TY - JOUR T1 - Microbial oceanography in a sea of opportunity JF - NatureNature Y1 - 2009 A1 - Bowler, Chris A1 - Karl, David M. A1 - Rita R. Colwell KW - Astronomy KW - astrophysics KW - Biochemistry KW - Bioinformatics KW - Biology KW - biotechnology KW - cancer KW - cell cycle KW - cell signalling KW - climate change KW - Computational Biology KW - development KW - developmental biology KW - DNA KW - drug discovery KW - earth science KW - ecology KW - environmental science KW - Evolution KW - evolutionary biology KW - functional genomics KW - Genetics KW - Genomics KW - geophysics KW - immunology KW - interdisciplinary science KW - life KW - marine biology KW - materials science KW - medical research KW - medicine KW - metabolomics KW - molecular biology KW - molecular interactions KW - nanotechnology KW - Nature KW - neurobiology KW - neuroscience KW - palaeobiology KW - pharmacology KW - Physics KW - proteomics KW - quantum physics KW - RNA KW - Science KW - science news KW - science policy KW - signal transduction KW - structural biology KW - systems biology KW - transcriptomics AB - Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean's response to climate change, improving the predictive power of climate models. VL - 459 SN - 0028-0836 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 - Structure and expression of the Drosophila melanogaster gene for the U1 small nuclear ribonucleoprotein particle 70K protein. JF - Mol Cell Biol Y1 - 1990 A1 - Mancebo, R A1 - Lo, P C A1 - Mount, S M KW - