TY - JOUR T1 - Genomic variation. Impact of regulatory variation from RNA to protein. JF - Science Y1 - 2015 A1 - Battle, Alexis A1 - Khan, Zia A1 - Wang, Sidney H A1 - Mitrano, Amy A1 - Ford, Michael J A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - 3' Flanking Region KW - 5' Flanking Region KW - Cell Line KW - Exons KW - Gene Expression Regulation KW - Genetic Variation KW - HUMANS KW - PHENOTYPE KW - Protein Biosynthesis KW - Quantitative Trait Loci KW - Ribosomes KW - RNA, Messenger KW - Transcription, Genetic AB -

The phenotypic consequences of expression quantitative trait loci (eQTLs) are presumably due to their effects on protein expression levels. Yet the impact of genetic variation, including eQTLs, on protein levels remains poorly understood. To address this, we mapped genetic variants that are associated with eQTLs, ribosome occupancy (rQTLs), or protein abundance (pQTLs). We found that most QTLs are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, eQTLs tend to have significantly reduced effect sizes on protein levels, which suggests that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we identified a class of cis QTLs that affect protein abundance with little or no effect on messenger RNA or ribosome levels, which suggests that they may arise from differences in posttranslational regulation.

VL - 347 CP - 6222 M3 - 10.1126/science.1260793 ER - TY - JOUR T1 - Primate transcript and protein expression levels evolve under compensatory selection pressures. JF - Science Y1 - 2013 A1 - Khan, Zia A1 - Ford, Michael J A1 - Cusanovich, Darren A A1 - Mitrano, Amy A1 - Pritchard, Jonathan K A1 - Gilad, Yoav KW - Animals KW - Evolution, Molecular KW - Gene Expression Regulation KW - HUMANS KW - Macaca mulatta KW - Pan troglodytes KW - Protein Biosynthesis KW - RNA, Messenger KW - Selection, Genetic KW - Species Specificity KW - Transcription, Genetic AB -

Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

VL - 342 CP - 6162 M3 - 10.1126/science.1242379 ER - TY - JOUR T1 - The genome and its implications. JF - Adv Parasitol Y1 - 2011 A1 - Teixeira, Santuza M A1 - El-Sayed, Najib M A1 - Araújo, Patrícia R KW - Animals KW - Antigens, Protozoan KW - Chagas Disease KW - Chromosomes KW - Comparative Genomic Hybridization KW - DNA, Protozoan KW - Gene Expression Regulation KW - Genetic Variation KW - Genome, Protozoan KW - Host-Parasite Interactions KW - HUMANS KW - Species Specificity KW - Synteny KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi AB -

Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.

VL - 75 M3 - 10.1016/B978-0-12-385863-4.00010-1 ER - TY - JOUR T1 - Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model JF - Journal of virologyJournal of virology Y1 - 2011 A1 - Shan, Liang A1 - Yang, Hung-Chih A1 - Rabi, S. Alireza A1 - Héctor Corrada Bravo A1 - Shroff, Neeta S. A1 - Irizarry, Rafael A. A1 - Zhang, Hao A1 - Margolick, Joseph B. A1 - Siliciano, Janet D. A1 - Siliciano, Robert F. KW - CD4-Positive T-Lymphocytes KW - Cells, Cultured KW - Gene Expression Profiling KW - Gene Expression Regulation, Viral KW - HIV-1 KW - HUMANS KW - Transcription, Genetic KW - Virus Integration KW - Virus Latency AB - Human immunodeficiency virus type 1 (HIV-1) establishes a latent reservoir in resting memory CD4(+) T cells. This latent reservoir is a major barrier to the eradication of HIV-1 in infected individuals and is not affected by highly active antiretroviral therapy (HAART). Reactivation of latent HIV-1 is a possible strategy for elimination of this reservoir. The mechanisms with which latency is maintained are unclear. In the analysis of the regulation of HIV-1 gene expression, it is important to consider the nature of HIV-1 integration sites. In this study, we analyzed the integration and transcription of latent HIV-1 in a primary CD4(+) T cell model of latency. The majority of integration sites in latently infected cells were in introns of transcription units. Serial analysis of gene expression (SAGE) demonstrated that more than 90% of those host genes harboring a latent integrated provirus were transcriptionally active, mostly at high levels. For latently infected cells, we observed a modest preference for integration in the same transcriptional orientation as the host gene (63.8% versus 36.2%). In contrast, this orientation preference was not observed in acutely infected or persistently infected cells. These results suggest that transcriptional interference may be one of the important factors in the establishment and maintenance of HIV-1 latency. Our findings suggest that disrupting the negative control of HIV-1 transcription by upstream host promoters could facilitate the reactivation of latent HIV-1 in some resting CD4(+) T cells. VL - 85 N1 - http://www.ncbi.nlm.nih.gov/pubmed/21430059?dopt=Abstract ER - TY - JOUR T1 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. JF - Environ Microbiol Y1 - 2005 A1 - Boonyaratanakornkit, Boonchai B A1 - Simpson, Anjana J A1 - Whitehead, Timothy A A1 - Fraser, Claire M A1 - el-Sayed, Najib M A A1 - Clark, Douglas S KW - Adaptation, Physiological KW - Archaeal Proteins KW - Cold Temperature KW - Gene Expression Profiling KW - Gene Expression Regulation, Archaeal KW - Heat-Shock Proteins KW - Hot Temperature KW - Methanococcus KW - Temperature KW - Transcription, Genetic AB -

Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85 degrees C to 65 degrees C and 95 degrees C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95 degrees C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an alpha subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65 degrees C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.

VL - 7 CP - 6 M3 - 10.1111/j.1462-2920.2005.00751.x ER - TY - JOUR T1 - Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. JF - Nucleic Acids Res Y1 - 2003 A1 - Haas, Brian J A1 - Delcher, Arthur L A1 - Mount, Stephen M A1 - Wortman, Jennifer R A1 - Smith, Roger K A1 - Hannick, Linda I A1 - Maiti, Rama A1 - Ronning, Catherine M A1 - Rusch, Douglas B A1 - Town, Christopher D A1 - Salzberg, Steven L A1 - White, Owen KW - algorithms KW - Alternative Splicing KW - Arabidopsis KW - DNA, Complementary KW - Expressed Sequence Tags KW - Genome, Plant KW - Introns KW - Plant Proteins KW - RNA, Plant KW - sequence alignment KW - software KW - Transcription, Genetic KW - Untranslated Regions AB -

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.

VL - 31 CP - 19 ER - TY - JOUR T1 - Analysis of stage-specific gene expression in the bloodstream and the procyclic form of Trypanosoma brucei using a genomic DNA-microarray. JF - Mol Biochem Parasitol Y1 - 2002 A1 - Diehl, Susanne A1 - Diehl, Frank A1 - El-Sayed, Najib M A1 - Clayton, Christine A1 - Hoheisel, Jörg D KW - Animals KW - Blotting, Northern KW - Escherichia coli KW - Gene expression KW - Gene Expression Profiling KW - Genes, Protozoan KW - HUMANS KW - Life Cycle Stages KW - Molecular Sequence Data KW - Oligonucleotide Array Sequence Analysis KW - Polymerase Chain Reaction KW - Transcription, Genetic KW - Trypanosoma brucei brucei AB -

A microarray comprising 21,024 different PCR products spotted on glass slides was constructed for gene expression studies on Trypanosoma brucei. The arrayed fragments were generated from a T. brucei shotgun clone library, which had been prepared from randomly sheared and size-fractionated genomic DNA. For the identification of stage-specific gene activity, total RNA from in vitro cultures of the human, long slender form and the insect, procyclic form of the parasite was labelled and hybridised to the microarray. Approximately 75% of the genomic fragments produced a signal and about 2% exhibited significant differences between the transcript levels in the bloodstream and procyclic forms. A few results were confirmed by Northern blot analysis or reverse-transcription and PCR. Three hundred differentially regulated clones have been selected for sequencing. So far, of 33 clones that showed about 2-fold or more over-expression in bloodstream forms, 15 contained sequences similar to those of VSG expression sites and at least six others appeared non-protein-coding. Of 29 procyclic-specific clones, at least eight appeared not to be protein-coding. A surprisingly large proportion of known regulated genes was already identified in this small sample, and some new ones were found, illustrating the utility of genomic arrays.

