AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation Science
Alu ElementsIntronsBase SequenceMolecular Sequence DataRepetitive Sequences, Nucleic AcidLong Interspersed Nucleotide ElementsExonsShort Interspersed Nucleotide ElementsDNA Transposable ElementsGenome, HumanSequence Homology, Nucleic AcidRetroelementsPrimatesEvolution, MolecularRNA SplicingStrepsirhiniPhylogenyPromoter Regions, GeneticTranscription, GeneticDNA3' Flanking RegionHominidaeRNA Splice SitesAmino Acid SequenceSequence AlignmentRNA EditingCloning, MolecularSequence Analysis, DNAPan troglodytesResponse ElementsCercopithecidaeRNA, MessengerMutagenesis, InsertionalEnhancer Elements, GeneticPolymerase Chain ReactionRegulatory Sequences, Nucleic AcidAlternative SplicingGene Expression RegulationGorilla gorillaBiological EvolutionModels, GeneticRestriction MappingRNA Polymerase IIIChromosome MappingGene ConversionGenes, Neurofibromatosis 1MutationConsensus SequenceGenetic VariationSpliceosomesNucleic Acid ConformationGenomeDNA PrimersRNAGenesHeLa CellsBase CompositionComputational BiologyInosineBinding SitesChromosome BreakageMultigene FamilyRNA PrecursorsPolymorphism, GeneticCpG IslandsRecombination, GeneticCell LineTerminal Repeat Sequences3' Untranslated RegionsConserved SequenceGene RearrangementTranscription FactorsPoly ADNA MethylationTrace ElementsFinite Element Analysis
Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Sequence Data: 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.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.PrimatesEvolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Strepsirhini: A suborder of PRIMATES consisting of the following five families: CHEIROGALEIDAE; Daubentoniidae; Indriidae; LEMURIDAE; and LORISIDAE.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).3' Flanking Region: The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.Hominidae: Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. It includes modern man (HOMO SAPIENS) and the great apes: gorillas (GORILLA GORILLA), chimpanzees (PAN PANISCUS and PAN TROGLODYTES), and orangutans (PONGO PYGMAEUS).RNA Splice Sites: Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.RNA Editing: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Cercopithecidae: The family of Old World monkeys and baboons consisting of two subfamilies: CERCOPITHECINAE and COLOBINAE. They are found in Africa and part of Asia.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Gorilla gorilla: This single species of Gorilla, which is a member of the HOMINIDAE family, is the largest and most powerful of the PRIMATES. It is distributed in isolated scattered populations throughout forests of equatorial Africa.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA Polymerase III: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Gene Conversion: The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.Genes, Neurofibromatosis 1: Tumor suppressor genes located on the long arm of human chromosome 17 in the region 17q11.2. Mutation of these genes is thought to cause NEUROFIBROMATOSIS 1, Watson syndrome, and LEOPARD syndrome.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Genetic Variation: Genotypic differences observed among individuals in a population.Spliceosomes: Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear RNA molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Inosine: A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Chromosome Breakage: A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Trace Elements: A group of chemical elements that are needed in minute quantities for the proper growth, development, and physiology of an organism. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Finite Element Analysis: A computer based method of simulating or analyzing the behavior of structures or components.
AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation Science
Alu ElementsIntronsBase SequenceMolecular Sequence DataRepetitive Sequences, Nucleic AcidLong Interspersed Nucleotide ElementsExonsShort Interspersed Nucleotide ElementsDNA Transposable ElementsGenome, HumanSequence Homology, Nucleic AcidRetroelementsPrimatesEvolution, MolecularRNA SplicingStrepsirhiniPhylogenyPromoter Regions, GeneticTranscription, GeneticDNA3' Flanking RegionHominidaeRNA Splice SitesAmino Acid SequenceSequence AlignmentRNA EditingCloning, MolecularSequence Analysis, DNAPan troglodytesResponse ElementsCercopithecidaeRNA, MessengerMutagenesis, InsertionalEnhancer Elements, GeneticPolymerase Chain ReactionRegulatory Sequences, Nucleic AcidAlternative SplicingGene Expression RegulationGorilla gorillaBiological EvolutionModels, GeneticRestriction MappingRNA Polymerase IIIChromosome MappingGene ConversionGenes, Neurofibromatosis 1MutationConsensus SequenceGenetic VariationSpliceosomesNucleic Acid ConformationGenomeDNA PrimersRNAGenesHeLa CellsBase CompositionComputational BiologyInosineBinding SitesChromosome BreakageMultigene FamilyRNA PrecursorsPolymorphism, GeneticCpG IslandsRecombination, GeneticCell LineTerminal Repeat Sequences3' Untranslated RegionsConserved SequenceGene RearrangementTranscription FactorsPoly ADNA MethylationTrace ElementsFinite Element Analysis
Noncoding DNANoncoding DNA
Many introns appear to be mobile genetic elements. Studies of group I introns from Tetrahymena protozoans indicate that some ... Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. ... Maston, Glenn; Sarah Evans; Michael Green (23 May 2006). "Transcriptional regulatory elements in the Human Genome" (PDF). ... doi:10.5779/hypothesis.v7i1.146. Callaway, Ewen (March 2010). "Junk DNA gets credit for making us who we are". New Scientist. ...
Alu elementAlu element
The discovery of Alu subfamilies led to the hypothesis of master/source genes, and provided the definitive link between ... The functional retinoic acid response element hexamer sites are in upper case and overlap the internal transcriptional promoter ... introns), where they have little discernible impact on the bearer. Mutations in the introns (or non-coding regions of RNA) have ... Alu elements in primates form a fossil record that is relatively easy to decipher because Alu elements insertion events have a ...
MutationMutation
Häsler J, Strub K (November 2006). "Alu elements as regulators of gene expression". Nucleic Acids Research. Oxford University ... There can also be silent mutations in nucleotides outside of the coding regions, such as the introns, because the exact ... For instance, association of Steroid Binding Domain can create a transcriptional switch that can change the expression of a ... Zhang J, Wang X, Podlaha O (May 2004). "Testing the chromosomal speciation hypothesis for humans and chimpanzees". Genome ...
MutationMutation
"Alu elements as regulators of gene expression". Nucleic Acids Research. 34 (19): 5491-7. doi:10.1093/nar/gkl706. PMC 1636486. ... There can also be silent mutations in nucleotides outside of the coding regions, such as the introns, because the exact ... For instance, association of Steroid Binding Domain can create a transcriptional switch that can change the expression of a ... "Testing the chromosomal speciation hypothesis for humans and chimpanzees". Genome Research. 14 (5): 845-51. doi:10.1101/gr. ...
RNARNA
Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA), or the introns can be ... these cis-regulatory elements regulate the activity of that mRNA. The untranslated regions can also contain elements that ... However, many RNAs do not code for protein (about 97% of the transcriptional output is non-protein-coding in eukaryotes). These ... Liang, Kung-Hao; Yeh, Chau-Ting (2013). "A gene expression restriction network mediated by sense and antisense Alu sequences ...
MicroRNAMicroRNA
As many as 40% of miRNA genes may lie in the introns or even exons of other genes. These are usually, though not exclusively, ... For example, miR16 contains a sequence complementary to the AU-rich element found in the 3'UTR of many unstable mRNAs, such as ... Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP (August 2011). "A ceRNA hypothesis: the Rosetta Stone of a hidden RNA ... RNA polymerase III (Pol III) transcribes some miRNAs, especially those with upstream Alu sequences, transfer RNAs (tRNAs), and ...
AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation Science
Alu ElementsIntronsBase SequenceMolecular Sequence DataRepetitive Sequences, Nucleic AcidLong Interspersed Nucleotide ElementsExonsShort Interspersed Nucleotide ElementsDNA Transposable ElementsGenome, HumanSequence Homology, Nucleic AcidRetroelementsPrimatesEvolution, MolecularRNA SplicingStrepsirhiniPhylogenyPromoter Regions, GeneticTranscription, GeneticDNA3' Flanking RegionHominidaeRNA Splice SitesAmino Acid SequenceSequence AlignmentRNA EditingCloning, MolecularSequence Analysis, DNAPan troglodytesResponse ElementsCercopithecidaeRNA, MessengerMutagenesis, InsertionalEnhancer Elements, GeneticPolymerase Chain ReactionRegulatory Sequences, Nucleic AcidAlternative SplicingGene Expression RegulationGorilla gorillaBiological EvolutionModels, GeneticRestriction MappingRNA Polymerase IIIChromosome MappingGene ConversionGenes, Neurofibromatosis 1MutationConsensus SequenceGenetic VariationSpliceosomesNucleic Acid ConformationGenomeDNA PrimersRNAGenesHeLa CellsBase CompositionComputational BiologyInosineBinding SitesChromosome BreakageMultigene FamilyRNA PrecursorsPolymorphism, GeneticCpG IslandsRecombination, GeneticCell LineTerminal Repeat Sequences3' Untranslated RegionsConserved SequenceGene RearrangementTranscription FactorsPoly ADNA MethylationTrace ElementsFinite Element Analysis
Institute of Bioinformatics WWU MünsterInstitute of Bioinformatics WWU Münster
showed that a point mutation in an Alu element residing in the third intron of the ornithine aminotransferase gene activated a ... element resulted in a truncated protein and ornithine aminotransferase deficiency. This discovery led to the hypothesis that a ... motifs for new transcriptional regulatory elements, polyadenylation signals, and protein-coding sequences. The last of these is ... Early DNA association studies showed that the human genome is full of repeated segments, such as Alu elements, that are ...
bioinformatics.uni-muenster.de
Molecular roles and function of circular RNAs in eukaryotic cells | SpringerLinkMolecular roles and function of circular RNAs in eukaryotic cells | SpringerLink
... of introns flanking the circularization event by binding to AU-rich motifs in reverse-complementary Alu elements in the introns ... a EIciRNAs and ciRNAs stimulate RNAP II-dependent transcriptional initiation at the transcriptional start site of a protein- ... 1c), the hypothesis emerged that transcription speed may be a decisive factor choosing between linear splicing and backsplicing ... such as in the form of inversely oriented Alu elements [41]. There are , 1 million Alu insertions sites in the human genome [42 ...
link.springer.com
Noncoding DNA - WikipediaNoncoding DNA - Wikipedia
Many introns appear to be mobile genetic elements. Studies of group I introns from Tetrahymena protozoans indicate that some ... Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. ... Maston, Glenn; Sarah Evans; Michael Green (23 May 2006). "Transcriptional regulatory elements in the Human Genome" (PDF). ... doi:10.5779/hypothesis.v7i1.146. Callaway, Ewen (March 2010). "Junk DNA gets credit for making us who we are". New Scientist. ...
en.wikipedia.org
Alu element - WikipediaAlu element - Wikipedia
The discovery of Alu subfamilies led to the hypothesis of master/source genes, and provided the definitive link between ... The functional retinoic acid response element hexamer sites are in upper case and overlap the internal transcriptional promoter ... introns), where they have little discernible impact on the bearer. Mutations in the introns (or non-coding regions of RNA) have ... Alu elements in primates form a fossil record that is relatively easy to decipher because Alu elements insertion events have a ...
en.wikipedia.org
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian...Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian...
After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. In ... and sequence conservation influence TE insertion/fixation in mammalian introns. Moreover, we provide the first report showing ... Transposable elements (TEs) represent more than 45% of the human and mouse genomes. Both parasitic and mutualistic features ... The frequencies of these elements were calculated on TE-free intron size and no significant differences were identified in ...
genomebiology.biomedcentral.com
Is junk DNA bunk? A critique of ENCODE | PNASIs junk DNA bunk? A critique of ENCODE | PNAS
Because our genomes have introns, Alu elements, and endogenous retroviruses, these things must be doing us some good. Because a ... Why should either function or nonfunction for a class of elements be taken as the null hypothesis, and why should evidence for ... Suppose that there had been (and probably, some day, there will be) ENCODE projects aimed at enumerating, by transcriptional ... Even when an entire genetic element seems relevant or necessary (whole introns must be removed even if only certain sites are ...
