Genomes analyses homeodomain sequences. Medical search. Frequent questions

Purpose: To determine the genetic basis of autosomal dominant cornea plana (CNA1) through the performance of a genome-wide linkage analysis and screening of the decorin (DCN), dermatan sulfate proteoglycan 3 (DSPG3), forkhead box C1 (FOXC1), keratocan (KERA), lumican (LUM,) and paired-like homeodomain transcription factor 2 (PITX2) genes in members of an affected multigenerational family. (llu.edu)
The absence of genomic resources renders the search for paralogous cuttlefish genes dependent upon the presence of highly conserved protein motifs within genes of interest, thus we used a degenerate primer strategy to isolate partial coding sequence from the conserved domains specific to these families. (europa.eu)
Spatial expression analysis of both genes revealed that Sof-RXR is expressed ubiquitously in all cells of the embryo, including the chondrocytes, whereas Sof-ALDH was expressed only in a sub-set of epithelial cells and no expression at the level of chondrocytes was observed. (europa.eu)
Using SVS software for their statistical analysis for genetic association as well as haplotype association, the team used the results of their study to provide evidence of genetic association of widely used SNV's in both genes with PCOS in this Tunisian population, suggesting they are good markers for PCOS in this region of the world. (goldenhelix.com)
SVS was used to filter and prioritize candidate genes in their WES analysis, which was based on the Human Genome annotation, GRCh37/hg19. (goldenhelix.com)
In this study, 23 HD-Zip genes distributed on 6 chromosomes were identified from the peach ( Prunus persica ) genome, and named PpHDZ01-23 according to their positions on the chromosomes. (biomedcentral.com)
Time-series analysis of whole-genome expression data during Drosophila melanogaster development indicates that up to 86% of its genes change their relative transcript level during embryogenesis. (nih.gov)
The ms4 locus was fine mapped to a 216 kb region, which contains 23 protein-coding genes including Glyma.02G243200 , an ortholog of Arabidopsis MALE MEIOCYTE DEATH 1 ( MMD1 ), which is a Plant Homeodomain (PHD) protein involved in male fertility. (biomedcentral.com)
Mutant analysis revealed complex genetic interactions between FLK and several major SA pathway genes. (nsf.gov)
RNA sequencing experiments indicated that >7000 genes are mis‐expressed in the Mting2‐1 mutant, consistent with its strong mutant phenotypes. (nsf.gov)
Genetic analysis of plant architecture has led to the discovery of key genes that function in meristems, including the maize ( Zea mays ) transcription factor knotted1 ( kn1 ), the founding member of the kn1 homeobox ( knox ) gene family (Vollbrecht et al. (grassius.org)
The presence of a homeodomain (HD), which comprises 60 amino acids, makes a three-helix tertiary structure, that binds the promoter regions of specific target genes (Sharif et al. (grassius.org)
Since the discovery of the Kn1 gene, a large number of transcription factor (TF) genes encoding proteins with homeodomains have been found in all plants and there are about 135 family members in maize. (grassius.org)
Large tumor genome sequencing projects have now uncovered a few hundred genes involved in the onset of tumorigenesis, or drivers, in some two dozen malignancies. (biomedcentral.com)
The catalog of driver genes involved in the development of several malignancies has grown in recent years, as a result of whole-exome and whole-genome analyses of cohorts of tumors, mainly within the framework of large international consortia [ 3 , 4 ]. (biomedcentral.com)
There are two main reasons why the catalogs of cancer drivers produced by the aforementioned projects and others need to be broken down into related sets of genes for deeper analysis. (biomedcentral.com)
NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. (gao-lab.org)
Expression analysis of several Hox genes in human embryos. (cnr.it)
Isolation of the murine homologs of the otd and ems homeobox containing genes and analysis of their expression during brain development. (cnr.it)
In this study, we identified 22 ZF-HD genes in the tomato genome and classified them into seven groups located on six chromosomes. (ashs.org)
Based on previous phylogenetic analyses in arabidopsis ( Arabidopsis thaliana ), our results showed that some tomato SL-ZH ( S. lycopersicum zinc-finger homeodomain) genes cluster into the same neighbor-joining (NJ) branch as arabidopsis, indicating that these genes may share similar structures and functions in these plants. (ashs.org)
Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. (lookformedical.com)
The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS. (lookformedical.com)
The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. (cam.ac.uk)
Many of these pattern-forming genes encode DNA binding proteins that regulate each others expression, and subsequently instruct the rest of the genome in a manner appropriate to each position in the organism. (jefferson.edu)
Mutational analysis of two positional candidate susceptibility genes for bipolar disorder on chromosome 12q23-q24: phenylalanine hydroxylase and human LIM-homeobox LHX5. (wikigenes.org)

The predicted protein sequence contained a highly conserved homeodomain and the WUS-box domain, which is present in some members of the WOX protein family. (gc.ca)
Both predicted proteins are highly conserved with other known homologous sequences, with the exception of two small domains present only in the Sof-RXR. (europa.eu)
HD-Zip protein usually contain two highly conserved domains: homeodomain (HD) and leucine zipper (LZ) [ 1 ]. (biomedcentral.com)

The homeodomain transcription factor EMX2 is critical for central nervous system and urogenital development. (wikipedia.org)
HD-Zip transcription factors belong to the Homeodomain (HD) transcription factor superfamily and are only found in plants. (biomedcentral.com)
The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome. (biomedcentral.com)

With no known attempts to investigate the heritable factors using next generation sequencing (NGS) and whole exome sequencing (WES), a research team from Mexico endeavored to better understand the genetic basis of the defect in a family with a recurrence of gastroschisis. (goldenhelix.com)

The homeodomain domain is generally composed of about 60 amino acids encoded homeobox, which form three alpha helices. (biomedcentral.com)
A homeobox (HB) encodes a protein domain, the homeodomain (HD), which is a conserved 60-amino acid motif present in transcription factors found in all the eukaryotic organisms. (gao-lab.org)
Isolation and expression analysis both in invertebrate and vertebrate embryos of a new homeobox containing gene named Orthopedia (Otp). (cnr.it)
Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)

Alliance of Genome Resources Consortium. (caltech.edu)
2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)

Although a controversial topic, the team intends to take advantage of recent advancements in next generation sequencing to assist with selecting embryos for implantation to prevent early life fatal genetic conditions which adversely affect the quality of life of the afflicted individuals and their families. (goldenhelix.com)
The genome contains all the genetic information of a given organism. (oist.jp)
By decoding genomes of target marine organisms (mainly invertebrates), we wish to understand genetic and developmental mechanisms underlying diversity of marine organisms. (oist.jp)
Our understanding of the landscape of pediatric cancer genomics has improved markedly in the past 20 years with the advent of next generation sequencing and other high throughput genetic sequencing. (medscape.com)
For a genetic analysis of the inheritance of behavior, the genetic tools were simply not available at that time. (balzan.org)
DNA methylation is considered a "soft" and potentially reversible change to the genome that can define or adapt to tumor biology and is functionally equivalent to genetic changes like mutation or deletion ( Kulis and Esteller, 2010 ). (frontiersin.org)
Recently, genome-wide association studies (GWAS) performed in populations of European-descent have identified several genetic variants associated with AF [ 3 ]. (e-arrhythmia.org)

These 23 PpHDZ transcription factors all contained a homeomorphism box domain and a leucine zipper domain, were divided into 4 subfamilies(I-IV) according to the evolutionary analysis, and their promoters contained many different cis-acting elements. (biomedcentral.com)

In addition, we use bioinformatic analysis across twelve Drosophila genomes to identify putative cis-regulatory sequences that may be capable of facilitating specific promoter-enhancer interactions at the bithorax complex and propose a model for their molecular function during development. (nih.gov)
Isolation and expression analysis in murine embryos of Dlx5 and Dlx6, two murine homologues of the Drosophila Distal-less gene. (cnr.it)
Mutations in the gene for the antennapedia homeodomain protein are associated with the conversion of antenna to leg or leg to antenna DROSOPHILA. (lookformedical.com)

