• DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. (wikidata.org)
  • Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that have these sequences near their promoters. (wikipedia.org)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • A Conserved Structural Signature of the Homeobox Coding DNA in HOX genes. (utmb.edu)
  • We have learned that genes in mammalian cells are transcribed into messenger RNAs (mRNAs), which are to be translated into polypeptides (proteins). (intechopen.com)
  • For example, steroid and thyroid hormones directly bind to nuclear receptors, which induce expression of specific genes. (intechopen.com)
  • J Virol, 79 2005), a DNA sequence that is responsible for the regulation of estrogen responsive genes in animals. (usda.gov)
  • Tumor suppressor genes encode proteins that normally provide negative control of cell proliferation. (medscape.com)
  • This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. (plos.org)
  • 2 3 The HGP demonstrated that a relatively limited number of genes could be identified in the human genome, which substantiated the theory that complex biological processes were regulated on other levels than DNA sequence alone. (bmj.com)
  • 8 The MeCP2 protein, initially characterized by its ability to bind single methylated CG nucleotides, 9 plays a significant role in the transcriptional silencing of genes. (neurology.org)
  • Their work had found that the protein produced by the Prdm9 gene determines where in the genome maternal and paternal chromosomes exchange genetic information: a process known as recombination, which controls how genes are passed down through a species. (ox.ac.uk)
  • In addition, these alterations affect 3 principal categories of genes, as follows: proto-oncogenes, tumor suppressor genes, and DNA repair genes. (medscape.com)
  • Like Rb protein, many of the proteins encoded by tumor suppressor genes act at specific points in the cell cycle. (medscape.com)
  • Even if the DNA sequence - the set of genes - is the same in all cells, only certain genes are expressed, i.e. only information from certain genes is copied (transcribed) and used to build protein structures or regulate processes. (lu.se)
  • Gene expression generally produces proteins, but there are also non-coding genes that produce RNA molecules (rRNA, tRNA). (lu.se)
  • DNA methylation is a chemical process that regulates the function of the genes. (lu.se)
  • It is not only the genes that code for proteins that are methylated, but also parts of the DNA that code for regulatory functions (RNA molecules), which can have a greater effect than genes. (lu.se)
  • Genes are arranged linearly along the DNA of chromosomes. (msdmanuals.com)
  • These proteins organize the DNA into a compact structure called chromatin. (wikipedia.org)
  • Other non-specific DNA-binding proteins in chromatin include the high-mobility group (HMG) proteins, which bind to bent or distorted DNA. (wikipedia.org)
  • Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers. (shengsci.com)
  • DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. (shengsci.com)
  • The laboratory is particularly interested in studying how specific DNA sequences, DNA binding proteins, and chromatin. (rochester.edu)
  • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (genomeweb.com)
  • Sso10a is a member of a group of DNA-binding proteins thought to be important in chromatin structure and regulation in the hyperthermophilic archaeon Sulfolobus solfataricus. (rcsb.org)
  • Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates within Model Chromatin Complexes David R. Chafin and Jeffrey J. Hayes 11. (nhbs.com)
  • It is a nuclear protein that is largely chromatin-bound and has a strong preference for binding to methylated DNA sequences in vivo . (portlandpress.com)
  • Chromatin Immunoprecipitation (ChIP) is a widely utilized experimental technique to monitor the association of proteins with specific DNA sequences. (sigmaaldrich.com)
  • ChIP has also been used to determine the temporal regulation underlying the occupation of the particular chromatin locus by multiple proteins. (sigmaaldrich.com)
  • When performing ChIP, chromatin from cells and tissues needs to be fragmented so that it becomes soluble and resolution can be achieved in detecting protein-DNA interaction at specific loci. (sigmaaldrich.com)
  • For example, foaming and overheating associated with sonication can result in protein denaturation or incomplete chromatin fragmentation. (sigmaaldrich.com)
  • The protein structure that surrounds the DNA, chromatin, largely comprises histone proteins and can be open or closed and thus allow or prevent factors binding to the DNA. (lu.se)
  • Bullock and Fersht 8 have shown that mutations of DNA-binding residues, such as those on the tumor repressor protein P53, may predispose individuals to cancer. (nature.com)
  • Scope includes mutations and abnormal protein expression. (cancerindex.org)
  • Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing. (genomeweb.com)
  • Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. (genomeweb.com)
