Identification and characterization of a gene activated by the deformed homeoprotein

Development ◽  
1993 ◽  
Vol 118 (1) ◽  
pp. 203-214 ◽  
Author(s):  
J.W. Mahaffey ◽  
D.F. Jones ◽  
J.A. Hickel ◽  
C.M. Griswold
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Direct Interaction ◽  
Homeotic Genes ◽  
Binding Assays ◽  
Transcript Accumulation ◽  
Enhancer Element ◽  
Control Segment ◽  
The Individual

In Drosophila, the homeotic genes encode transcription factors which control segment identity during embryogenesis by specifying the appropriate set of ‘target’ genes necessary to produce the individual segmental characteristics. Though we know much about the homeotic genes and the proteins they encode, we know little of their targets. Here we identify and characterize one such target gene, a gene activated by the product of the homeotic gene Deformed. DNA binding assays and expression of reporter gene constructs indicate that activation of this gene requires a direct interaction between the Deformed protein and an upstream enhancer element at this target gene. However, although Deformed is required to activate this gene in cells of the maxillary segment, ectopically expressed Deformed does not activate the gene in other regions of the embryo. We conclude from this and other observations that additional factors may be required to activate the target gene, and, therefore, Deformed may participate in either a combinatorial or hierarchical activation signal in the maxillary cells. This newly identified gene encodes a novel protein of unknown function, though proteins with similar amino acid composition have been found. The pattern of transcript accumulation during embryogenesis indicates that this gene may be regulated by other homeoproteins in addition to Deformed.

scholarly journals Mutant Alleles of the Drosophila trithorax Gene Produce Common and Unusual Homeotic and Other Developmental Phenotypes

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 319-344
Author(s):  
Thomas R Breen
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Protein Isoforms ◽  
Homeotic Genes ◽  
Set Domain ◽  
Human Homologue ◽  
Terminal Set ◽  
Hypomorphic Alleles ◽  
Different Levels ◽  
Target Gene Transcription

Abstract trithorax (trx) encodes chromosome-binding proteins required throughout embryogenesis and imaginal development for tissue- and cell-specific levels of transcription of many genes including homeotic genes of the ANT-C and BX-C. trx encodes two protein isoforms that contain conserved motifs including a C-terminal SET domain, central PHD fingers, an N-terminal DNA-binding homology, and two short motifs also found in the TRX human homologue, ALL1. As a first step to characterizing specific developmental functions of TRX, I examined phenotypes of 420 combinations of 21 trx alleles. Among these are 8 hypomorphic alleles that are sufficient for embryogenesis but provide different levels of trx function at homeotic genes in imaginal cells. One allele alters the N terminus of TRX, which severely impairs larval and imaginal growth. Hypomorphic alleles that alter different regions of TRX equivalently reduce function at affected genes, suggesting TRX interacts with common factors at different target genes. All hypomorphic alleles examined complement one another, suggesting cooperative TRX function at target genes. Comparative effects of hypomorphic genotypes support previous findings that TRX has tissue-specific interactions with other factors at each target gene. Some hypomorphic genotypes also produce phenotypes that suggest TRX may be a component of signal transduction pathways that provide tissue- and cell-specific levels of target gene transcription.

scholarly journals MyDGR: a server for identification and characterization of diversity-generating retroelements

2019 ◽  
Vol 47 (W1) ◽  
pp. W289-W294 ◽  
Author(s):  
Fatemeh Sharifi ◽  
Yuzhen Ye
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Web Server ◽  
Nucleotide Sequences ◽  
Bacterial Genomes ◽  
Fasta Format ◽  
Reverse Transcriptases ◽  
Identification And Characterization ◽  
The Web

Abstract MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background MicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results Total RNA from milk exosomes was collected from healthy cows (n = 3, the control group) and S. aureus infected cows (n = 6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. The expression of two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2 fold changes (> 3.5) was significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

2019 ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results: Total RNA from milk exosomes was collected from healthy cows (n=3, the control group) and S. aureus infected cows (n=6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log 2 fold changes (>3.5) were significantly higher in mastitic milk infected with S. aureus. One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B, MLLT3, HP1BP3, NPR2 and PGM1) of bta-miR-185 were validated. Conclusion: DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

scholarly journals Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus

2019 ◽  
Author(s):  
Shaoyang Ma ◽  
Chao Tong ◽  
Eveline M. Ibeagha-Awemu ◽  
Xin Zhao
Keyword(s):  
Staphylococcus Aureus ◽  
Target Gene ◽  
Protein Transport ◽  
Target Genes ◽  
Bovine Milk ◽  
Differentially Expressed ◽  
Control Group ◽  
Mastitic Milk ◽  
Identification And Characterization

Abstract Background: MicroRNAs (miRNA) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected by Staphylococcus aureus (S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated. Results: Total RNA from milk exosomes was collected from healthy cows (n=3, the control group) and S. aureus infected cows (n=6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. Two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log 2 fold changes (>3.5) were significantly higher in mastitic milk infected with S. aureus. One target gene (V AT1L) of bta-miR-378 and five target genes (DYRK1B , MLLT3 , HP1BP3 , NPR2 and PGM1) of bta-miR-185 were validated. Conclusion: DE miRNAs in exosomes from normal and S. aureus infected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.