2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)

PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)

The sequence consisted of 2045 bp, and contained an open reading frame (ORF), encoded 322 amino acids. (gc.ca)

Phylogenetic analysis suggested that Ae. (gc.ca)
Gene identity was determined initially based upon BLAST similarity and confirmed by phylogenetic analysis. (europa.eu)
Phylogenetic analysis showed presence of a homolog protein (MS4_homolog) encoded by the Glyma.14G212300 gene. (biomedcentral.com)

The comparative expression analysis of Ms4 and Ms4_homologs across the soybean developmental and reproductive stages showed significantly higher expression of Ms4 in early flowering (flower bud differentiation) stage than its homolog. (biomedcentral.com)
The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental processes in plants, such as embryonic patterning, stem-cell maintenance and organ formation. (gao-lab.org)
Transcription factors (TFs), which bind to specific nucleotide sequences, have been shown to play important roles in the regulatory networks of numerous developmental processes in plants. (ashs.org)
Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL). (lookformedical.com)
Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. (cam.ac.uk)

Massively parallel experimental assays, particularly DNA microarrays and sequencing, have revolutionized genomics research in the last decades. (nature.com)
Since 2009, the Marine Genomics Unit (MGU) has conducted research in the realm of genome-based biological sciences. (oist.jp)
Additionally, translational genomics and genome editing technologies can be utilized to generate new male-sterile lines in other plant species. (biomedcentral.com)

Current work in the laboratory is focused on understanding two major aspects of nuclear genome regulation in eukaryotic organisms that affect genome organization in 3 dimensions. (jefferson.edu)

In this study, a putative WOX2 homolog was isolated and characterized from Aegilops tauschii, the donor of D genome of Triticum aestivum. (gc.ca)
The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. (bvsalud.org)

TP53 encodes the protein p53, which is known as the "guardian of the genome. (medscape.com)
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. (sdbonline.org)

The molecular mass of the expressed protein was identical to that predicted by the cDNA sequence. (gc.ca)

Along with the core binding motif, the flanking sequence context can play a role in DNA-TF recognition. (bvsalud.org)
The binding sequences for each factor were aligned by using the motif-assembly program, and the binding specificities of each factor were modeled with position weight matrices (PWMs). (sdbonline.org)
The sequence variant rs2106261 is an intronic SNP located in the ZFHX3 gene, also called AT motif-binding factor 1 ( ATBF1 ), on chromosome 16q22, and was highly associated with AF in a Chinese GeneID study [ 8 ]. (e-arrhythmia.org)

With the help of VarSeq software for the single nucleotide polymorphism (SNP) and indel analysis, they classified the variants according to ACMG standards and guidelines. (goldenhelix.com)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)
It is also called nucleotide sequence. (lookformedical.com)

We are using state-of-the-art next generation sequencing combined with bioinformatic strategies, and developing stem cell-based approaches for gene therapy and drug discovery. (nih.gov)

None of the identified sequence variants demonstrated complete segregation with the affected phenotype in the pedigree. (llu.edu)
Multivariate Cox regression analysis showed that persistent AF (OR 1.677, 95% CI 1.176-2.381, p =0.004) and the number of variants (OR 1.552, 95% CI 1.099-2.222, p =0.015) were independent predictors for recurrence of AF. (e-arrhythmia.org)

A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. (grassius.org)

In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. (nature.com)
High-throughput sequencing-RNA affinity profiling (HiTS-RAP) 22 is conceptually similar to RNA-MaP, but uses the E. coli replication terminator protein Tus to stall the RNA polymerase after transcribing the variable section of the DNA library. (nature.com)
Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). (bvsalud.org)

