• The heterochromatin consists mainly of short, simple sequence elements repeated for many megabases, occasionally interrupted by inserted transposable elements, and tandem arrays of ribosomal RNA genes. (harvard.edu)
  • Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions. (prolekarniky.cz)
  • In yeast, ribosomal protein genes are generally duplicated and evidence has emerged that paralogs might have specific roles. (prolekarniky.cz)
  • Our aim is not only to understand and predict the function of individual smORFs, but of smORFs as a whole, as a new class of genes in the genome. (cabd.es)
  • Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
  • We constructed sex-specific genetic networks associated with alcohol-dependent modulation of gene expression that include protein-coding genes, Novel Transcribed Regions (NTRs, postulated to encode long non-coding RNAs) and female-specific coordinated regulation of snoRNAs that regulate pseudouridylation of ribosomal RNA. (biomedcentral.com)
  • There is significant and sex-specific natural genetic variation in the transcriptional response to developmental exposure to ethanol in Drosophila that comprises networks of genes affecting nervous system development and ethanol metabolism as well as networks of regulatory non-coding RNAs. (biomedcentral.com)
  • As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. (genetex.com)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
  • More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. (biomedcentral.com)
  • The human mitochondrial genome is encoded in multiple copies of ~16.6 kb circular double-stranded DNA molecules (mtDNA) present in mitochondrial nucleoids in the mitochondrial matrix. (nature.com)
  • The complete mitochondrial genome of the West African honey bee Apis mellifera adansonii (Insecta: Hymenoptera: Apidae), Mitochondrial DNA, Part B, 2020a, vol. 5, no. 1, pp. 11 12. (cytgen.com)
  • Using this approach neural-specific decay kinetics were observed, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. (escholarship.org)
  • ribosomal proteins and histones have higher fractions of optimal codons while transcriptional regulators and mRNAs predicted to be localized to synapses have lower fractions of optimal codons. (escholarship.org)
  • Unlike yeast, most mammalian ribosomal proteins are thought to be encoded by a single gene copy, raising the possibility that heterogenous populations of ribosomes are unique to yeast. (prolekarniky.cz)
  • Ribosome synthesis is a highly controlled process, whereby three distinct RNA polymerases are synchronously coordinated to produce equimolar amounts of four rRNAs and 79 mammalian ribosomal proteins (RPs) [1] - [4] . (prolekarniky.cz)
  • Here, a genome-wide analysis of the human mitochondrial transcriptome shows that 2'- O -methylation is limited to residues of the mitoribosomal large subunit (mtLSU) 16S mt-rRNA, introduced by MRM1, MRM2 and MRM3, with the modifications installed by the latter two proteins being interdependent. (nature.com)
  • The protein belongs to the S6E family of ribosomal proteins. (genetex.com)
  • This not been done thoroughly at a genomic scale in any metazoan species, and we are using Poly-Ribo-Seq, our improvement of Ribosomal profiling that allows genome-wide identification of translated sequences, and proteomics. (cabd.es)
  • Finally, C) hundreds of thousands of intergenic smORFs appear in the genome as DNA sequences neither conserved nor transcribed, but resembling dwarf smORFs in the other aspects. (cabd.es)
  • The phylogenetic relationships of methanol-assimilating yeasts based on the partial sequences of 18S and 26S ribosomal RNAs: the proposal of Komagataella gen. nov. (boku.ac.at)
  • The m 7 G-cap of the mRNA is recognized by the 43S translation preinitiation complex comprised of the 40S ribosomal subunit and the eIF2-GTP-Met-tRNAi ternary complex. (biorxiv.org)
  • His Gene study is mostly concerned with Homing endonuclease, Genetic code, Cytochrome c oxidase subunit I and Ribosomal RNA. (research.com)
  • A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. (colorado.edu)
  • This gene encodes a cytoplasmic ribosomal protein that is a component of the 40S subunit. (genetex.com)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
  • We also generated genome-wide maps of PARIS occupancy using ChIP-seq in human SH-SY5Y cells. (nature.com)
  • The MZT marks the transfer of control of development from the mother to the zygote as maternal mRNAs are degraded, transcription from the zygotic genome begins, and embryonic development becomes dependent on zygotic gene products ( Tadros and Lipshitz, 2009 ). (elifesciences.org)