  • Some of these mutations change single protein building blocks (amino acids) in euchromatic histone methyltransferase 1. (medlineplus.gov)
  • In conjunction with RNA sequencing data, the researchers used MIRA to identify mutations in binding sites that altered RNA expression and splicing. (aacr.org)
  • Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X-linked methyl CpG binding protein 2 ( MeCP2 ) gene. (neurology.org)
  • One hundred sixteen patients with classical and atypical RTT were studied for mutations of the MeCP2 gene by using DHPLC and direct sequencing. (neurology.org)
  • [ 8 ] Both mutations created stop codons leading to truncation of the PAX3 protein. (medscape.com)
  • Spontaneous mutations happen as a result of apparently chance errors in the formation of DNA during cell division. (lu.se)
  • When a cell divides, the mutations are passed on to the daughter cells, but only mutations that occur in the DNA of the gametes are passed on to the next generation. (lu.se)
  • Kornberg 7 has presented that the interactions between DNA and histones are involved in chromosome packaging in the cell nucleus. (nature.com)
  • DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. (wikipedia.org)
  • A critical function of telomeres is to prevent the ligation of chromosome ends by DNA repair enzymes. (ens-lyon.fr)
  • However, Drosophila capping proteins can bind chromosome extremities in a DNA sequence-independent manner. (ens-lyon.fr)
  • This epigenetic protection of fly telomeres has been essentially studied in somatic cells where capping proteins such as HOAP or HP1 are essential in preventing chromosome end-to-end fusions. (ens-lyon.fr)
  • Most people with Kleefstra syndrome are missing a sequence of about 1 million DNA building blocks (base pairs) on one copy of chromosome 9 in each cell. (medlineplus.gov)
  • The researchers discovered that this strange binding pattern came about because over many generations, the normal mouse PRDM9 protein erodes the DNA sequence it binds to, resulting in the asymmetric chromosome binding pattern seen in the infertile hybrids. (ox.ac.uk)
  • For example, the TP53 gene, located on chromosome 17, encodes a 53-kd nuclear protein that functions as a cell cycle checkpoint. (medscape.com)
  • Computational methods to identify the DNA binding sequence specificity have been proposed to make a good use of the abundant sequence data in the post-genomic era. (wikipedia.org)
  • The repE gene is not expressed by mitotically dividing cells, and repE mRNA is first detected during the aggregation phase of development when the cells have ceased dividing and replicating genomic DNA. (nih.gov)
  • Regulation of transcription factors via natural decoys in genomic DNA. (utmb.edu)
  • The structure of Sso10a provides insight into the structures of the conserved domain represented by COG3432, a group of more than 20 hypothetical transcriptional regulators coded in the genomic sequences of both crenarchaeota and euryarchaeota. (rcsb.org)
  • We divide the field of genomics into genotyping (focused on the genome sequence), transcriptomics (focused on genomic expression) and epigenomics (focused on epigenetic regulation of genome expression). (bmj.com)
  • Extractions of genomic DNA were made from the dental root after exposure to high temperatures (600ºC, 800ºC and 1000ºC), during 10, 30 and 60 minutes. (bvsalud.org)
  • In contrast, other proteins have evolved to bind to specific DNA sequences. (wikipedia.org)
  • We have previously reported on seven 46,XX true hermaphrodites and one 45,X mixed gonadal dysgenesis case all presenting with testicular tissue in their gonads in the apparent absence of Y-specific DNA sequences. (nih.gov)
  • Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. (nature.com)
  • An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
  • Deciphering protein–protein interactions. (crossref.org)
  • Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. (wikipedia.org)
  • These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. (wikipedia.org)
  • The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to read the DNA sequence. (wikipedia.org)
  • Protein-DNA interactions occur when a protein binds a molecule of DNA, often to regulate the biological function of DNA, usually the expression of a gene. (wikipedia.org)
  • Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions. (scilifelab.se)
  • We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin. (shengsci.com)
  • Selective microfluidics-based ligand enrichment followed by sequencing, or SMiLE-seq, combines antibody arrays, mechanical trapping, and next-generation sequencing readouts to provide a new platform for characterizing DNA-protein interactions. (genomeweb.com)
  • That year, the two published a paper in Science describing a method to trap low-affinity DNA-protein interactions, specifically those of transcription factors. (genomeweb.com)
