• repeats
  • Evidence for co-evolution between human microRNAs and Alu-repeats. (nih.gov)
  • Base-pair complementarity could be demonstrated between the seed sequence of a subset of human microRNAs and Alu repeats that are integrated parallel (sense) in mRNAs. (nih.gov)
  • This model includes on one hand the fact that 3p-miRNAs of C19MC are enriched in number and production quantity and on the other hand that gene duplication events leading to growth of the cluster was facilitated by minus strand Alu repeats. (nih.gov)
  • RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures - a requisite for ADAR editing. (biomedcentral.com)
  • While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. (biomedcentral.com)
  • We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. (biomedcentral.com)
  • Adjacent inverted Alu repeats can pair and form long stable stem-loop structures, which are favorable editing substrates, and are also potentially highly abundant in humans (there are 228,607 inverted Alu pairs within 1 kb in genes from the NCBI Reference Sequence (RefSeq) database). (biomedcentral.com)
  • The analysis of SINEs - Short INterspersed Elements - LINEs - Long INterspersed Elements - or truncated LTRs - Long Terminal Repeats - as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data. (wikipedia.org)
  • gene
  • A primate-specific gene cluster on chromosome 19 encodes the majority of miRNAs that target the most conserved sense Alu site. (nih.gov)
  • Gene duplication events in this locus are supported by comparing repeat length variations of the LINE elements within the cluster with those in the rest of the chromosome. (nih.gov)
  • We propose a mechanistic model for this Alu -mediated replacement event, which deleted the 92-bp exon and thus inactivated the human hydroxylase gene. (pnas.org)
  • One is loss of exon 34 in the tropoelastin gene, which was possibly facilitated by Alu -mediated recombination events ( 6 ). (pnas.org)
  • The gene encoding BC200 RNA arose from a monomeric Alu element. (springer.com)
  • This study highlights the importance of noncoding RNA and transposable elements in the regulation of gene expression and in the evolution of gene expression networks in mammalian genomes," said coauthor Manuel Ares, professor of molecular, cell, and developmental biology at UC Santa Cruz. (eurekalert.org)
  • GSS with low coverage can generate abundant information of gene content and putative regulatory elements of comparative species. (wikipedia.org)
  • RNAs
  • 2007, EMBO J, 26:2670-2681) but also by intermolecular base-pairing either between the Alu element of an mRNA 3'UTR and a partially complementary Alu element in one or more Alu element-containing long noncoding (lnc)RNAs (Gong and Maquat, 2011, Nature, 470:284-288) or between the 3'UTR Alu elements of two different mRNAs (Gong et al. (rochester.edu)
  • cytoplasmic
  • In other studies, we have found that STAU1 (and probably STAU2) binding to 3'UTR inverted Alu elements competes with binding of the largely nuclear paraspeckle protein p54nrb and largely cytoplasmic protein kinase R (PKR) to mediate, respectively, the nuclear export and cytoplasmic translation of a number of mRNAs that contain these elements. (rochester.edu)
  • Thus, STAU1 binding to 3'UTR inverted Alu elements, like removal of these elements by alternative RNA 3'-end cleavage and polyadenylation, obviates a PKR-mediated innate immune response to cytoplasmic 3'UTR inverted Alu elements. (rochester.edu)
  • human
  • In genetics, presence or lack thereof of a recently inserted Alu element may be a good property to consider when studying human evolution. (wikipedia.org)
  • An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. (peerj.com)
  • Were the Alu elements that have spread to fixation in human populations spread by a selective advantage that they conveyed? (peerj.com)
  • By using special Alu sequence as target locus, specific human DNA can be obtained from clone of TAC, BAC, PAC or human-mouse cell hybrid. (wikipedia.org)
  • BC200
  • BC200 emerged from retrotransposed Alu domain, while BC1 originated from retrotransposed tRNAAla. (wikipedia.org)
  • The biosynthesis of BC200 RNA occurs at the cell body of a neuron and requires upstream promoter elements, downstream internal promoter elements (intragenic A and B boxes), at least two transcription factor binding sites, a TATA-like sequence, TATA-box binding protein (TBP), and RNA polymerase III. (wikipedia.org)