VL - 123 CP - 2 ER - TY - JOUR T1 - Trypanosoma cruzi: RNA structure and post-transcriptional control of tubulin gene expression. JF - Exp Parasitol Y1 - 2002 A1 - Bartholomeu, Daniella C A1 - Silva, Rosiane A A1 - Galvão, Lucia M C A1 - el-Sayed, Najib M A A1 - Donelson, John E A1 - Teixeira, Santuza M R KW - Animals KW - Base Sequence KW - Blotting, Northern KW - DNA, Complementary KW - DNA, Protozoan KW - Gene Expression Regulation KW - Half-Life KW - Life Cycle Stages KW - Molecular Sequence Data KW - RNA Processing, Post-Transcriptional KW - RNA, Messenger KW - RNA, Protozoan KW - Transcription, Genetic KW - Transfection KW - Trypanosoma cruzi KW - Tubulin AB -

Changes in tubulin expression are among the biochemical and morphological adaptations that occur during the life cycle of Trypanosomatids. To investigate the mechanism responsible for the differential accumulation of tubulin mRNAs in Trypanosoma cruzi, we determine the sequences of alpha- and beta-tubulin transcripts and analyzed their expression during the life cycle of the parasite. Two beta-tubulin mRNAs of 1.9 and 2.3 kb were found to differ mainly by an additional 369 nucleotides at the end of the 3' untranslated region (UTR). Although their transcription rates are similar in epimastigotes and amastigotes, alpha- and beta-tubulin transcripts are 3- to 6-fold more abundant in epimastigotes than in trypomastigotes and amastigotes. Accordingly, the half-lives of alpha- and beta-tubulin mRNAs are significantly higher in epimastigotes than in amastigotes. Transient transfection experiments indicated that positive regulatory elements occur in the 3' UTR plus downstream intergenic region of the alpha-tubulin gene and that both positive and negative elements occur in the equivalent regions of the beta-tubulin gene.