  • By physically restraining bound molecules against an antibody array, they capture both transient interactions, which yeast two-hybrid or tandem mass spectrometry methods don't, and weak interactions, which are usually obliterated by the wash in protein-DNA microarrays. (genomeweb.com)
  • The transcription factors bind to any number of DNA motifs in the library, those interactions are trapped, and then the readout matches up each motif with the transcription factor via the barcode. (genomeweb.com)
  • Deplancke also worked in advanced bioinformatics to derive predictive models for binding interactions. (genomeweb.com)
  • Possible DNA-binding interactions are discussed on the basis of comparisons to other winged helix proteins. (rcsb.org)
  • In 'DNA-Protein Interactions: Principles and Protocols, Third Edition', this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. (nhbs.com)
  • Comprehensive and authoritative, 'DNA-Protein Interactions: Principles and Protocols, Third Edition' serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research. (nhbs.com)
  • Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Manon Gaudreault, Marie-Eve Gingras, Maryse Lessard, Steeve Leclerc, and Sylvain L. Guerin 3. (nhbs.com)
  • Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper Athanasios G. Papavassiliou 14. (nhbs.com)
  • One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. (cshlpress.com)
  • Since the mid-20th century, from discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. (cshlpress.com)
  • Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. (cshlpress.com)
  • A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create a unified view of the field and a fuller understanding of protein-DNA interactions. (cshlpress.com)
  • These DNA targets can occur throughout an organism's genome. (wikipedia.org)
  • Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. (shengsci.com)
  • Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. (shengsci.com)
  • The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. (utmb.edu)
  • In terms of predicting where in the genome the transcription factors bind, the models we're able to derive seem to be, in general, actually better than the other assays. (genomeweb.com)
  • The dynamics of genome replication using deep sequencing. (genomeweb.com)
  • TP53 encodes the protein p53, which is known as the "guardian of the genome. (medscape.com)
  • We used whole-genome sequencing to compare these isolates with a worldwide collection of current and historical clinical strains for characterizing population structures. (cdc.gov)
  • High numbers of repetitive DNA elements (RepMPs), designated RepMP1, RepMP2/3, RepMP4, and RepMP5, comprise ≈8% of the M. pneumoniae genome and play essential roles in survival niches of M. pneumoniae by engaging in recombination events to generate surface antigen diversity ( 5 ). (cdc.gov)
  • P1 adhesin causes antigenic variation between clinical strains as a result of homologous recombination between RepMP2/3 and RepMP4 domains located within their open reading frames and at repetitive DNA elements at other sites in the bacterial genome ( 8 ). (cdc.gov)
  • Most notably, are the applications for genome sequencing and metagenomics. (wikidoc.org)
  • This can make the process of genome assembly more difficult, particularly for sequence containing a large amount of repetitive DNA . (wikidoc.org)
  • The OMICS field ranges from genomics (focused on the genome) to proteomics (focused on large sets of proteins, the proteome) and metabolomics (focused on large sets of small molecules, the metabolome). (bmj.com)
  • This technique has been used to study patterns of histone modifications and to map binding sites of various proteins on a genome-wide scale with the aid of microarray technology. (sigmaaldrich.com)
  • The groups replaced the region of the mouse Prdm9 gene responsible for DNA binding with the equivalent sequence from humans, thus completely changing where recombination happened along the genome. (ox.ac.uk)
  • This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). (cdc.gov)
  • METHOD: The Cipro-panel was selected using whole genome sequencing, bioinformatic tools, and antimicrobial susceptibility testing (AST) data. (cdc.gov)
  • In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. (wikipedia.org)
  • In this article, we reconcile this inconsistency by showing that, in a defined in vitro system with plasmid DNA templates, a variety of sequence-specific DNA-binding proteins, such as the bacteriophage λ O replication initiator or the E. coli lactose or galactose repressors, strikingly stimulate transcription-coupled DNA supercoiling. (johnshopkins.edu)
  • Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. (shengsci.com)
  • We describe an improved model of DNA replication in Xenopus egg extracts, in which a circular plasmid immobilized on paramagnetic beads is used as a template. (shengsci.com)
  • Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: "Disentangling DNA molecules" by Alexander Vologodskii. (utmb.edu)
