GenesPaired-like homeodomain transcriptionProteinsAnnotationProteinChromosomeTranscription factorsHomeoboxMutationsChromosomalWhole exome2002ExonEncodesGeneticChromatinREGULATIONNCBI2022VariantsLociVertebrateHumanInsulatorsSubsetsGene SequencesBioinformaticSpecificityEmbryoAnalysisRegulatoryApproachesViralRegionsAmino acidTargetsNext generationMolecularDevelopmentNucleotideCloneResultsExpressionFamilies
Genes19
- 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)
- Subsequent analysis using targeted bisulfite massive parallel sequencing showed hypermethylation of the promoters of specific genes in miscarriages with trisomy 16 but not miscarriages with other aneuploidies. (bvsalud.org)
- 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)
- Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.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)
- The CsNps was located at a 13.4-kb genomic region on chromosome 3, which region contains three predicted genes. (biomedcentral.com)
- NRL interacts with homeodomain protein CRX and numerous other regulatory factors to control expression of most rod-expressed genes. (nih.gov)
- 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)
- 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)
- As a scientist she has been involved in mapping the human genome and identifying genes and mutations, which give rise to heritable disorders. (bepress.com)
- Gene transcription is mainly regulated by transcription factors (TFs) that bind to specific DNA sequences (called motifs) located in the promoter regions of genes [ 1 ]. (biomedcentral.com)
- 2016. An Isogenic Human ESC Platform for Functional Evaluation of Genome-wide-Association-Study-Identified Diabetes Genes and Drug Discovery. . (cornell.edu)
- 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)
- 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)
- 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)
- In this study, we first identified all the CAMTA homologous genes in the whole genome of maize. (frontiersin.org)
Paired-like homeodomain transcription1
- The PITX gene encode the paired-like homeodomain transcription factor family. (nature.com)
Proteins10
- 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)
- Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL). (lookformedical.com)
- The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.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)
- Interleukin-10 expression in macrophages during phagocytosis of apoptotic cells is mediated by homeodomain proteins Pbx1 and Prep-1. (cornell.edu)
- The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. (beds.ac.uk)
- The C-terminal domain shows strong sequence similarity to human, frog, and yeast Orc4 proteins, including conserved ATP-binding motifs. (embl.de)
- We have classified these motifs into three types according to their sequence similarity and have found that they are prevalent in many eukaryotic nuclear proteins in single or multiple copies. (embl.de)
- Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). (embl.de)
Annotation1
- 2022). Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. (caltech.edu)
Protein9
- 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)
- 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)
- Using pattern searches and position-dependent matrices, we have extracted the AT-hook motifs present in a non-redundant protein sequence database. (embl.de)
- PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
- One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
Chromosome4
- 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)
- Previously, we developed statistical tools to identify association between the sites of provirus establishment and chromosome marks - as determined by chromatin immuno-precipitation with massively parallel DNA sequencing (ChIPSeq) [ 18 , 19 ]. (biomedcentral.com)
- 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)
- HG975520.1 Solanum lycopersicum chromosome ch08, complete genome. (gao-lab.org)
Transcription factors1
- By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, genomic regions containing unusually high concentrations of predicted binding sites were identified for these factors. (sdbonline.org)
Homeobox1
- The homeobox transcription factor HOXC13 upregulates human papillomavirus E1 gene expression and contributes to viral genome maintenance. (nih.gov)
Mutations2
- Cancer genome sequencing reveals diverse acquired mutations in CTCF , which we have shown, functions as a tumour suppressor gene. (preprints.org)
- 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)
Chromosomal1
Whole exome2
- 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)
- performed whole-exome sequencing in a Palestinian family with hereditary hearing loss and identified a novel mutation in the gene, GPSM2 , which had been hidden in the autosomal recessive hearing loss locus (DFNB32) first identified by Masmoudi et al. (biomedcentral.com)
20022
- PWMs are a useful way to represent binding specificities and provide a statistical framework for searching for novel instances of the motif in genome sequences (Berman, 2002). (sdbonline.org)
- Release of the drosophila sequence was in 2002 ( link ). (bcm.edu)
Exon2
- The KDM5A (JARID1A) sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain. (atlasgeneticsoncology.org)
- 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)
Encodes1
