• 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)
  • NOTE: features (genes or exons) that are only partially contained within the sequence are completely excluded. (uu.nl)
  • 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)
  • Candidate clusters are cloned into reporter genes, transformed into the genome, and tested for in vivo activity by in situ hybridization experiments. (nyu.edu)
  • 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)
  • The genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. (nih.gov)
  • The changes provide powerful assays for identifying the trans -acting factors that regulate the homeotic genes and the cis -acting sequences through which they act. (nih.gov)
  • Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. (biomedcentral.com)
  • 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)
  • The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
  • Bicoid is a homeodomain-containing transcription factor that is expressed in a long-range anterior gradient in the early embryo (Figure 2). (nyu.edu)
  • HD-Zip transcription factors belong to the Homeodomain (HD) transcription factor superfamily and are only found in plants. (biomedcentral.com)
  • 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)
  • A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. (biomedcentral.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)
  • 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)
  • Antennapedia homeodomain protein. (lookformedical.com)
  • Antennapedia homeodomain protein is a homeobox protein involved in limb patterning in ARTHROPODS. (lookformedical.com)
  • 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)
  • HD-Zip protein usually contain two highly conserved domains: homeodomain (HD) and leucine zipper (LZ) [ 1 ]. (biomedcentral.com)
  • TP53 encodes the protein p53, which is known as the "guardian of the genome. (medscape.com)
  • The 14/SATB1 monoclonal antibody specifically binds to the special AT-rich sequence binding protein 1 that is encoded by the SATB1 (SATB homeobox 1) gene. (bdbiosciences.com)
  • SATB1 is a homeodomain MAR binding protein. (bdbiosciences.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)
  • 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)
  • 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)
  • The homeodomain domain is generally composed of about 60 amino acids encoded homeobox, which form three alpha helices. (biomedcentral.com)
  • We used this information to develop the BrassicaEDB, including eFP, Treatment, Coexpression, and SRA Project modules based on gene expression profiles and Gene Feature, qPCR Primer, and BLAST modules based on gene sequences. (preprints.org)
  • Human genomic databases including The Cancer Genome Atlas (TCGA) were interrogated to identify DPP9 LoF variants and associated cancers. (preprints.org)
  • It recognizes ATC sequences that consist of stretches of A's, T's, and C's on one DNA strand. (bdbiosciences.com)
  • 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)
  • 2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)
  • We then extended these sequences in both directions using rapid-amplification of complementary deoxyribonucleic acid (c-DNA) ends (RACE) to obtain full length transcripts, all of which will be deposited in the public database GenBank. (europa.eu)
  • 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)
  • Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
  • However, they do not simultaneously and directly measure the affinity parameters relevant to biological function and are biased towards strongly binding sequences. (nature.com)
  • While collecting an ever-growing number of Bcd-dependent elements, we are using data mining techniques to identify sequence motifs or binding site arrangements that correlate with target gene positioning. (nyu.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)
  • By decoding genomes of target marine organisms (mainly invertebrates), we wish to understand genetic and developmental mechanisms underlying diversity of marine organisms. (oist.jp)
  • 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)
  • Quantitative analysis of RNA on a massively parallel array (RNA-MaP) 21 , 23 starts with ssDNA sequencing libraries including an RNA polymerase promoter region, a stall sequence, and a variable region complementary to the desired RNA. (nature.com)
  • Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. (biomedcentral.com)
  • 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)
  • The genome contains all the genetic information of a given organism. (oist.jp)
  • Recently, genome-wide association studies (GWAS) performed in populations of European-descent have identified several genetic variants associated with AF [ 3 ]. (e-arrhythmia.org)
  • molecular studies are difficult due to the absence of genome sequence data for any cephalopod. (europa.eu)
  • 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)
  • We examined the consequences of CTCF depletion in immortalised human and mouse cells using shRNA knockdown and CRISPR/Cas9 genome editing and examined the growth and development of heterozygous Ctcf ( Ctcf +/- ) mice. (preprints.org)
  • 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)
  • This 60-amino acid sequence folds into a characteristic three-helix structure that is able to interact specifically with DNA. (gao-lab.org)
  • The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)
  • 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)
  • Improving delivery systems for CRISPR/Cas9 nucleases for therapeutic applications - We are collaborating the the Khvorova, Sontheimer and Watts laboratories (UMMS-RTI) to improve delivery systems for CRISPR-Cas nucleases in the context of the NIH Somatic Cell Genome Editing program . (umassmed.edu)
  • The gene with 5 kb flanks (if sufficient flanking sequence is available). (uu.nl)
  • 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)
  • We are currently attempting to identify the cis -regulatory DNA sequences in the Scr that are required for Polycomb-group silencing in the second and third legs. (nih.gov)
  • 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)
  • 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)
  • 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)
  • And the arrangement of the three helices determines the difference in the specific binding of homeodomain to DNA. (biomedcentral.com)
  • After the DNA library is sequenced on the Illumina flow cell, it is enzymatically double stranded by extension of a 5′ biotinylated primer. (nature.com)
  • Using this information we can build simple qualitative models of recognition that allow the design of homeodomains with novel DNA-binding specificity. (umassmed.edu)