pnas.org
Frontiers in Bioscience 17, 1329-1344, January 1, 2012]Frontiers in Bioscience 17, 1329-1344, January 1, 2012]
... heavily depends on the orientation and sequence homology of Alu elements within introns and relies on the base-pairing of Alu ... of direct interference by Alu elements with normal human gene expression through the transcriptional activity of the Alu ... Some of the hypotheses dealing with potential contribution of TEs to the epigenetic regulation of the mammalian genome were ... LINE-1 elements 4.2. Alu elements 4.3. SVA elements 4.4. HERVs 4.5. DNA transposons 5. Perspective 6. Acknowledgments 7. ...
bioscience.org
Cancers | Free Full-Text | Global Decrease of Histone H3K27 Acetylation in ZEB1-Induced Epithelial to Mesenchymal Transition...Cancers | Free Full-Text | Global Decrease of Histone H3K27 Acetylation in ZEB1-Induced Epithelial to Mesenchymal Transition...
SEMA3F intron 13 (SEMA3F-neg) and Alu sequences [9] (Supplementary Material). Together, these results demonstrate that ZEB1 ... In the present study, we tested the hypothesis that ZEB1 directly binds ST14, EpCAM, and ESRP1 genes in H358 non-small cell ... Decrease in lysine acetylation on ZEB1 target genes is in accordance with the mechanism of transcriptional repression induced ... We tested ZEB1 binding to these elements by chromatin immunoprecipitation (ChIP) coupled to quantitative real-time PCR analyses ...
mdpi.com
Circular RNAs: analysis, expression and potential functions | DevelopmentCircular RNAs: analysis, expression and potential functions | Development
The reported enrichment of Alu elements in the introns flanking circularized exons, and the base-pairing interactions ... Some circRNAs have also been implicated in transcriptional or post-transcriptional gene regulation of their host genes. The ... 5B). This hypothesis was tested using short hairpin RNA (shRNA)-mediated knockdown of ADAR and revealed a subset of circRNAs ... named exon-intron circRNAs (EIciRNAs), has been identified and appears to play a role in transcriptional regulation (Li et al ...
dev.biologists.org
Свердлов Евгений Давидович - ИБХ РАНСвердлов Евгений Давидович - ИБХ РАН
CTCF binding sites were mapped within gene introns and intergenic regions, and some of them contained Alu-like repeated ... To test this hypothesis, we constructed two modified double promoters, where the proximal PhSurv promoter was replaced either ... Here, we describe mapping of transcriptional start sites within solitary and proviral LTRs of the HERV-K (HML-2) human-specific ... HERVs can modify expression of host cell genes through their cis-regulatory elements concentrated in their long terminal ...
ibch.ru
Prostatespecific Promoters - Prostate CancerProstatespecific Promoters - Prostate Cancer
... and a downstream deletion of an Alu transcription-silencing repeat. PSES showed significantly stronger transcriptional activity ... The human OC promoter contains numerous regulatory elements, including a vitamin D-responsive element, making it inducible by ... Recently, the PSMA enhancer (PSME) was discovered within the third intron of the PSMA gene, FOLH1 (71). Lee et al. have ... developed a novel chimeric promoter, PSES, under the hypothesis that AREc and PSME could function synergistically in any ...
europeanmedical.info
Frontiers | Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs | GeneticsFrontiers | Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs | Genetics
In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the ... In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the ... Since Alu elements are not found outside of primates, lncRNAs must use other elements, especially in non-primates. In addition ... These zinc finger proteins likely repress transposable element activity primarily through transcriptional silencing, although ...
frontiersin.org
The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK | Science SignalingThe RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK | Science Signaling
... with most of these located in Alu repetitive elements. The editing of Alu sequences has several implications, such as " ... 5F). Collectively, our data suggest that ADAR binds to region A in intron 26 of FAK and edits FAK on an intronic site chr8: ... An alternative hypothesis is that the function of ADAR is dependent on tumor progression. Under certain pressures (such as ... It is well-documented that FAK transcriptional activity is increased in cancer cells by nuclear factor κB, Nanog, and Ago2 ...
stke.sciencemag.org
Polyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1 | proLékaře.czPolyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1 | proLékaře.cz
MartignettiJA, BrosiusJ (1993) BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc Natl ... White boxes represent exons and the small black box corresponds to the SNORD60 snoRNA located in the SHG60 intron. The TRAF7 ... Článek A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation ... SalmenaL, PolisenoL, TayY, KatsL, PandolfiPP (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146: ...