  • In addition to upstream elements, there is an upstream TATGAAA sequence (similar to TATA box sequence) at positions -28 to -22 which, when deleted, compromises transcription, revealing this TATA-like sequence as another critical player in the synthesis of BC200 RNA. (wikipedia.org)
  • Both upstream and internal promoter elements are also essential for BC200 RNA synthesis. (wikipedia.org)
  • nucleotides
  • There are two types of upstream promoter elements in the 100 base pair region: one proximal to the transcription start site and associated with downstream transcription factor binding sites, and the other between nucleotides -36 to -100 and not associated with downstream binding sites. (wikipedia.org)
  • proteins
  • Alu elements replication and mobilization begins by interactions with signal recognition particles (SRPs), which aid newly translated proteins reach final destinations. (wikipedia.org)
  • transcript
  • This is of great interest as Alu is a retro-element that can transpose in a cycle containing a free Alu transcript, which is always in sense orientation. (nih.gov)
  • promoter
  • The functional retinoic acid response element hexamer sites are in upper case and overlap the internal transcriptional promoter. (wikipedia.org)
  • The internal promoter elements are intragenic A and B boxes with A located at position +5 to +15 and B located at position +78 to +88. (wikipedia.org)
  • evolution
  • It is suggested that Alu elements have played potentially important roles in genotypic and phenotypic evolution in the hominid lineage. (pnas.org)
  • protein
  • Alu elements do not encode for protein products. (wikipedia.org)
  • Alu RNA forms a specific RNA:protein complex with a protein heterodimer consisting of SRP9 and SRP14. (wikipedia.org)
  • An alternatively-spliced protein variant, called Bcl-rambo beta, is composed of only the BH4 domain, completely lacking the BH domains 1 through 3 due to an in-frame stop codon inserted by an Alu element. (wikipedia.org)
  • evolutionary
  • The most common target site coincides with the evolutionary most conserved part of Alu. (nih.gov)
  • Thus, a dual relationship exists between an evolutionary young miRNA cluster and their Alu targets that may have evolved in the same time window. (nih.gov)
  • The target sites are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is not large and may even be negligible over evolutionary time scales. (wikipedia.org)
  • hypothesis
  • In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. (deepdyve.com)
  • Considering these effects of viruses, the "X chromosome-nucleolus nexus" hypothesis, which proposed disruption of the inactive X by the nucleolus during stress, is now expanded here to propose subsequent disruption of the nucleolus by previously sequestered Alu elements, which can fragment the nucleolus, leading to generation of autoantigens. (frontiersin.org)
  • strand
  • The mutation was caused when a strand of DNA, known as Alu, inserted a copy of itself into the Y chromosome. (wikipedia.org)
  • occurs
  • citation needed]This is because insertion of an Alu element occurs only 100 - 200 times per million years, and no known mechanism of deletion of one has been found. (wikipedia.org)
  • Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. (biomedcentral.com)
  • targets
  • Model for dual relationship between Alu elements and miRNAs in the C19MC cluster.During the phase of rapid extension of Alu copy number, a miRNA containing cassette was duplicated from which the mature miRNA targets free (duplicating) Alu RNA. (nih.gov)
  • cassette
  • The unique design of the cluster's miRNA duplication cassette, as well as the cluster's sense Alu target capacity and the miRNA expression data were the basis to postulate a dual interaction model (Figure 6). (nih.gov)
  • thus
  • The study of Alu Y elements (the more recently evolved) thus reveals details of ancestry because individuals will only share a particular Alu element insertion if they have a common ancestor. (wikipedia.org)
  • These results indicate that this cis -acting structural element, downstream of the sequence required for A-to-I catalysis, increases the local concentration of the editing enzyme by attracting ADAR, thus enabling editing in the vicinity. (biomedcentral.com)