VL - 102 CP - 3-4 ER - TY - JOUR T1 - The genome sequence of Drosophila melanogaster. JF - Science Y1 - 2000 A1 - Adams, M D A1 - Celniker, S E A1 - Holt, R A A1 - Evans, C A A1 - Gocayne, J D A1 - Amanatides, P G A1 - Scherer, S E A1 - Li, P W A1 - Hoskins, R A A1 - Galle, R F A1 - George, R A A1 - Lewis, S E A1 - Richards, S A1 - Ashburner, M A1 - Henderson, S N A1 - Sutton, G G A1 - Wortman, J R A1 - Yandell, M D A1 - Zhang, Q A1 - Chen, L X A1 - Brandon, R C A1 - Rogers, Y H A1 - Blazej, R G A1 - Champe, M A1 - Pfeiffer, B D A1 - Wan, K H A1 - Doyle, C A1 - Baxter, E G A1 - Helt, G A1 - Nelson, C R A1 - Gabor, G L A1 - Abril, J F A1 - Agbayani, A A1 - An, H J A1 - Andrews-Pfannkoch, C A1 - Baldwin, D A1 - Ballew, R M A1 - Basu, A A1 - Baxendale, J A1 - Bayraktaroglu, L A1 - Beasley, E M A1 - Beeson, K Y A1 - Benos, P V A1 - Berman, B P A1 - Bhandari, D A1 - Bolshakov, S A1 - Borkova, D A1 - Botchan, M R A1 - Bouck, J A1 - Brokstein, P A1 - Brottier, P A1 - Burtis, K C A1 - Busam, D A A1 - Butler, H A1 - Cadieu, E A1 - Center, A A1 - Chandra, I A1 - Cherry, J M A1 - Cawley, S A1 - Dahlke, C A1 - Davenport, L B A1 - Davies, P A1 - de Pablos, B A1 - Delcher, A A1 - Deng, Z A1 - Mays, A D A1 - Dew, I A1 - Dietz, S M A1 - Dodson, K A1 - Doup, L E A1 - Downes, M A1 - Dugan-Rocha, S A1 - Dunkov, B C A1 - Dunn, P A1 - Durbin, K J A1 - Evangelista, C C A1 - Ferraz, C A1 - Ferriera, S A1 - Fleischmann, W A1 - Fosler, C A1 - Gabrielian, A E A1 - Garg, N S A1 - Gelbart, W M A1 - Glasser, K A1 - Glodek, A A1 - Gong, F A1 - Gorrell, J H A1 - Gu, Z A1 - Guan, P A1 - Harris, M A1 - Harris, N L A1 - Harvey, D A1 - Heiman, T J A1 - Hernandez, J R A1 - Houck, J A1 - Hostin, D A1 - Houston, K A A1 - Howland, T J A1 - Wei, M H A1 - Ibegwam, C A1 - Jalali, M A1 - Kalush, F A1 - Karpen, G H A1 - Ke, Z A1 - Kennison, J A A1 - Ketchum, K A A1 - Kimmel, B E A1 - Kodira, C D A1 - Kraft, C A1 - Kravitz, S A1 - Kulp, D A1 - Lai, Z A1 - Lasko, P A1 - Lei, Y A1 - Levitsky, A A A1 - Li, J A1 - Li, Z A1 - Liang, Y A1 - Lin, X A1 - Liu, X A1 - Mattei, B A1 - McIntosh, T C A1 - McLeod, M P A1 - McPherson, D A1 - Merkulov, G A1 - Milshina, N V A1 - Mobarry, C A1 - Morris, J A1 - Moshrefi, A A1 - Mount, S M A1 - Moy, M A1 - Murphy, B A1 - Murphy, L A1 - Muzny, D M A1 - Nelson, D L A1 - Nelson, D R A1 - Nelson, K A A1 - Nixon, K A1 - Nusskern, D R A1 - Pacleb, J M A1 - Palazzolo, M A1 - Pittman, G S A1 - Pan, S A1 - Pollard, J A1 - Puri, V A1 - Reese, M G A1 - Reinert, K A1 - Remington, K A1 - Saunders, R D A1 - Scheeler, F A1 - Shen, H A1 - Shue, B C A1 - Sidén-Kiamos, I A1 - Simpson, M A1 - Skupski, M P A1 - Smith, T A1 - Spier, E A1 - Spradling, A C A1 - Stapleton, M A1 - Strong, R A1 - Sun, E A1 - Svirskas, R A1 - Tector, C A1 - Turner, R A1 - Venter, E A1 - Wang, A H A1 - Wang, X A1 - Wang, Z Y A1 - Wassarman, D A A1 - Weinstock, G M A1 - Weissenbach, J A1 - Williams, S M A1 - Worley, K C A1 - Wu, D A1 - Yang, S A1 - Yao, Q A A1 - Ye, J A1 - Yeh, R F A1 - Zaveri, J S A1 - Zhan, M A1 - Zhang, G A1 - Zhao, Q A1 - Zheng, L A1 - Zheng, X H A1 - Zhong, F N A1 - Zhong, W A1 - Zhou, X A1 - Zhu, S A1 - Zhu, X A1 - Smith, H O A1 - Gibbs, R A A1 - Myers, E W A1 - Rubin, G M A1 - Venter, J C KW - Animals KW - Biological Transport KW - Chromatin KW - Cloning, Molecular KW - Computational Biology KW - Contig Mapping KW - Cytochrome P-450 Enzyme System KW - DNA Repair KW - DNA Replication KW - Drosophila melanogaster KW - Euchromatin KW - Gene Library KW - Genes, Insect KW - Genome KW - Heterochromatin KW - Insect Proteins KW - Nuclear Proteins KW - Protein Biosynthesis KW - Sequence Analysis, DNA KW - Transcription, Genetic AB -