prolekare.cz
Alu elements shape the primate transcriptome by cis-regulation of RNA editing | Genome Biology | Full TextAlu elements shape the primate transcriptome by cis-regulation of RNA editing | Genome Biology | Full Text
The Alu element in NEIL1 increases the local concentration of ADAR. Our hypothesis is that a long stem-loop structure forming ... To prove that editing of NEIL1 is induced by the upstream Alu elements, we made a NEIL1 minigene including intron 5 (with the ... RNA editing by adenosine deamination is a co- or post-transcriptional alteration of mRNA as well as non-coding RNA, which ... Inverted Alu elements and site-selective editing in ZFP14. (a) Top: UCSC genome browser view. Inverted Alu elements are ...
genomebiology.biomedcentral.com
Beverly S. Mitchell, M.D. | Stanford Medicine ProfilesBeverly S. Mitchell, M.D. | Stanford Medicine Profiles
We have characterized the type I and type II genes and identified elements important in the transcriptional regulation of both ... The hypothesis is that survival disparities for blacks and Hispanics with AML will be explained by older age at diagnosis and ... However, the intron structures are completely divergent, resulting in disparities in gene length (18 kilobases for type I and ... The P1 promoter that regulates the transcription of this mRNA has a high degree of sequence identity to an Alu repetitive ...
med.stanford.edu
Junk DNA: evolutionary discards or Gods tools? - creation...'Junk' DNA: evolutionary discards or God's tools? - creation...
Cytosine methylation inactivates the promoters of most viruses and transposons (including retroviruses and Alu elements). In ... The presence of introns throughout genes allows the proper levels to be maintained, and indeed introns reflect the general ... mobile elements as a group. A new hypothesis formulated by genomicist and creationist Wood addresses the past and present ... Wightman, B., Ha, I. and Ruvkun, G., Post-transcriptional regulation of the heterochronic gene lin-14 by lin-4 mediates ...
creation.com
Plus itPlus it
Comparative analysis of transposed element insertion within human and mouse genomes reveals Alus unique role in shaping the ... into introns; 4) into exons; and 5) into the untranslated regions (UTR). b) The role of TEs in the development of (complex) ... A challenging hypothesis may be that the heterogeneity of asthma is due to differences with respect to TE-regulated asthma- ... Such findings suggest that TEs are intrinsic components of the transcriptional region of protein coding loci with crucial ...
erj.ersjournals.com
Complex regulation of ADAR-mediated RNA-editing across tissues | BMC Genomics | Full TextComplex regulation of ADAR-mediated RNA-editing across tissues | BMC Genomics | Full Text
This is thought to be related to hyper editing of Alu repeat elements within the 3 UTRs of human transcripts. Alu repeats are ... Additional file 2 Figure S3. The percent of genic RDDs within introns versus the percent of genic reads mapped to introns. The ... There are several possible hypotheses to explain differential or tissue specific RNA-editing. One hypothesis is that the ... RNA-editing is an enzyme-mediated post-transcriptional modification whereby individual nucleotide residues are altered in the ...
bmcgenomics.biomedcentral.com
Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice VariantsPrimate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants
The creation of splicing signals was accompanied not only by exaptation of an L1 element but also by exonization of an Alu ... 2009). Another hypothesis explains the high expression of retrogenes in testis by the fact that these are, in most cases, ... common feature of all newly evolved transcripts regardless of their chromosomal localization and may reflect a transcriptional ... Previous analyses of introns in the vertebrate genomes did not uncover any intron gain in mammals (Roy et al. 2003). Our study ...
pubmedcentralcanada.ca
Cureus | Apolipoprotein(a) is the Product of a Pseudogene: Implications for the Pathophysiology of Lipoprotein(a)Cureus | Apolipoprotein(a) is the Product of a Pseudogene: Implications for the Pathophysiology of Lipoprotein(a)
... this hypothesis has implications for the therapy of elevated Lp(a) and atherothrombosis theory. Because apo(a) is functionless ... This hypothesis explains many of the unusual features of Lp(a) and apo(a). Also, ... two Alu elements, the most common type of SINE (short interspersed nuclear element), are present in the untranslated 5 region ... A second mutation which destroys a consensus splicing site is found in a large intron separating the exon coding for the leader ...
cureus.com
Hyperconserved CpG domains underlie Polycomb-binding sites | PNASHyperconserved CpG domains underlie Polycomb-binding sites | PNAS
In any case, the depletion of Alu elements from HCGDs/PRC2 domains, together with recent experimental evidence (19), suggests ... Negating this null hypothesis for a genomic interval is an indication for some regional modulation of CpG divergence rates that ... The joint distribution was reconstructed separately for intergenic and intronic sequences, with very similar results, intron ... larger than standard transcription factor-binding sites may play an important role in Polycomb recruitment and transcriptional ...
pnas.org
Gene Report for G00002031 - Genes2Cognition Neuroscience Research ProgrammeGene Report for G00002031 - Genes2Cognition Neuroscience Research Programme
Alu-element insertion in an OPA1 intron sequence associated with autosomal dominant optic atrophy.. Gallus GN, Cardaioli E, ... We present the hypothesis that this pathway regulates mitochondrial morphology and serves as an early response to prevent ... Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative ... Results: We identified an Alu-element insertion located in intron 7 of OPA1 causing an in-frame deletion of exon 8 in 18 family ...
genes2cognition.org
First log on First log on
... including length of introns flanking circularized exons, repetitive elements such as Alu elements and SINEs, competition score ... Two hypothesis tests on the overall mediation effect are proposed and their statistical significance is estimated by ... MotivationGene fusions are an important class of transcriptional variants that can influence cancer development and can be ... Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic ...
library.wur.nl
Andrew Gentles | Stanford Medicine ProfilesAndrew Gentles | Stanford Medicine Profiles
We analyze minisatellites derived from Alu fragments corresponding approximately to the first 44 bases of human Alu consensus ... Reporter assays revealed that LMO2 increases transcriptional activity of NFATc1 and decreases transcriptional activity of LEF1 ... the initial intron tends to be the largest among introns; single-exon gene length is approximately the mean gene exon number ... Our hypothesis is that by segregating CLL according to BAGS, we can identify subtypes with prognostic implications in support ...
med.stanford.edu
AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation Science
Alu ElementsIntronsBase SequenceMolecular Sequence DataRepetitive Sequences, Nucleic AcidLong Interspersed Nucleotide ElementsExonsShort Interspersed Nucleotide ElementsDNA Transposable ElementsGenome, HumanSequence Homology, Nucleic AcidRetroelementsPrimatesEvolution, MolecularRNA SplicingStrepsirhiniPhylogenyPromoter Regions, GeneticTranscription, GeneticDNA3' Flanking RegionHominidaeRNA Splice SitesAmino Acid SequenceSequence AlignmentRNA EditingCloning, MolecularSequence Analysis, DNAPan troglodytesResponse ElementsCercopithecidaeRNA, MessengerMutagenesis, InsertionalEnhancer Elements, GeneticPolymerase Chain ReactionRegulatory Sequences, Nucleic AcidAlternative SplicingGene Expression RegulationGorilla gorillaBiological EvolutionModels, GeneticRestriction MappingRNA Polymerase IIIChromosome MappingGene ConversionGenes, Neurofibromatosis 1MutationConsensus SequenceGenetic VariationSpliceosomesNucleic Acid ConformationGenomeDNA PrimersRNAGenesHeLa CellsBase CompositionComputational BiologyInosineBinding SitesChromosome BreakageMultigene FamilyRNA PrecursorsPolymorphism, GeneticCpG IslandsRecombination, GeneticCell LineTerminal Repeat Sequences3' Untranslated RegionsConserved SequenceGene RearrangementTranscription FactorsPoly ADNA MethylationTrace ElementsFinite Element Analysis
ExonsSequenceGenomesMammalianEukaryoticMRNAChromatinRepeatsMutationsThird intronMechanismInsertionsPrimateGenomicHighly conservedEpigeneticLong interspersedPolymeraseProteinsRegulationTransposonsEvolutionaryInsertionTranscriptsPseudogenesEndogenous retrovirusesAbstractDeletion of exonMammalsRepetitiveAbundantRepressorRetrotransposonCopiesGenetic elementsHexamerTransposable elementDistalSubfamiliesParasiticRegulatory elementsGene mutationTandem repeatTranslational
Exons11
Sequence17
Genomes14
Mammalian6
Eukaryotic4
MRNA3
Chromatin3