A genome-wide linkage analysis did not indicate or exclude linkage to the region on chromosome 12 to which CNA1 has been previously mapped, and did not provide a single or multipoint LOD score greater than 2.0 for any of the 400 microsatellite markers. (llu.edu)
Chromosome Architecture and Gene Regulation by Chromatin Insulators, Epigenetic Gene Regulation by Polycomb-group Proteins, and Cooperative DNA binding by Sequence-specific Transcription Factors. (jefferson.edu)
The second aspect of genome regulation that we study is the organization of chromosomal loops by chromatin insulators, which impacts several chromosome functions. (jefferson.edu)

These regulatory modules include promoters, insulators, silencers, enhancers, promoter targeting sequences and the recently identified promoter tethering element (PTE). (nih.gov)
This is a major function of insulators in eukaryotic genomes, to stabilize boundaries between repressive and active chromatin. (jefferson.edu)

Isolation and sequencing of Glyma.02G243200 from the ms4 mutant line showed a single base insertion in the 3rd exon causing a premature stop codon resulting in truncated protein production. (biomedcentral.com)
The KDM5A (JARID1A) sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain. (atlasgeneticsoncology.org)

Once considered a unique feature of vertebrate patterning, components of the retinoic acid (RA) signalling pathway, including both RA and the retinoid (RX) class of receptors, have been found within invertebrate genomes. (europa.eu)

molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
Decoding the genome therefore provides the molecular basis for understanding every biological phenomenon. (oist.jp)
Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. (oist.jp)

We have performed comprehensive analysis of homeodomain and Cys2His2 zinc finger specificities in D. melanogaster - (fruit fly) in collaboration with Michael Brodsky (UMMS-MCCB) & Gary Stormo (Wash. U). We have coupled this data with specificity data from artificial zinc fingers and homeodomains that we have selected using our bacterial one-hybrid system. (umassmed.edu)
This dataset can also be used to broadly predict the specificity of homeodomains ( http://stormo.wustl.edu/flyhd/ ) and zinc fingers ( http://stormo.wustl.edu/ZFModels/ ). (umassmed.edu)
The zinc finger-homeodomain (ZF-HD) TFs, containing a conserved zinc finger (ZF) domain in the N-terminal and a homeodomain (HD) in the C-terminal. (grassius.org)
Members of the zinc-finger homeodomain (ZF-HD) family play a key role in the control of plant growth and development, which are involved in plant responses to stress. (ashs.org)

The first step in this process is the identification of regions of the genome that contain regulatory information. (sdbonline.org)

HD-Zips (Homeodomain-Leucine Zippers) are a class of plant-specific transcription factors that play multiple roles in plant growth and development. (biomedcentral.com)
1991). The maize Kn1 gene was found to encode a homeodomain-containing protein, the first identified in the plant kingdom. (grassius.org)
PHD: plant homeodomain fingers or LAP domains. (atlasgeneticsoncology.org)

Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. (biomedcentral.com)

Australian researchers performed a pilot study to test the value of whole genome sequencing (WGS) intended to aid in embryo selection in high-risk couples engaged in in vitro fertilization (IVF) treatment. (goldenhelix.com)
In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. (bvsalud.org)
The MtING2 PHD finger bound H3K4me2/3 peptides weakly in vitro , but analysis of gene‐edited mutants indicated that it was dispensable to MtING2 function in wild‐type plants. (nsf.gov)

Dr. Koki Nishitsuji(middle left) and Dr. Asuka Arimoto(left) were awarded the Research Encouragement Prize of Okinawa 2019 as recognition for their contribution to Okinawa for their work on deciphering the genomes of many algal crops, including Okinawa mozuku and Umi-budo. (oist.jp)
Here, we report results of jellyfish genomes, which was published in Nature Ecology and Evolution 3:811-822 (2019) with cover photo of the journal. (oist.jp)

However, they do not simultaneously and directly measure the affinity parameters relevant to biological function and are biased towards strongly binding sequences. (nature.com)