  • We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance. (biologists.com)
  • Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. (wikipedia.org)
  • Abstract: '[Researchers] have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. (harvard.edu)
  • P. 2194 middle column 2nd paragraph: 'Genome assembly relied on the use of several types of data, including clone-based sequence, whole-genome sequence from libraries with three insert sizes [2 kb, 10 kb, and 130 kb], and a Bacterial Artificial Chromosome (BAC)-based sequence-tagged site (STS) content map. (harvard.edu)
  • The genome sequence of the rice blast fungus Magnaporthe grisea. (genscript.com)
  • Based on ribosomal gene sequence data, P. pastoris was re-classified in 1995 into a new phylogenetically distinct genus, Komagataella [4], which was later split into several species based on 26S rRNA sequencing data [5]. (boku.ac.at)
  • 2009. Genome sequence of the recombinant protein production host Pichia pastoris. (boku.ac.at)
  • 2011. High-quality genome sequence of Pichia pastoris CBS7435. (boku.ac.at)
  • Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. (geneticsmr.com)
  • rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes. (wikipedia.org)
  • 5S rDNA is also present in independent tandem repeats as in Drosophila. (wikipedia.org)
  • It was found that in the genome of A. m. carnica there are at least two classes of 5S rDNA, each of which includes several structural variants. (cytgen.com)
  • The genomes of the two studied races of the Carpathian breed and that of the A. m. carnica from Genbank differ in the sets of such variants, while the 5S rDNA repeated units of the of A. cerana are identical within the genome. (cytgen.com)
  • The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. (flybase.org)
  • Whole mouse genome microarrays of paired placentas and cortices were performed to establish the transcriptomic inter-organ "placenta-cortex" signature in control and PAE groups at gestational day 20. (bvsalud.org)
  • We developed a novel technique to profile polysomal fractions (Poly-Ribo-Seq): RNAs bound by multiple ribosomes (and thus actively translated) are purified and the exact position of the translating ribosomes determined by ribosomal profiling. (cabd.es)
  • Almost half of these MRPs are evolutionarily exclusive to mitochondrial ribosomes, some of which were repurposed and accreted during reductive genome evolution 4 , 5 . (nature.com)
  • HOT1 expresses recombination-stimulating activity when it is inserted into novel locations in the yeast genome. (wikipedia.org)
  • Valuable insight into these important enzymes has already emerged from the analysis of the yeast and worm genomes. (rupress.org)
  • In addition, interventions leading to reduced translation, such as dietary restriction and reduced 60S ribosomal protein expression, elicits lifespan extension in yeast, worms and files [10] - [13] . (prolekarniky.cz)
  • This database hosts up-to-date annotation information of the genome of the methylotrophic yeast Pichia pastoris ( Komagataella spp. (boku.ac.at)
  • We employed conditional translating ribosome affinity purification (TRAP) followed by RNA sequencing (TRAP-seq) for transcriptome profiling of DA neurons in transgenic Drosophila lines expressing human PARIS wild type (WT) or mutant (C571A). (nature.com)
  • Modulation of the Drosophila transcriptome by developmental exposure t" by Vijay Shankar, Tatiana V. Morozova et al. (clemson.edu)
  • He was instrumental in the creation of the consortium, having initiated, along with Bikram Gill, discussions with interested colleagues on sequencing the wheat genome, at the ITMI meeting in Winnipeg in 2002, and organized, in 2003 in Washington, the first workshop designed to push forward the sequencing of the bread wheat genome. (wheatgenome.org)
  • 2002). Arabidopsis map-based cloning in the post-genome era. (geneticsmr.com)
  • Harmonizing model organism data in the Alliance of Genome Resources. (flybase.org)
  • Alliance of Genome Resources Portal: unified model organism research platform. (flybase.org)
  • 1996. Ribosomal RNA: small nucleolar RNAs make their mark. . (umd.edu)
  • In Xenopus, zebrafish, and Drosophila the major activation of zygotic transcription occurs as the cell cycle lengthens and gastrulation begins, a developmental period referred to as the midblastula transition. (elifesciences.org)
