Anterior movement of ventral diencephalic precursors separates the primordial eye field in the neural plate and requires cyclops

Development ◽  
1999 ◽  
Vol 126 (24) ◽  
pp. 5533-5546 ◽  
Author(s):  
Z.M. Varga ◽  
J. Wegner ◽  
M. Westerfield
Keyword(s):  
Gene Function ◽  
Neural Plate ◽  
Wild Type ◽  
Morphogenetic Movements ◽  
Eye Field ◽  
Left And Right ◽  
Single Field ◽  
Ventral Diencephalon

A currently favored hypothesis postulates that a single field of cells in the neural plate forms bilateral retinas. To learn how retinal precursors segregate, we followed individual labeled neural plate cells in zebrafish. In the late gastrula, a single field of odd-paired-like-expressing cells contributed to both retinas, bordered posteriorly by diencephalic precursors expressing mariposa. Median mariposa-expressing cells moved anteriorly, separating the eyes, and formed ventral anterior diencephalon, the presumptive hypothalamus. In cyclops mutants, corresponding cells failed to move anteriorly, a ventral diencephalon never formed, and the eyes remained fused. Ablation of the region containing these cells induced cyclopia in wild types. Our results indicate that movement of a median subpopulation of diencephalic precursors separates retinal precursors into left and right eyes. Wild-type cyclops gene function is required for these morphogenetic movements.

scholarly journals Characterization of the DNA-binding activity of GCR1: in vivo evidence for two GCR1-binding sites in the upstream activating sequence of TPI of Saccharomyces cerevisiae.

1992 ◽  
Vol 12 (6) ◽  
pp. 2690-2700 ◽  
Author(s):  
M A Huie ◽  
E W Scott ◽  
C M Drazinic ◽  
M C Lopez ◽  
I K Hornstra ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Fusion Protein ◽  
Binding Site ◽  
Gene Function ◽  
Binding Sites ◽  
Sequence Motif ◽  
Wild Type ◽  
Upstream Activating Sequence ◽  
Sequence Elements

GCR1 gene function is required for high-level glycolytic gene expression in Saccharomyces cerevisiae. Recently, we suggested that the CTTCC sequence motif found in front of many genes encoding glycolytic enzymes lay at the core of the GCR1-binding site. Here we mapped the DNA-binding domain of GCR1 to the carboxy-terminal 154 amino acids of the polypeptide. DNase I protection studies showed that a hybrid MBP-GCR1 fusion protein protected a region of the upstream activating sequence of TPI (UASTPI), which harbored the CTTCC sequence motif, and suggested that the fusion protein might also interact with a region of the UAS that contained the related sequence CATCC. A series of in vivo G methylation protection experiments of the native TPI promoter were carried out with wild-type and gcr1 deletion mutant strains. The G doublets that correspond to the C doublets in each site were protected in the wild-type strain but not in the gcr1 mutant strain. These data demonstrate that the UAS of TPI contains two GCR1-binding sites which are occupied in vivo. Furthermore, adjacent RAP1/GRF1/TUF- and REB1/GRF2/QBP/Y-binding sites in UASTPI were occupied in the backgrounds of both strains. In addition, DNA band-shift assays were used to show that the MBP-GCR1 fusion protein was able to form nucleoprotein complexes with oligonucleotides that contained CTTCC sequence elements found in front of other glycolytic genes, namely, PGK, ENO1, PYK, and ADH1, all of which are dependent on GCR1 gene function for full expression. However, we were unable to detect specific interactions with CTTCC sequence elements found in front of the translational component genes TEF1, TEF2, and CRY1. Taken together, these experiments have allowed us to propose a consensus GCR1-binding site which is 5'-(T/A)N(T/C)N(G/A)NC(T/A)TCC(T/A)N(T/A)(T/A)(T/G)-3'.

scholarly journals Comparative analysis and mutation effects of fpp2–fpp1 tandem genes encoding proteolytic extracellular enzymes of Flavobacterium psychrophilum

Microbiology ◽  
2011 ◽  
Vol 157 (4) ◽  
pp. 1196-1204 ◽  
Author(s):  
David Pérez-Pascual ◽  
Esther Gómez ◽  
Beatriz Álvarez ◽  
Jessica Méndez ◽  
Pilar Reimundo ◽  
...  
Keyword(s):  
Gene Function ◽  
Type Strain ◽  
Wild Type Strain ◽  
Proteolytic Enzymes ◽  
Function Analysis ◽  
Phenotypic Characterization ◽  
Pcr Analysis ◽  
Wild Type ◽  
Flavobacterium Psychrophilum ◽  
Genes Encoding

Flavobacterium psychrophilum is a very significant fish pathogen that secretes two biochemically characterized extracellular proteolytic enzymes, Fpp1 and Fpp2. The genes encoding these enzymes are organized as an fpp2–fpp1 tandem in the genome of strain F. psychrophilum THC02/90. Analysis of the corresponding encoded proteins showed that they belong to two different protease families. For gene function analysis, new genetic tools were developed in F. psychrophilum by constructing stable isogenic fpp1 and fpp2 mutants via single-crossover homologous recombination. RT-PCR analysis of wild-type and mutant strains suggested that both genes are transcribed as a single mRNA from the promoter located upstream of the fpp2 gene. Phenotypic characterization of the fpp2 mutant showed lack of caseinolytic activity and higher colony spreading compared with the wild-type strain. Both characteristics were recovered in the complemented strain. One objective of this work was to assess the contribution to virulence of these proteolytic enzymes. LD50 experiments using the wild-type strain and mutants showed no significant differences in virulence in a rainbow trout challenge model, suggesting instead a possible nutritional role. The gene disruption procedure developed in this work, together with the knowledge of the complete genome sequence of F. psychrophilum, open new perspectives for the study of gene function in this bacterium.

scholarly journals An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9

2018 ◽  
Author(s):  
Han Wang ◽  
Heenam Park ◽  
Jonathan Liu ◽  
Paul W. Sternberg
Keyword(s):  
Dna Repair ◽  
Caenorhabditis Elegans ◽  
Genome Editing ◽  
Gene Function ◽  
Unique Sequence ◽  
Target Site ◽  
Null Alleles ◽  
Wild Type ◽  
C Elegans ◽  
Null Mutants

AbstractNull mutants are essential for analyzing gene function. Here, we describe a simple and efficient method to generate Caenorhabditis elegans null mutants using CRISPR/Cas9 and short single stranded DNA oligo repair templates to insert a universal 43-nucleotide-long stop knock-in (STOP-IN) cassette into the early exons of target genes. This cassette has stop codons in all three reading frames and leads to frameshifts, which will generate putative null mutations regardless of the reading frame of the insertion position in exons. The STOP-IN cassette also contains an exogenous Cas9 target site that allows further genome editing and provides a unique sequence that simplifies the identification of successful insertion events via PCR. As a proof of concept, we inserted the STOP-IN cassette right at a Cas9 target site in aex-2 to generate new putative null alleles by injecting preassembled Cas9 ribonucleoprotein and a short synthetic single stranded DNA repair template containing the STOP-IN cassette and two 35-nucleotide-long homology arms identical to the sequences flanking the Cas9 cut site. We showed that these new aex-2 alleles phenocopied an existing loss-of-function allele of aex-2. We further showed that the new aex-2 null alleles could be reverted back to the wild-type sequence by targeting exogenous Cas9 cut site included in the STOP-IN cassette and providing a single stranded wild-type DNA repair oligo. We applied our STOP-IN method to generate new putative null mutants for additional 20 genes, including three pharyngeal muscle-specific genes (clik-1, clik-2, and clik-3), and reported a high insertion rate (46%) based on the animals we screened. We showed that null mutations of clik-2 cause recessive lethality with a severe pumping defect and clik-3 null mutants have a mild pumping defect, while clik-1 is dispensable for pumping. We expect that the knock-in method using the STOP-IN cassette will facilitate the generation of new null mutants to understand gene function in C. elegans and other genetic model organisms.SummaryWe report a simple and efficient CRISPR/Cas9 genome editing strategy to generate putative null C. elegans mutants by inserting a small universal stop knock-in (STOP-IN) cassette with stop codons in three frames and frameshifts. The strategy is cloning-free, with the mixture consisting of preassembled Cas9 ribonucleoprotein and single stranded repair DNA oligos directly injected into gonads of adult C. elegans. The universal STOP-IN cassette also contains a unique sequence that simplifies detection of successful knock-in events via PCR and an exogenous Cas9 target sequence that allows further genome editing.

scholarly journals Donor plasmids for phenotypically neutral chromosomal gene insertions in Enterobacteriaceae

Microbiology ◽  
2020 ◽  
Vol 166 (12) ◽  
pp. 1115-1120 ◽  
Author(s):  
Emma R. Holden ◽  
Gregory J. Wickham ◽  
Mark A. Webber ◽  
Nicholas M. Thomson ◽  
Eleftheria Trampari
Keyword(s):  
Homologous Recombination ◽  
Gene Function ◽  
Copy Number ◽  
Chromosomal Gene ◽  
Wild Type ◽  
Bacterial Genomes ◽  
Inexpensive Method ◽  
In Trans ◽  
Λ Red ◽  
Insertion Mutants

Recombineering using bacteriophage lambda Red recombinase (λ-Red) uses homologous recombination to manipulate bacterial genomes and is commonly applied to disrupt genes to elucidate their function. This is often followed by the introduction of a wild-type copy of the gene on a plasmid to complement its function. This is often not, however, at a native copy number and the introduction of a chromosomal version of a gene can be a desirable solution to provide wild-type copy expression levels of an allele in trans. Here, we present a simple methodology based on the λ-Red-based ‘gene doctoring’ technique, where we developed tools used for chromosomal tagging in a conserved locus downstream of glmS and found no impact on a variety of important phenotypes. The tools described provide an easy, quick and inexpensive method of chromosomal modification for the creation of a library of insertion mutants to study gene function.

MUTATIONS WITH DOMINANT EFFECTS ON THE BEHAVIOR AND MORPHOLOGY OF THE NEMATODE CAENORHABDITIS ELEGANS

Genetics ◽  
1986 ◽  
Vol 113 (4) ◽  
pp. 821-852
Author(s):  
Eun-Chung Park ◽  
H Robert Horvitz
Keyword(s):  
Caenorhabditis Elegans ◽  
Random Sample ◽  
Gene Function ◽  
The Novel ◽  
Wild Type ◽  
Nematode Caenorhabditis Elegans ◽  
Type Function ◽  
C Elegans ◽  
Wild Type Phenotype ◽  
Gene Functions

ABSTRACT We have analyzed 31 mutations that have dominant effects on the behavior or morphology of the nematode Caenorhabditis elegans. These mutations appear to define 15 genes. We have studied ten of these genes in some detail and have been led to two notable conclusions. First, loss of gene function for four of these ten genes results in a wild-type phenotype; if these genes represent a random sample from the genome, then we would estimate that null mutations in about half of the genes in C. elegans would result in a nonmutant phenotype. Second, the dominant effects of mutations in nine of these ten genes are caused by novel gene functions, and in all nine cases the novel function is antagonized by the wild-type function.

Abstract 18321: Analysis of a Consanguineous Cohort to Identify and Characterize Human Knockouts

Circulation ◽  
2015 ◽  
Vol 132 (suppl_3) ◽  
Author(s):  
Danish Saleheen ◽  
Pradeep Nataranjan ◽  
Wei Zhao ◽  
Asif Rasheed ◽  
Sumeet Khetarpal ◽  
...  
Keyword(s):  
Gene Function ◽  
Large Fraction ◽  
Model Organisms ◽  
Wild Type ◽  
Gene Copies ◽  
Apolipoprotein C ◽  
Genome Wide ◽  
Whole Exome ◽  
Phenotypic Screen ◽  
Complete Disruption

Background: Experimental disruption of both gene copies (“knockout”) in model organisms has proven useful to understand gene function. Identification of “human knockouts” (i.e., individuals in which null mutations disrupt both copies of a given gene) should therefore provide valuable insights to a gene function that could be of direct relevance to humans. Objective and Methods: We leverage naturally-occurring null mutations and consanguinity in the human population in order to: 1) identify humans knocked out for genes; and 2) characterize the phenotypic consequences of complete gene disruption. We performed whole-exome sequencing in 7,078 individuals living in Pakistan, a region of the world with high levels of consanguinity, and tested whether knockouts differed from wild-type participants across a range of >200 cardiometabolic traits. Results: Median length of genome-wide homozygosity among Pakistani participants was 6-7 times higher than participants of European (CEU, TSI), East Asian (CHB, JPT, CHD) and African ancestries (YRI, MKK), respectively. In Pakistanis, we were able to enumerate 47,656 mutations predicted to be null (nonsense, frameshift, or canonical splice-site); variants were further filtered based on MAF, transcript position, splice sites, and conservation to identify 36,850 “high-confidence” null mutations across 12,131 autosomal genes. Across all participants, 961 distinct genes were completely disrupted by homozygous null mutations. 1,306 participants (18.4%) had at least one gene knocked out. In a phenotypic screen, homozygosity for null mutations at APOC3 was associated with absent plasma apolipoprotein C-III levels; at PLAG27 , with absent enzymatic activity of lipoprotein-associated phospholipase A2 in the blood; at CYP2F1 , with higher plasma interleukin-8 concentrations; and at either A3GALT2 or NRG4 , with markedly reduced plasma insulin C-peptide concentrations. After physiologic challenge with oral fat, APOC3 knockouts, when compared to wild-type family members, displayed marked blunting of the usual post-prandial rise in plasma triglycerides. Conclusion: These observations provide a roadmap to understand the consequences of complete disruption of a large fraction of genes in the human genome.