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We 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. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

VL - 287 CP - 5461 ER - TY - JOUR T1 - Characterization of enhancer-of-white-apricot in Drosophila melanogaster. JF - Genetics Y1 - 1990 A1 - Peng, X B A1 - Mount, S M KW - Alleles KW - Animals KW - Blotting, Northern KW - DNA Transposable Elements KW - Drosophila melanogaster KW - Eye Color KW - Female KW - Heterozygote KW - Homozygote KW - Male KW - Nucleic Acid Hybridization KW - PHENOTYPE KW - Poly A KW - Reproduction KW - RNA KW - RNA, Messenger KW - Transcription, Genetic AB -

The white-apricot (wa) allele differs from the wild-type white gene by the presence of the retrovirus-like transposable element copia within the transcription unit. Most RNAs derived from wa have 3' termini within this insertion, and only small amounts of structurally normal RNA are produced. The activity of wa is reduced in trans by a semidominant mutation in the gene Enhancer-of-white-apricot (E(wa). Flies that are wa and heterozygous for the enhancer have eyes which are much lighter than the orange-yellow of wa alone while E(wa) homozygotes have white eyes. This semidominant effect on pigmentation is correlated with a corresponding decrease in white RNA having wild type structure, and flies homozygous for E(wa) have increased levels of aberrant RNAs. Three reverant alleles of E(wa) generated by reversion of the dominant enhancer phenotype with gamma radiation are noncomplementing recessive lethals, with death occurring during the larval stage. The effects on wa eye pigmentation of varying doses of the original E(wa) allele, the wild type allele, and the revertant alleles suggest that the original E(wa) allele produces a product that interferes with the activity of the wild type gene and that the revertants are null alleles. We propose that the E(wa) gene product influences the activity of the downstream copia long terminal repeat in 3' end formation.

VL - 126 CP - 4 ER - TY - JOUR T1 - Lessons from mutant globins. JF - Nature Y1 - 1983 A1 - Mount, S A1 - Steitz, J KW - Globins KW - HUMANS KW - Mutation KW - RNA, Messenger KW - Thalassemia KW - Transcription, Genetic VL - 303 CP - 5916 ER - TY - JOUR T1 - Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites. JF - Cell Y1 - 1983 A1 - Bernstein, L B A1 - Mount, S M A1 - Weiner, A M KW - Animals KW - Base Sequence KW - DNA KW - genes KW - HUMANS KW - Nucleic Acid Conformation KW - Rats KW - Recombination, Genetic KW - Repetitive Sequences, Nucleic Acid KW - RNA KW - RNA, Small Nuclear KW - RNA-Directed DNA Polymerase KW - Templates, Genetic KW - Transcription, Genetic AB -

We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3' end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5' end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.