  • The new data-coming from high-throughput analyses of transcriptional and chromatin landscapes, transcription factor footprints, and long-range chromosomal interactions-support many current population genetic studies linking human diseases to supposedly nongenic regions, and they are truly impressive in scope and depth ( 5 ). (pnas.org)
  • Our data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms. (beds.ac.uk)
  • Its noncoding status immediately implied that RNA itself could be an effector of chromatin and transcriptional change, an idea substantiated years later by the isolation of Xist's first interacting factors, Polycomb repressive complex 2 (PRC2) ( 17 ) and YY1 ( 18 ). (sciencemag.org)
Repeats8
Mutations3
Third intron2
Mechanism5
Insertions4
Primate2
Genomic7
Highly conserved1
  • A homozygous substitution of the highly conserved isoleucine at position 26 by threonine (I26T) in the transcriptional repressor HESX1 has been associated with anterior pituitary hypoplasia in a human patient, with no forebrain or eye defects. (biologists.org)
Epigenetic6
  • Recent studies suggest an important role for Alu elements in epigenetic gene regulation by linANRIL 17 . (nature.com)
  • Notably, at least the non-long terminal repeat retrotransposons are still able to cause disease by insertional mutagenesis, recombination, providing enzymatic activities for other mobile DNA, and perhaps by transcriptional overactivation and epigenetic effects. (beds.ac.uk)
  • As we usher in the era of genome-scale studies, it is clear that these elements have the potential to cause intra-individual and inter-individual variation and probably common disease through structural variation, deregulated transcriptional activity or epigenetic effects. (beds.ac.uk)
  • While the interpretation of the genome data is still in its initial stages, this new volume looks at the evolving understanding of molecular mechanisms involved in cellular processes, gene function associated with complex traits, epigenetic components involve in gene control and the creation of hypothesis-free genome-wide approaches. (stanford.edu)
  • Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. (plos.org)
  • A gene can also lose its functionality by epigenetic mechanisms, such as transcriptional or posttranscriptional downregulation ( 7 , 38 , 55 , 79 ). (asm.org)
Long interspersed2
Polymerase3
Proteins4
  • We describe how circRNAs impact gene expression of their host gene locus by affecting transcriptional initiation and elongation or splicing, and how they partake in controlling the function of other molecules, for example by interacting with microRNAs and proteins. (springer.com)
  • Alu elements replication and mobilization begins by interactions with signal recognition particles (SRPs), which aid newly translated proteins reach final destinations. (wikipedia.org)
  • Heterochromatin proteins can recognize and silence transposable elements, some of which target heterochromatin for insertion. (asmscience.org)
  • Varied and tissue-specific disease phenotypes associated with the perturbation of ribosomal proteins as well as posttranscriptional and posttranslational modifications of ribosomal components ( 1 , 2 ) have renewed interest in the hypothesis that functionally distinct ribosome subpopulations may exist in the cell ( 3 - 5 ), often referred to as specialized ribosomes ( 6 ). (sciencemag.org)
Regulation5
Transposons2
Evolutionary7
Insertion6
Transcripts1
Pseudogenes1
Endogenous retroviruses2
Abstract1
Deletion of exon1
Mammals2
Repetitive5
Abundant1
Repressor1
Retrotransposon1
Copies2
Genetic elements5
Hexamer1
Transposable element3
Distal1
  • Although this editing inducer element (IE) is hyper-edited, mutational analysis shows that it is the double-stranded structure rather than editing that is important for the distal editing induction. (biomedcentral.com)
Subfamilies1
  • In 1988, Jerzy Jurka and Temple Smith discovered that Alu elements were split in two major subfamilies known as AluJ (named after Jurka) and AluS (named after Smith), and other Alu subfamilies were also independently discovered by several groups. (wikipedia.org)
Parasitic1
Regulatory elements3
Gene mutation1
Tandem repeat1
  • We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1 ), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5' CCCTCT element being one of the variable regions. (beds.ac.uk)
Translational1