The Drosophila homeotic target gene centrosomin (cnn) encodes a novel centrosomal protein with leucine zippers and maps to a genomic region required for midgut morphogenesis

Development ◽  
1995 ◽  
Vol 121 (11) ◽  
pp. 3861-3876 ◽  
Author(s):  
J.G. Heuer ◽  
K. Li ◽  
T.C. Kaufman
Keyword(s):  
Leucine Zipper ◽  
Target Genes ◽  
Developmental Process ◽  
Coiled Coil ◽  
Regional Identity ◽  
Homeotic Genes ◽  
Structural Protein ◽  
Accumulation Pattern ◽  
Visceral Mesoderm

The products of the homeotic genes in Drosophila are transcription factors that are necessary to impose regional identity along the anterior-posterior axis of the developing embryo. However, the target genes under homeotic regulation that control this developmental process are largely unknown. We have utilized an immunopurification method to clone target genes of the Antennapedia protein (ANTP). We present here the characterization of centrosomin (cnn), one of the target genes isolated using this approach. The spatial and temporal expression of the cnn gene in the developing visceral mesoderm (VM) of the midgut and the central nervous system (CNS) of wild-type and homeotic mutant embryos is consistent with the idea that cnn is a homeotic target. In the VM, Antp and abdominal-A (abd-A) negatively regulate cnn, while Ultrabithorax (Ubx) shows positive regulation. In the CNS, cnn is regulated positively by Antp and negatively by Ubx and abd-A. Characterization of a cDNA encoding CNN predicts a novel structural protein with three leucine zipper motifs and several coiled-coil domains exhibiting limited homology to the rod portion of myosin. Immunocytochemical results demonstrate that the cnn encoded protein is localized to the centrosome and the accumulation pattern is coupled to the nuclear and centrosome duplication cycles of cleavage. In addition, evidence suggests that the expression of the cnn gene in the VM correlates with the morphogenetic function of Ubx in that tissue, i.e., the formation of the second midgut construction. The centrosomal localization of CNN and the involvement of microtubules in midgut morphogenesis suggest that this protein may participate in mitotic spindle assembly and the mechanics of morphogenesis through an interaction with microtubules, either directly or indirectly.

scholarly journals Regulation by Homeoproteins: A Comparison of Deformed-Responsive Elements

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 677-686
Author(s):  
Jeffrey A Pederson ◽  
James W LaFollette ◽  
Cornelius Gross ◽  
Alexey Veraksa ◽  
William McGinnis ◽  
...  
Keyword(s):  
Binding Sites ◽  
Target Genes ◽  
Gene Selection ◽  
Consensus Sequence ◽  
Cooperative Binding ◽  
Homeotic Genes ◽  
Specific Expression ◽  
Enhancer Element

Abstract Homeotic genes of Drosophila melanogaster encode transcription factors that specify segment identity by activating the appropriate set of target genes required to produce segment-specific characteristics. Advances in understanding target gene selection have been hampered by the lack of genes known to be directly regulated by the HOM-C proteins. Here we present evidence that the gene 1.28 is likely to be a direct target of Deformed in the maxillary segment. We identified a 664-bp Deformed Response Element (1.28 DRE) that directs maxillary-specific expression of a reporter gene in transgenic embryos. The 1.28 DRE contains in vitro binding sites for Deformed and DEAF-1. The Deformed binding sites do not have the consensus sequence for cooperative binding with the cofactor Extradenticle, and we do not detect cooperative binding to these sites, though we cannot rule out an independent role for Extradenticle. Removing the four Deformed binding sites renders the 1.28 DRE inactive in vivo, demonstrating that these sites are necessary for activation of this enhancer element, and supporting the proposition that 1.28 is activated by Deformed. We show that the DEAF-1 binding region is not required for enhancer function. Comparisons of the 1.28 DRE with other known Deformed-responsive enhancers indicate that there are multiple ways to construct Deformed Response Elements.

scholarly journals Tools for Characterization of Escherichia coli Genes of Unknown Function

2002 ◽  
Vol 184 (16) ◽  
pp. 4573-4581 ◽  
Author(s):  
Christophe Merlin ◽  
Sean McAteer ◽  
Millicent Masters
Keyword(s):  
Escherichia Coli ◽  
Target Gene ◽  
Target Genes ◽  
Functional Characterization ◽  
Phenotypic Characterization ◽  
Gene Encoding ◽  
Flp Recombinase ◽  
Short Scar