  • Here we show that in young proliferating embryonic fibroblasts (MEFs) the Polycomb Repressive Complex 2 (PRC2) member EZH2 together with PRC1 members BMI1 and M33 are strongly expressed and localized at the INK4/ARF regulatory domain (RD) identified as a DNA replication origin. (plos.org)
  • Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. (plos.org)
  • Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. (plos.org)
  • Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. (plos.org)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • More precisely, we suggest that some nucleoprotein complexes, perhaps those that contain sharply bent DNA, can form barriers that impede the diffusion and merger of independent chromosomal supercoil domains. (johnshopkins.edu)
  • Localization of DNA supercoils by nucleoprotein complexes may serve as a general mechanism for modulating DNA transactions that are sensitive to DNA superhelicity. (johnshopkins.edu)
  • In particular, X-ray structures of BEN domain DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. (bvsalud.org)
  • When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). (plos.org)
  • Hydroxyl Radical Footprinting of Protein-DNA Complexes Indu Jagannathan and Jeffrey J. Hayes 6. (nhbs.com)
  • Ethylation Interference Footprinting of DNA-Protein Complexes Iain W. Manfield and Peter G. Stockley 10. (nhbs.com)
  • RFX forms cooperative DNA binding complexes with x2bp and cbf/nf-y. (lu.se)
  • The p16INK4A protein is a cell-cycle inhibitor that acts by inhibiting activated cyclin D:CDK4/6 complexes, which play a crucial role in the control of the cell cycle by phosphorylating Rb protein. (medscape.com)
  • You are seeking a database of transcription factor binding specificities. (stackexchange.com)
  • Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. (scilifelab.se)
  • Bacteria often can't support over-expression needed to get workable quantities of protein for an assay, and in vitro expression often can't synthesize a fully functional transcription factor. (genomeweb.com)
  • p53 is a transcription factor whose expression is increased by DNA damage and blocks cell division at the G1 phase of the cell cycle to allow DNA repair. (medscape.com)
  • Classification tasks included the prediction of enhancer and promoter sequences and transcription factor binding sites. (nvidia.com)
  • Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots Athanasios G. Papavassiliou 15. (nhbs.com)
  • The CDK4-cyclinD complex normally phosphorylates the retinoblastoma protein (Rb protein), leading to release of the E2F transcription factor and cell cycle progression. (medscape.com)
  • The knowledge about DNA-binding residues, binding specificity and binding affinity helps to not only understand the recognition mechanism of protein-DNA complex, but also give clues for protein function annotation. (nature.com)
  • Mathematical descriptions of protein-DNA binding taking into account sequence-specificity, and competitive and cooperative binding of proteins of different types are usually performed with the help of the lattice models. (wikipedia.org)
  • This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins. (nih.gov)
  • DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. (wikipedia.org)
  • Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity. (utmb.edu)
  • Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. (nature.com)
  • Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. (nhbs.com)
  • The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. (wikipedia.org)
  • These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA. (nature.com)
  • These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form chromosomes. (wikipedia.org)
  • They found that the infertile mouse hybrids showed a striking pattern: the mouse PRDM9 protein would bind to one of their chromosomes or the other, but not both. (ox.ac.uk)
  • The researchers think that asymmetric binding makes it more difficult for chromosomes to successfully identify and make contact with each other as egg and sperm cells are formed. (ox.ac.uk)
  • The result is that in many different hybrid mice, asymmetric PRDM9 binding is associated with an increasing failure rate in chromosomes making contact correctly, leading to more and more fertility problems. (ox.ac.uk)
  • We think that the symmetric marking of chromosomes by PRDM9 facilitates their pairing: where PRDM9 binding is very asymmetric, this leads to difficulties in pairing, failure in recombination repair and, at one extreme, the infertility we see in some mouse hybrids', says Professor Donnelly. (ox.ac.uk)
  • The fertilised egg inherits its DNA unchanged from the parents' sex chromosomes. (lu.se)
  • DNA (deoxyribonucleic acid) is the cell's genetic material, contained in chromosomes within the cell nucleus and mitochondria. (msdmanuals.com)
  • Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. (wikidata.org)
  • Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. (shengsci.com)
  • DNA synthesis occurred on either circular or linear plasmids coupled to the beads, but only DNA synthesis on the circular plasmid was inhibited by geminin and a. (shengsci.com)
  • Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle developed by Mostafa Ronaghi and Pål Nyrén (published in Analytical Biochemistry 1996 and Science 1998). (wikidoc.org)
  • In vitro synthesis of variola virus DNA exceeding a designated length requires explicit authorization by WHO, as does mutagenesis of orthopoxvirus DNA, larger than a designated length, with the aim of producing the corresponding variola virus sequence. (who.int)
  • Protein synthesis, folding, and tertiary and quaternary structure ultimately determine much of the body's structure and function. (msdmanuals.com)
  • Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. (bvsalud.org)
  • Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. (bvsalud.org)
  • Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins . (bvsalud.org)
  • Identification of binding sites of EVI1 in mammalian cells. (rochester.edu)
  • Each run would cost about 8 to 9 thousand USD, thereby, de novo sequencing of mammalian genomes are in million dollar range. (wikidoc.org)
  • We have determined the nucleotide sequence of the C gene. (shengsci.com)
  • Example of a pyrogram showing the nucleotide sequence in a specific section of DNA. (wikidoc.org)
  • The tops represent light emission and nucleotide binding. (wikidoc.org)
  • Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed. (shengsci.com)
  • Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules. (lu.se)
  • Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (nih.gov)
  • Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. (shengsci.com)
  • Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. (nature.com)
  • A gene, the basic unit of heredity, is a segment of DNA containing all the information necessary to synthesize a polypeptide (protein) or a functional RNA molecule. (msdmanuals.com)
  • A gene is a segment of DNA that provides the code to construct a protein or RNA molecule. (msdmanuals.com)
  • Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. (scilifelab.se)
  • The chicken infectious anemia virus (CAV) gene promoter fused to the gene for enhanced green fluorescent protein (EGFP) was used to measure virus activity in response to estrogen. (usda.gov)
  • The virus promoter-enhancer DNA sequence was also found to bind some of the proteins that recongnize a consensus estrogen response element (ERE) (Miller et al. (usda.gov)
  • A long virus promoter construct that included sequences downstream from the transcription start point (TSP) expressed lower levels of EGFP than a shorter sequence that stopped at the TSP. (usda.gov)
  • Mutation of an E box-like sequence at the TSP restored expression of this longer promoter to the same level as the short promoter. (usda.gov)
  • Expression of enhanced green fluorescent protein (EGFP) under control of the promoter-enhancer of chicken infectious anemia virus (CAV) is increased in an estrogen receptor-enhanced cell line when treated with estrogen. (usda.gov)
  • This promoter-enhancer also binds unidentified proteins that recognize a consensus estrogen response element (ERE) (Miller et al. (usda.gov)
  • In front of every gene is a DNA sequence called a promoter. (lu.se)
  • Transcription factors bind alongside the promoter and set off the gene expression. (lu.se)
  • In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. (bvsalud.org)
  • The predicted protein encodes a leucine zipper motif. (nih.gov)
  • We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). (nature.com)
  • Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide. (rochester.edu)
  • Another motif, DPHK, is in the DNA-binding domain. (cdc.gov)
  • The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. (cdc.gov)
  • This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. (cdc.gov)
  • PTEN encodes a protein kinase of the same name and functions as a tumor suppressor through regulation of cell proliferation. (medscape.com)
  • In a paper published in Nature Methods this week, a Switzerland-based team of researchers, led by bioengineer Bart Deplancke of the École Polytechnique Fédérale de Lausanne (EPFL), showcased the assay's ability to determine DNA-binding specificities for transcription factors. (genomeweb.com)
  • Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins . (bvsalud.org)
  • As well as DNA methylation, there are also other epigenetic mechanisms such as modification of histone proteins. (lu.se)
  • Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor. (utmb.edu)
  • SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
  • The Use of Diethyl Pyrocarbonate (DEPC) and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA Brenda F. Kahl and Marvin R. Paule 7. (nhbs.com)
  • InsertionMapper: a pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. (genomeweb.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)
  • HipHop and K81 are two recently identified paralogous capping proteins with complementary expression patterns. (ens-lyon.fr)
  • Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it. (wikidoc.org)