- 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)
Genetic8
- 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)
- Recently, genome-wide association studies (GWAS) performed in populations of European-descent have identified several genetic variants associated with AF [ 3 ]. (e-arrhythmia.org)
- In Arabidopsis , as giant single epidermal cells, trichomes have become an excellent model system to study cell differentiation and development because it is easy to analyze them at the genetic, genomic and cell biology levels. (biomedcentral.com)
- We are analyzing how long-range repression and activation occur over an entire genetic locus, even skipped ( eve ), and its genomic neighborhood, through the regulation of chromatin structure. (jefferson.edu)
- Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. (bcm.edu)
Chromatin2
- This is a major function of insulators in eukaryotic genomes, to stabilize boundaries between repressive and active chromatin. (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)
REGULATION2
- 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)
- Regulation of actin dynamics and analysis of genomic influences on actin function. (upstate.edu)
NCBI1
- Flybase BLAST -Searches all Drosophila reads and provides links to the individual matched sequences through the NCBI. (bcm.edu)
20221
- 2022). Harmonizing model organism data in the Alliance of Genome Resources. (caltech.edu)
Variants2
- Human genomic databases including The Cancer Genome Atlas (TCGA) were interrogated to identify DPP9 LoF variants and associated cancers. (preprints.org)
- Among them, variants at 4q25, located upstream of PITX2 , far exceeded the preset threshold for genome-wide significance and demonstrate strong association with AF in both Europeans and Japanese popupations. (nature.com)
Loci1
- identified six AF susceptibility loci ( PRRX1 , CAV1 , C9orf3 , SYNPO2L , SYNE2 , and HCN4 ) in addition to three previously reported loci ( PITX2 , ZFHX3 , and KCNN3 ) by a genome-wide association study (GWAS) conducted in individuals of European ancestry. (nature.com)
Vertebrate2
- 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)
- Vertebrate genomes contain retroviral sequences that are believed to be remnants of exogenous retroviral infection from the distant past [ 1 ]. (biomedcentral.com)
Human6
- 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)
- The Drosophila genome is about one twentieth the size of the human genome. (nih.gov)
- How do numerous non-coding variations in the human genome affect gene expression in the retina? (nih.gov)
- 2001. Integration of telomere sequences with the draft human genome sequence. . (cornell.edu)
- 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences" . (en-academic.com)
- The Drosophila Genome Project was funded by the National Human Genome Research Institute , National Cancer Institute , and Howard Hughes Medical Institute . (bcm.edu)
Insulators1
- These regulatory modules include promoters, insulators, silencers, enhancers, promoter targeting sequences and the recently identified promoter tethering element (PTE). (nih.gov)
Subsets1
- Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes. (atlasgeneticsoncology.org)
Gene Sequences1
- 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)
Bioinformatic2
- 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 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)
Specificity1
- Our findings establish Sox17 as a tissue -specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/β-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and β-catenin/Tcf transcriptional complexes. (xenbase.org)
Embryo1
- 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)
Analysis1
- 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)
Regulatory5
- The transcription of Abd-B is tightly controlled by an array of cis-regulatory modules that direct its expression over extended genomic distances. (nih.gov)
- 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)
- 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)
Approaches2
- Here, using genomic approaches and epistasis experiments, we define the Sox17 -governed endoderm GRN in Xenopus gastrulae. (xenbase.org)
- Introduction: genomic approaches in infectious diseases. (cornell.edu)
Viral1
Regions2
- Specific genomic DNA segments that interact with the nuclear matrix are called scaffold or matrix attachment regions (SARs or MARs). (bdbiosciences.com)
- Meiotic DSBs are not randomly distributed within the genome but mostly occur at discrete regions, called hotspots (Baudat et al. (springer.com)
Amino acid1
- 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)
Targets1
- Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. (xenbase.org)
Next generation1
- 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)
Molecular3
- 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)
Development1
Nucleotide1
- It is also called nucleotide sequence. (lookformedical.com)
Clone1
- No member sequence or clone is mapped. (cornell.edu)
Results1
- 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)
Expression1
- The gene expression before and after Wnt activation is compared within each intestinal origin and across the three locations using RNA sequencing. (biomedcentral.com)
Families1
- By comparison with DNA sequences from exogenous retrovirus families, three main classes of HERVs, gamma, beta, and delta have been identified [ 2 ]. (biomedcentral.com)