 50 mg/L) of [Cnmim]NO3 (n = 2, 4, 6) for 1 week. Subsequently, the F1 offspring were cultured in clean water for 96 h. [Cnmim]NO3 (n = 2, 4, 6) exposure inhibited spermatogenesis and oogenesis in F0 adults, even causing obvious lacunae in the testis and atretic follicle oocytes in ovary. After parental exposure to [Cnmim]NO3 (n = 2, 4, 6), the body length and locomotor behavior were measured in F1 larvae at 96 hours post‐fertilization (hpf). The results showed that the higher the concentration of [Cnmim]NO3 (n = 2, 4, 6), the shorter the body length and swimming distance, and the longer the immobility time. Besides, a longer alkyl chain length of [Cnmim]NO3 had a more negative effect on body length and locomotor behavior. RNA‐seq analysis revealed several downregulated differentially expressed genes (DEGs)—grin1b, prss1, gria3a, and gria4a—enriched in neurodevelopment‐related pathways, particularly the pathway for neuroactive ligand–receptor interaction. Moreover, several upregulated DEGs, namely col1a1a, col1a1b, and acta2, were mainly associated with skeletal development. Expression of DEGs was tested by RT‐qPCR, and the outcomes were consistent with those obtained from RNA‐Seq. We provide evidence showing the effects of parental exposure to ILs on the regulation of nervous and skeletal development in F1 offspring, demonstrating intergenerational effects.

show abstract

“…rerio . It should also be borne in mind that harmful phenotype changes in mutants, but not in morphants, may be buffered by the activity of the mechanism underlying genetic compensation ( 43 , 44 ). Therefore, conclusions reached from studies on haematopoiesis in zebrafish can be and are indeed used for modelling studies on haematopoiesis and its disorders in humans ( 20 , 32 ).…”

Section: Danio Rerio As a Model Organism In Studies On Haema...mentioning

confidence: 99%

Haematopoiesis in Zebrafish (Danio Rerio)

Stosik

Tokarz–Deptuła²,

Deptuła³

2022

Front. Immunol.

View full text Add to dashboard Cite

Haematopoiesis in fish and mammals is a complex process, and many aspects regarding its model and the differentiation of haematopoietic stem cells (HSCs) still remain enigmatic despite advanced studies. The effects of microenvironmental factors or HSCs niche and signalling pathways on haematopoiesis are also unclear. This review presents Danio rerio as a model organism for studies on haematopoiesis in vertebrates and discusses the development of this process during the embryonic period and in adult fish. It describes the role of the microenvironment of the haematopoietic process in regulating the formation and function of HSCs/HSPCs (hematopoietic stem/progenitor cells) and highlights facts and research areas important for haematopoiesis in fish and mammals.

show abstract

The recent advances and future perspectives of genetic compensation studies in the zebrafish model

Cited by 21 publications

References 75 publications

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Intergenerational toxic effects of parental exposure to [C_nmim]NO₃ (n = 2,4,6) on nervous and skeletal development in zebrafish offspring

Haematopoiesis in Zebrafish (Danio Rerio)

Contact Info

Product

Resources

About

The recent advances and future perspectives of genetic compensation studies in the zebrafish model

Cited by 21 publications

References 75 publications

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Long read sequencing and expression studies ofAHDC1deletions in Xia‐Gibbs syndrome reveal a novel genetic regulatory mechanism

Intergenerational toxic effects of parental exposure to [Cnmim]NO3 (n = 2,4,6) on nervous and skeletal development in zebrafish offspring

Haematopoiesis in Zebrafish (Danio Rerio)

Contact Info

Product

Resources

About

Intergenerational toxic effects of parental exposure to [C_nmim]NO₃ (n = 2,4,6) on nervous and skeletal development in zebrafish offspring