  • DNA polymerase incorporates the correct, complementary dNTPs onto the template. (wikidoc.org)
  • The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. (nature.com)
  • United States Patent 8,932,814 CRISPR-Cas nickase systems, methods and compositions for sequence manipulation in eukaryotes. (stanford.edu)
  • Currently, a limitation of the method is that the lengths of individual reads of DNA sequence are in the neighborhood of 300-500 nucleotides, shorter than the 800-1000 obtainable with chain termination methods (e.g. (wikidoc.org)
  • For comparisons of proteins with limited sequence and backbone-fold similarity, where coordinate-based methods typically fail, ZEAL can often find alignments with substantial surface-shape correspondence. (lu.se)
  • Consequently, a lot of effort is put into identifying the constituent proteins using mass spectrometric methods. (lu.se)
  • We demonstrate further that this stimulation requires the presence in the DNA template of a recognition sequence for the relevant DNA-binding protein and depends on the production of long RNA chains by an RNA polymerase. (johnshopkins.edu)
  • The winged helix domains are at opposite ends of the extended coiled coil with two putative DNA-recognition helices separated by 55A and rotated by 83 degrees. (rcsb.org)
  • The assay could help accelerate efforts to map where transcription factors bind the genomes of humans and model organisms, Deplancke said. (genomeweb.com)
  • As of 2007, pyrosequencing is most commonly used for resequencing or sequencing of genomes for which the sequence of a close relative is already available. (wikidoc.org)
  • Attempts to synthesize full-length variola virus genomes or infectious variola viruses from smaller DNA fragments remain strictly prohibited. (who.int)
  • Assays showed that multiple proteins can bind to this sequence and that one of these is the transcription regulator delta-EF1 (dEF1). (usda.gov)
  • This alters the accessibility of the DNA template to the polymerase. (wikipedia.org)
  • Transcription by RNA polymerase can stimulate localized DNA supercoiling in Escherichia coli. (johnshopkins.edu)
  • In vivo, there is extensive experimental support for a "twin-domain" model in which positive DNA supercoils are generated ahead of a translocating RNA polymerase complex and negative supercoils are formed behind it. (johnshopkins.edu)
  • Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface. (utmb.edu)
  • First, the general TFs (GTFs), including preinitiation complex components TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and THIIH, are the primary protein factors that are required for the initiation of transcription from the TATA box (or TATA element), then elongation is executed by RNA polymerase II (RNA pol II) [ 1 ]. (intechopen.com)
  • DNA sequencing using electrical conductance measurements of a DNA polymerase. (genomeweb.com)
  • ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase , ATP sulfurylase , luciferase and apyrase , and with the substrates adenosine 5´ phosphosulfate (APS) and luciferin . (wikidoc.org)
  • PCR (polymerase chain reaction) technique has achieved increased importance for post-mortem DNA analysis in forensic cases 8 because of the millions of copies amplified from one specific sequence of DNA. (bvsalud.org)
  • Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart 9. (nhbs.com)
  • Evidence from model systems shows that MeCP2 can recruit the Sin3a co-repressor complex to promoters leading to transcriptional repression, therefore suggesting that MeCP2 can interpret the DNA methylation signal to bring about gene silencing. (portlandpress.com)
  • Future studies of MeCP2 promise to shed light upon brain function, neurological disease and the biology of DNA methylation. (portlandpress.com)
  • Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
  • Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
  • DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein-DNA interfaces. (biomedcentral.com)
  • The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. (cdc.gov)
  • Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. (biomedcentral.com)
  • Transcription factors are a group of proteins that are needed for a gene to start being copied to RNA, i.e. for transcription to start. (lu.se)
  • DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. (wikipedia.org)
  • The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. (genomeweb.com)
  • Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
  • Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. (nhbs.com)
  • The method can be used for automated detection of chemical/post- translational modifications, quality control of experiments and labelling approaches, and to control the modification settings of protein identification tools. (lu.se)
  • Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. (nature.com)
  • Electromobility shift assays were done to find if proteins from the nucleus bind to the DNA sequence at the TSP. (usda.gov)
  • Electromobility shift assays showed that the transcription regulator delta-EF1 (dEF1) is one of the proteins that recognize the E box region. (usda.gov)