ABSTRACT Despite the power of sequencing and of emerging high-throughput technologies to collect data rapidly, the definitive functional characterization of unknown genes still requires biochemical and genetic analysis in case-by-case studies. This often involves the deletion of target genes and phenotypic characterization of the deletants. We describe here modifications of an existing deletion method which facilitates the deletion process and enables convenient analysis of the expression properties of the target gene by replacing it with an FRT-lacZ-aph-Plac -FRT cassette. The lacZ gene specifically reports the activity of the deleted gene and therefore allows the determination of the conditions under which it is actively expressed. The aph gene, encoding resistance to kanamycin, provides a selectable means of transducing a deleted locus between strains so that the deletion can be combined with other relevant mutations. The lac promoter helps to overcome possible polar effects on downstream genes within an operon. Because the cassette is flanked by two directly repeated FRT sites, the cassette can be excised by the Flp recombinase provided in trans. Removing the cassette leaves an in-frame deletion with a short scar which should not interfere with downstream expression. Replacements of yacF, yacG, yacH, yacK (cueO), yacL, ruvA, ruvB, yabB, and yabC made with the cassette were used to verify its properties.

Knockdown of calreticulin, laccase, and Snf7 Genes Through RNAi Is Not Effective to Control the Asian Citrus Psyllid (Hemiptera: Livideae)

2020 ◽  
Vol 113 (6) ◽  
pp. 2931-2940
Author(s):  
Jéssika Angelotti-Mendonça ◽  
Meire M Bassan ◽  
João Paulo R Marques ◽  
Pedro T Yamamoto ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Asian Citrus Psyllid ◽  
Diaphorina Citri ◽  
Transcript Accumulation ◽  
Citrus Industry ◽  
Murraya Paniculata ◽  
Knockdown Effect ◽  
Detached Leaves ◽  
Candidatus Liberibacter

Abstract The Asian citrus psyllid, Diaphorina citri Kuwayama, transmits the bacteria Candidatus Liberibacter associated with huanglongbing (HLB), a devastating disease of the citrus industry. The use of genetically modified plants is an alternative to control this vector. Conversely, technology based on RNA interference (RNAi) for silencing specific genes of a target insect could be attempted. This work evaluated the knockdown effect of the target genes calreticulin (DcCRT), laccase (DcLAC), and Snf7 (DcSnf7) by RNAi through feeding D. citri in Murraya paniculata leaves after the uptake of an aqueous solution with dsRNA homologous to each vector target gene. Confocal microscopy revealed the uptake of the fluorescent-labeled dsRNA by detached leaves and the symplastic movement, allowing the ingestion by the feeding insect. A reduction in the survival rate was observed only 144 h after the beginning of feeding with dsRNA targeting DcSnf7; however, no reduction in transcript accumulation. The knockdown of the DcCRT and DcLAC genes was detected only 12 and 96 h after insect feeding, respectively. Additionally, a reduction in amino acid excretion from insects fed with dsRNA targets to DcCRT and DcLAC was observed 120 h after the beginning of feeding. However, the effects of the dsRNAs tested here appear to be minimal, both at the transcriptional and phenotype levels. For most concentrations and time points, no effects were observed. Therefore, the knockdown of genes DcCRT, DcLAC, and DcSnf7 do not appear to have the potential to control of D. citri through RNAi-mediated gene silencing.

Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis

Development ◽  
1999 ◽  
Vol 126 (24) ◽  
pp. 5599-5609 ◽  
Author(s):  
A. Di Gregorio ◽  
M. Levine
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Ciona Intestinalis ◽  
Subtractive Hybridization ◽  
Flanking Sequence ◽  
Binding Assays ◽  
Specific Staining ◽  
Direct Target Gene ◽  
Direct Target

Brachyury is a sequence-specific transcriptional activator that is essential for notochord differentiation in a variety of chordates. In vertebrates, Brachyury is expressed throughout the presumptive mesoderm, but becomes restricted to the notochord at later stages of development. In ascidians, such as Ciona intestinalis, Brachyury is expressed exclusively in the notochord and does not exhibit an early pan-mesodermal pattern. Subtractive hybridization screens were recently used to identify potential Ciona Brachyury (Ci-Bra) target genes (Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R. W., Levine, M. and Satoh, N. (1999). Genes Dev. 13, 1519–1523). Of the genes that were identified in this screen, one corresponds to a new member of the tropomyosin superfamily, Ciona tropomyosin (Ci-trop). Here we show that Ci-trop is specifically expressed in the developing notochord beginning at gastrulation, and expression persists in the notochord during tailbud and tadpole stages. A 3 kb region of the Ci-trop 5′-flanking sequence was characterized via electroporation of lacZ fusion genes into fertilized Ciona eggs. A minimal, 114 bp enhancer was identified that is sufficient to direct the expression of a heterologous promoter in the notochord. DNA binding assays indicate that this enhancer contains two sets of low-affinity Brachyury half-sites, which are bound in vitro by a GST/Ci-Bra fusion protein. Deletion of the distal sites inactivates the notochord-specific staining pattern mediated by an otherwise normal Ci-trop/lacZ transgene. These results suggest that Ci-trop is a direct target gene of Ci-Bra and that Brachyury plays an immediate role in the cellular morphogenesis of the notochord.

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