• 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)
  • Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
  • 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)
  • The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. (cam.ac.uk)
  • 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)
  • In this study, we first identified all the CAMTA homologous genes in the whole genome of maize. (frontiersin.org)
  • Most of these hearing loss genes have been detected using classical genetic methods, typically starting with linkage analysis in large families with hereditary hearing loss. (biomedcentral.com)
  • Eighty known hearing loss genes were selected and simultaneously sequenced by targeted next-generation sequencing (NGS) in 8 Korean families with autosomal dominant non-syndromic sensorineural hearing loss. (biomedcentral.com)
  • However, there are 54 candidate chromosomal loci at which causative genes have not yet been identified, although classical genetic studies such as linkage analysis have predicted that these loci contain novel hearing loss-associated genes (Hereditary Hearing loss Homepage, http://hereditaryhearingloss.org ). (biomedcentral.com)
  • Due to the limitation of the Sanger sequencing method, which is highly expensive and time-consuming, it has been difficult to sequence the hundreds of genes in these candidate chromosomal loci. (biomedcentral.com)
  • However, there have been no reports of the detection of pathogenic mutations by screening candidate hearing loss genes in small families without using linkage analysis. (biomedcentral.com)
  • Therefore, based on the hypothesis that causative mutations of hearing loss are more likely to exist in known hearing loss associated-genes than in novel genes, we performed exon capture and resequencing using Illumina library generation and Solexa sequencing methods. (biomedcentral.com)
  • We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. (preprints.org)
  • Enriched pathways analysis of these positively correlated genes featured Toll-like receptor and SUMOylation pathways. (preprints.org)
  • During productive infection, the 152-kb double-stranded HSV-1 genome is rapidly translocated to the nucleus where at least 80 viral genes are transcribed by the host cell RNA polymerase II (Pol II) [ 1 ]. (biomedcentral.com)
  • Sequences of previously described binding sites were collected for these five factors present in the cis-regulatory regions of known target genes. (sdbonline.org)
  • 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)
  • 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)
  • We focus our attention on three families of transcription factors that are known to have roles in vertebrate chondrogenesis: Sox and the Ant- and Prd- class families of the homeodomain proteins. (europa.eu)
  • 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)
  • The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.com)
  • As the authors point out, the function of approximately 40-50% of the proteins encoded by each genome cannot be determined on the basis of similarities to proteins of known function. (biomedcentral.com)
  • 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 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)
  • 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 comparative study based on four fully sequenced eukaryotic genomes has revealed profound differences in the sets of transcription factors used by plants, fungi and animals. (biomedcentral.com)
  • With the completed genome sequences of Saccharomyces cerevisiae (budding yeast), Caenorhabditis elegans and Drosophila melanogaster , complete proteomes from representatives of three eukaryotic kingdoms (plants, fungi and animals) are now available for comprehensive comparative studies. (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)
  • This is a major function of insulators in eukaryotic genomes, to stabilize boundaries between repressive and active chromatin. (jefferson.edu)
  • 2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)
  • 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)
  • 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)
  • 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)
  • The homeodomain transcription factor EMX2 is critical for central nervous system and urogenital development. (wikipedia.org)
  • The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
  • HD-Zip transcription factors belong to the Homeodomain (HD) transcription factor superfamily and are only found in plants. (biomedcentral.com)
  • 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)
  • HD-Zip protein usually contain two highly conserved domains: homeodomain (HD) and leucine zipper (LZ) [ 1 ]. (biomedcentral.com)
  • We introduced the human missense mutation into the orthologous position of the mouse Gjc2 gene and inserted the mCx47M282T coding sequence into the mouse genome via homologous recombination in embryonic stem cells. (prolekarniky.cz)
  • 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 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 include gene expression (by either facilitating or blocking interactions between enhancers and promoters), DNA recombination and repair (by influencing which linearly distant DNA sequences are accessible to each other and which are not), chromatin compaction during mitosis and meiosis, and epigenetic maintenance of gene expression. (jefferson.edu)
  • Therefore, it has been nearly impossible to identify the precise pathogenic mutations in affected individuals from small families who cannot be examined either through linkage analysis or standard capillary sequencing analysis. (biomedcentral.com)
  • Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
  • Using F 2 and BC 1 populations constructed from a cross between nps and '9930', the genetic analysis showed that the nps trait is controlled by a single recessive nuclear gene. (biomedcentral.com)
  • For a genetic analysis of the inheritance of behavior, the genetic tools were simply not available at that time. (balzan.org)
  • 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)
  • However, these classical strategies are not well suited for mutation analysis in smaller families who have insufficient genetic information. (biomedcentral.com)
  • These regulatory modules include promoters, insulators, silencers, enhancers, promoter targeting sequences and the recently identified promoter tethering element (PTE). (nih.gov)
  • 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)
  • Sequence analysis showed that only one single nucleotide mutation (C → T) between 9930 and nps was found in the second exon of Csa3G748220 , a plant-specific class I HD-Zip gene. (biomedcentral.com)
  • Exon shuffling has led to transcription factors unique to plants that contain both homeodomains and leucine zippers. (biomedcentral.com)
  • 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)
  • 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)
  • We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). (preprints.org)
  • 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)
  • The first DNA sequence of a cephalopod was published in 1983 and the first molecular paper focusing on cephalopods was published in 1994. (tonmo.com)
  • Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. (biomedcentral.com)
  • Human genomic databases including The Cancer Genome Atlas (TCGA) were interrogated to identify DPP9 LoF variants and associated cancers. (preprints.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)
  • 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)
  • Gene identity was determined initially based upon BLAST similarity and confirmed by phylogenetic analysis. (europa.eu)
  • The full-length US11 gene, which is composed of 459 bp (base pairs) and predicted to encode a protein of 152 amino acids, was amplified successfully from the HSV-1 (strain F) genome (Figure 1 , lane 1). (biomedcentral.com)
  • A detailed microscopic investigation has revealed how wild-type fungal hyphae, of the sequenced strain PH-1, colonised susceptible wheat ears and spread from spikelet to spikelet. (rothamsted.ac.uk)
  • 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)
  • The homeodomain domain is generally composed of about 60 amino acids encoded homeobox, which form three alpha helices. (biomedcentral.com)
  • Survival and gene signature analyses were performed on hepatocellular carcinoma (HCC) data. (preprints.org)
  • 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)
  • 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)
  • 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)
  • Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. (bvsalud.org)
  • 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 resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cells. (bvsalud.org)
  • 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)
  • Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes. (bvsalud.org)
  • The first step in this process is the identification of regions of the genome that contain regulatory information. (sdbonline.org)
  • 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)
  • Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. (bvsalud.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)
  • And the arrangement of the three helices determines the difference in the specific binding of homeodomain to DNA. (biomedcentral.com)
  • determined the entire complement of these regulators encoded by all four genomes. (biomedcentral.com)
  • Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. (bvsalud.org)
  • 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)
  • Next-generation sequencing (NGS) can overcome these limitations through its ability to perform parallel sequencing of billions of nucleotides at a low cost and high speed[ 1 - 4 ]. (biomedcentral.com)
  • Trichomes are excellent model systems for the analysis of cell differentiation and play essential roles in plant protection. (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)
  • We also improved the Ciona intestinalis genome to be nearly complete one. (oist.jp)
  • In this paper, we determined the complete mitochondrial genome of Octopus conispadiceus (Cephalopoda: Octopodidae). (tonmo.com)
  • 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)
  • We also analysed the impact of CTCF haploinsufficiency by examining gene expression changes in CTCF -altered endometrial carcinoma. (preprints.org)