  • 1. Filter-Binding Assays Peter G. Stockley 2. (nhbs.com)
  • Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
  • Next, an electropositive patch was found in the C-terminal region of IRIS-1, suggesting potential interaction with DNA. (lu.se)
  • Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. (genomeweb.com)
  • Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. (genomeweb.com)
  • EVI1 Interferes with Myeloid Maturation via Transcriptional Repression of Cebpa, via Binding to Two Far Downstream Regulatory Elements. (rochester.edu)
  • RFXANKbase: Mutation registry for Ankyrin repeat containing regulatory factor X-associated protein deficiency. (lu.se)
  • The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids. (lu.se)
  • A novel PAX3 heterozygous mutation of c.372-373delGA (p.N125fs) was found that gave rise to a frameshift and truncation of the PAX3 protein. (medscape.com)
  • Associate Professor of Biology Dr. Jason Kuehner was awarded a three-year, $372,026 grant from the National Science Foundation (NSF) Research in Undergraduate Institutions (RUI) to examine control of DNA traffic and regulation of gene expression. (emmanuel.edu)
  • Today we use epigenetics to mean changes to gene expression that are not caused by changes in the actual DNA sequence. (lu.se)
  • Gene expression is the process of several steps through which the information in a gene's DNA sequence is transferred to the structures and functions of a cell. (lu.se)
  • Changes in conformational dynamics of basic side chains upon protein-DNA association. (utmb.edu)
  • These tasks can help with understanding the dynamics of how DNA is translated into RNA and proteins, unlocking new clinical applications. (nvidia.com)
  • How proteins modify water dynamics. (lu.se)
  • Analysis of protein dynamics simulations by a stochastic point process approach. (lu.se)
  • Hydration dynamics of a halophilic protein in folded and unfolded states. (lu.se)
  • Slow internal protein dynamics from water 1 H magnetic relaxation dispersion. (lu.se)
  • Does the dynamic Stokes shift report on slow protein hydration dynamics? (lu.se)
  • Time scales of water dynamics at biological interfaces: peptides, proteins and cells. (lu.se)
  • Dynamics at the protein-water interface from 17 O spin relaxation in deeply supercooled solutions. (lu.se)
  • Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. (genomeweb.com)
  • Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
  • I am a computer scientist and we are working on protein function prediction algorithms. (stackexchange.com)
  • [ 1 ] His prediction was subsequently supported by the cloning of the retinoblastoma tumor suppressor gene ( RB1 ) and by functional studies of the retinoblastoma protein, Rb. (medscape.com)
  • We describe a statistical measure, Mass Distance Fingerprint, for automatic de novo detection of predominant peptide mass distances, i.e., putative protein mod- ifications. (lu.se)
  • Biophysical studies show that these architectural HMG proteins bind, bend and loop DNA to perform its biological functions. (wikipedia.org)
  • DNA-Binding Proteins (DBP) plays a pivotal role in biological system. (biomedcentral.com)
  • Due to this resilience against environmental changes (incineration, immersion, traumas, mutilation and decomposition), teeth represent an excellent source of DNA, when the other biological sources have been lost 20,29,30 . (bvsalud.org)
  • The 95 amino acid residue protein contains a winged helix DNA-binding domain with an extended C-terminal alpha-helix that leads to dimerization by forming a two-stranded, antiparallel coiled-coil rod. (rcsb.org)
  • Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. (plos.org)
  • The p19ARF protein, which is encoded by the same locus as p16, also leads to cell cycle arrest by inhibiting the ability of MDM2 to inactivate TP53. (medscape.com)
  • This locus, however, also encodes a protein from an alternative reading frame, designated p19ARF. (medscape.com)
  • Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. (nature.com)
  • For this, we would make use of datasets about containing DNA-binding proteins and the DNA sequences they bind to. (stackexchange.com)
  • In addition, it can stimulate apoptosis of cells containing damaged DNA. (medscape.com)
  • The TP53 gene is also capable of stimulating apoptosis of cells containing damaged DNA. (medscape.com)
  • Proteotoxic stress promotes entrapment of ribosomes and misfolded proteins in a shared cytosolic compartment. (shengsci.com)
  • Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins. (scilifelab.se)
  • We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site , which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non- DNA -binding BEN domains (BD1). (bvsalud.org)
  • Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. (genomeweb.com)
  • A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. (nih.gov)
  • Immunoglobulin gene transcription is activated by downstream sequence elements. (wikidata.org)