scholarly journals CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Hua Zhong ◽  
Yiyun Chen ◽  
Yumei Li ◽  
Rui Chen ◽  
Graeme Mardon
Keyword(s):  
Gene Function ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Photoreceptor Cells ◽  
Mutant Mice ◽  
Wild Type ◽  
Cell Degeneration ◽  
Rpe Cells ◽  
Mosaic Expression

Abstract The era of genomics has demanded the development of more efficient and timesaving approaches to validate gene function in disease. Here, we utilized the CRISPR-Cas9 system to generate Kcnj13 mutant mice by zygote injection to verify the pathogenic role of human KCNJ13, mutations of which are thought to cause Leber congenital amaurosis (LCA), an early-onset form of blindness. We found that complete loss of Kcnj13 is likely postnatal lethal. Among surviving F0-generation mice examined, 80% show mosaic KCNJ13 expression in the retinal pigment epithelium (RPE). Mosaic expression correlates with decreased response to light and photoreceptor degeneration, indicating that Kcnj13 mutant mice mimic human KCNJ13-related LCA disease. Importantly, mosaic animals enable us to directly compare Kcnj13 mutant and wild-type RPE cells in the same eye. We found that RPE cells lacking KCNJ13 protein still survive but overlying photoreceptors exhibit cell degeneration. At the same time, wild-type RPE cells can rescue neighboring photoreceptor cells that overlie mutant RPE cells. These results suggest that KCNJ13 expression is required for RPE cells to maintain photoreceptor survival. Moreover, we show that CRISPR-Cas9 engineered mosaicism can be used to rapidly test candidate gene function in vivo.

scholarly journals The R21C Mutation in Cardiac Troponin I Imposes Differences in Contractile Force Generation between the Left and Right Ventricles of Knock-In Mice

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Jingsheng Liang ◽  
Katarzyna Kazmierczak ◽  
Ana I. Rojas ◽  
Yingcai Wang ◽  
Danuta Szczesna-Cordary
Keyword(s):  
Papillary Muscle ◽  
Cardiac Troponin ◽  
Troponin I ◽  
Contractile Force ◽  
Cardiac Troponin I ◽  
Wild Type ◽  
Partial Loss ◽  
Left And Right ◽  
The Difference ◽  
State Force

We investigated the effect of the hypertrophic cardiomyopathy-linked R21C (arginine to cysteine) mutation in human cardiac troponin I (cTnI) on the contractile properties and myofilament protein phosphorylation in papillary muscle preparations from left (LV) and right (RV) ventricles of homozygous R21C+/+knock-in mice. The maximal steady-state force was significantly reduced in skinned papillary muscle strips from the LV compared to RV, with the latter displaying the level of force observed in LV or RV from wild-type (WT) mice. There were no differences in the Ca2+sensitivity between the RV and LV of R21C+/+mice; however, the Ca2+sensitivity of force was higher in RV-R21C+/+compared with RV-WT and lower in LV- R21C+/+compared with LV-WT. We also observed partial loss of Ca2+regulation at low [Ca2+]. In addition, R21C+/+-KI hearts showed no Ser23/24-cTnI phosphorylation compared to LV or RV of WT mice. However, phosphorylation of the myosin regulatory light chain (RLC) was significantly higher in the RV versus LV of R21C+/+mice and versus LV and RV of WT mice. The difference in RLC phosphorylation between the ventricles of R21C+/+mice likely contributes to observed differences in contractile force and the lower tension monitored in the LV of HCM mice.

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