Epigenetics acts through two mechanisms: (1) modifications to chromosomal proteins that alter the 3D conformation of the genome and/or protein-DNA interactions and (2) chemical modification of the DNA strand itself ( Kondo, 2009 ). (frontiersin.org)

We further decoded genomes of hemichordates and a brachiopod in 2015, a brown alga (Okinawa-mozuku) in 2016, Crown-Thorns-Starfish in 2017, and a nemertean, phoronid, and two dinoflagellate clades in 2018. (oist.jp)

Microsatellite genotyping was used for haplotype analysis. (molvis.org)

Based on their sequence conservation and functional properties, HD-ZIP can be further divided into four subfamilies (HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV) (Sharif et al. (grassius.org)

In addition, no pathogenic sequence variations were found in DCN, DSPG3, LUM, PITX2 and FOXC1, which have also been implicated in corneal and anterior segment dysgenesis. (llu.edu)

Marburg virus (MARV) is a lipid-enveloped virus harboring a negative sense RNA genome, which has caused sporadic outbreaks of viral hemorrhagic fever in Sub-Saharan Africa. (uci.edu)
Given that we previously defined the viral np9 gene, which is aberrantly activated in human leukemia, as a potent oncogene [ 1 ], we next attempted to search for cellular homologs of the viral oncogene np9 in NCBI database by performing alignment using Np9 protein sequence. (aging-us.com)

Recent global analyses of gene transcripts revealed that specific transcription factors (TFs) and their networking systems physiologically correspond to the onset of human diseases, including cancer. (intechopen.com)
Creating more precise CRISPR/Cas9 nucleases for gene therapy - We are utilzing our expertise in protein engineering and protein-DNA recognition to create hybrid CRISPR/Cas9 nucleases to achieve single-site cleavage precision within the human genome. (umassmed.edu)
Human endogenous retroviruses (HERVs) have resided in the human genome for several million years and makes up 8% of the human genome [ 1 - 4 ]. (aging-us.com)
How do numerous non-coding variations in the human genome affect gene expression in the retina? (nih.gov)
Expression analysis of the human Hox Complex in teratocarcinoma cells (N-tera2/D1) upon treatment with retinoic acid and the definition of temporal colinearity concept. (cnr.it)

While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. (bvsalud.org)
Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. (bvsalud.org)

Initial genome sequencing and analysis of multiple myeloma. (uchicago.edu)

However, the cis-regulatory sequence controlling this posterior expression pattern has not been precisely identified. (sdbonline.org)
We and others have shown that these regulatory systems have a major impact on the packaging and utilization of the genome. (jefferson.edu)

Relative levels of gene expression throughout development were determined by quantitative polymerase chain reaction (PCR) analysis and in cases where sufficient specific gene sequence was acquired, ribonucleic acid (RNA) probes were generated to evaluate the spatial expression patterns during the period of organogenesis. (europa.eu)
New genome editing approaches development using artificial nucleases (TALEN and CRISPR/Cas9). (viaf.org)
Combined expression analysis of Otx, Emx, Dlx and Otp during development and definition of brain segmentary identities. (cnr.it)

Anatomy8

Organisms20

Diseases1

Chemicals and Drugs41

Analytical, Diagnostic and Therapeutic Techniques and Equipment26

Phenomena and Processes89

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science14

Health Care1

Genes28

Highly conserved3

Transcription factor4

Whole exome1

Homeobox4

Alliance of Genome Resources2

Genetic7

Leucine zipper1

Drosophila3

20221

Mutations1

Amino acids1

Phylogenetic3

Developmental5

Genomics3

Organisms1

Putative2

Encodes2

CDNA1

Motif3

Nucleotide3

Bioinformatic1

Variants2

Proteins encoded1

High-throughput3

Chromosome3

Insulators2

Exon2

Invertebrate1

Molecular3

Zinc4

Identification1

Plant3

Interacts1

Vitro3

20192

Affinity1

Chromosomal1

20181

Haplotype1

Subfamilies1

Pathogenic1

Viral2

Human5

Modulate2

Initial1

Regulatory2

Development3