VL - 32 CP - 2 ER - TY - JOUR T1 - Small ribonucleoproteins from eukaryotes: structures and roles in RNA biogenesis. JF - Cold Spring Harb Symp Quant Biol Y1 - 1983 A1 - Steitz, J A A1 - Wolin, S L A1 - Rinke, J A1 - Pettersson, I A1 - Mount, S M A1 - Lerner, E A A1 - Hinterberger, M A1 - Gottlieb, E KW - Animals KW - Base Sequence KW - HeLa Cells KW - HUMANS KW - Mice KW - Molecular Weight KW - Nucleic Acid Conformation KW - Nucleic Acid Hybridization KW - Nucleoproteins KW - Ribonucleoproteins KW - Ribonucleoproteins, Small Nuclear KW - RNA Polymerase III KW - Transcription, Genetic VL - 47 Pt 2 ER - TY - JOUR T1 - Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein. JF - Cell Y1 - 1983 A1 - Padgett, R A A1 - Mount, S M A1 - Steitz, J A A1 - Sharp, P A KW - Adenoviruses, Human KW - Antigens KW - Autoantigens KW - Base Sequence KW - Cell Extracts KW - HeLa Cells KW - HUMANS KW - Immune Sera KW - Nucleic Acid Precursors KW - Ribonucleoproteins KW - Ribonucleoproteins, Small Nuclear KW - RNA KW - RNA Precursors KW - RNA Splicing KW - RNA, Messenger KW - RNA, Small Cytoplasmic KW - RNA, Viral KW - Transcription, Genetic AB -

A mouse monoclonal antibody and human autoimmune sera directed against various classes of small ribonucleoprotein particles have been tested for inhibition of mRNA splicing in a soluble in vitro system. The splicing of the first and second leader exons of adenovirus late RNA was inhibited only by those sera that reacted with U1 RNP. Both U1 RNP-specific human autoimmune serum and sera directed against the Sm class of small nuclear RNPs, including a mouse monoclonal antibody, specifically inhibited splicing. Antisera specific for U2 RNP had no effect on splicing nor did antisera specific for the La or Ro class of small RNPs. These results suggest that U1 RNP is essential for the splicing of mRNA precursors.

VL - 35 CP - 1 ER - TY - JOUR T1 - Structure and function of small ribonucleoproteins from eukaryotic cells. JF - Princess Takamatsu Symp Y1 - 1982 A1 - Steitz, J A A1 - Berg, C A1 - Gottlieb, E A1 - Hardin, J A A1 - Hashimoto, C A1 - Hendrick, J P A1 - Hinterberger, M A1 - Krikeles, M A1 - Lerner, M R A1 - Mount, S M KW - Antigen-Antibody Complex KW - Autoantibodies KW - HUMANS KW - Lupus Erythematosus, Systemic KW - Nucleoproteins KW - Ribonucleoproteins KW - RNA Polymerase III KW - Transcription, Genetic AB -

Autoantibodies from patients with systemic lupus erythematosus and other related diseases have been used to identify and study small RNA-protein complexes from mammalian cells. Properties of three previously described and several new classes of small ribonucleoproteins (RNPs) are reviewed. The sequence of Drosophila U1 RNA reveals that the region proposed to pair with 5' splice junctions is conserved, while that proposed to interact with 3' junctions diverges; this forces some revision of the model for U1 small nuclear (sn)RNP participation in hnRNA splicing. Further characterization of the Ro and La small RNPs has shown that the Ro small cytoplasmic (sc)RNPs are a subclass of La RNPs. Both tRNA and 5S rRNA precursors are at least transiently associated with the La protein. This raises the possibility that the La protein may be an RNA polymerase III transcription factor.

VL - 12 ER - TY - JOUR T1 - Transcription of cloned tRNA and 5S RNA genes in a Drosophila cell free extract. JF - Nucleic Acids Res Y1 - 1981 A1 - Dingermann, T A1 - Sharp, S A1 - Appel, B A1 - DeFranco, D A1 - Mount, S A1 - Heiermann, R A1 - Pongs, O A1 - Söll, D KW - Animals KW - Cell-Free System KW - Cloning, Molecular KW - Drosophila KW - In Vitro Techniques KW - RNA KW - RNA Polymerase III KW - RNA, Transfer KW - Transcription, Genetic KW - Xenopus laevis AB -

We describe the preparation of a cell-free extract from Drosophila Kc cells which allows transcription of a variety of cloned eukaryotic RNA polymerase III genes. The extract has low RNA-processing nuclease activity and thus the major products obtained are primary transcripts.

VL - 9 CP - 16 ER -