  • HOT1 includes an RNA polymerase I (PolI) transcription promoter that catalyzes 35S ribosomal rRNA gene transcription. (wikipedia.org)
  • Yet traditional genome-wide approaches fail to address complex patterns of gene expression, which include both synthesis and decay. (escholarship.org)
  • Expression of this genome entails several, highly regulated processes, with newly synthesised transcripts being cleaved, chemically modified, polyadenylated and further matured in neighbouring structures known as mitochondrial RNA granules (MRGs). (nature.com)
  • Using these methods on 122 cap analysis of gene expression (CAGE) samples of transcription start sites, we construct genome-wide 'promoteromes' in human and mouse consisting of a three-tiered hierarchy of transcription start sites, transcription start clusters, and transcription start regions. (biomedcentral.com)
  • To understand the differential gene expression in Anopheles following infection with drug-resistant Plasmodium , we conducted a genome-wide transcriptomic profiling analysis of Anopheles stephensi following feeding on mice with drug-resistant or drug-sensitive P. yoelii , observed changes in gene expression profiles and identified transcripts affected by the drug-resistant parasite. (biomedcentral.com)
  • We are one of the few groups worldwide that can apply functional genomics to the study of smORFs, due to our expertise in functional genetic analysis, bioinformatics, and ribosomal profiling. (cabd.es)
  • The Drosophila model allows strict control over the genetic background. (biomedcentral.com)
  • 1995. Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor. . (umd.edu)
  • Under non-stress conditions, start codons of these uORFs (uAUGs) have higher-than-background ribosomal association. (biorxiv.org)
  • 2004). Genome diversity and gene haplotypes in the grapevine (Vitis vinifera L.), as revealed by single nucleotide polymorphisms. (geneticsmr.com)
  • 1998). Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. (geneticsmr.com)
  • Yet, dopaminergic (DA) neuron-specific mechanistic underpinnings and genome-wide PARIS binding landscape has not been explored. (nature.com)
  • 12. Cherevatov, O.V. and Volkov, R.A., Molecular organization of 5S ribosomal DNA of Polyommatus icarus, Bull. (cytgen.com)
  • In the human genome there are 5 chromosomes with nucleolus organizer regions: the acrocentric chromosomes 13 (RNR1), 14 (RNR2), 15 (RNR3), 21 (RNR4) and 22 (RNR5). (wikipedia.org)
  • Whole genome sequencing of K. pastoris CBS704 and K. phaffii CBS7435 ([8 - 10]) confirmed the presence of four chromosomes and a chromosome rearrangement between K. pastoris and K. phaffii , as identified by pulsed field gel electrophoresis [11]. (boku.ac.at)
  • A concurrent subtractive assembly approach for identification of disease associated sub-meta-genomes. (stanford.edu)
  • After this initial stage of maternal control, which lasts for 1-2 mitotic divisions in mammals and 13 mitotic divisions in Drosophila, widespread transcription begins from the zygotic nuclei ( Tadros and Lipshitz, 2009 ). (elifesciences.org)
  • In this way a genome-wide picture of transcription start sites (TSSs) at single base-pair resolution can be obtained. (biomedcentral.com)
  • While the RNA components of the mitoribosome are mitochondrially-encoded, all MRPs and assembly factors are encoded in the nuclear genome, thus requiring coordination between two genomes for the assembly of these macromolecular complexes. (nature.com)
  • We propose that ribosome specificity may exist in mammals, providing evidence that one ribosomal protein can influence composition of the ribosome by regulating its own paralog. (prolekarniky.cz)
  • A JBrowse based genome browser is integrated into the annotation data website, displaying ORF annotation information, RNA-Seq data and flanking regions of particular features. (boku.ac.at)
  • Consistent with the hypothesis that either ribosomal protein can support translation, knockdown of Rpl22l1 impairs growth of cells lacking Rpl22 . (prolekarniky.cz)
  • We have successfully improved ribosomal profiling to detect, genome-wide, productive smORF translation. (cabd.es)
  • A multitasking plasma membrane protein coordinates cell division and energy metabolism in healthy-and perhaps also cancerous- Drosophila cells. (the-scientist.com)
  • Rudi has been a tireless advocate for sequencing the wheat genome and an energetic leader in advancing IWGSC strategies and research projects," said Kellye Eversole, Executive Director of the IWGSC. (wheatgenome.org)
  • Genome ResearchGenome Research. (umd.edu)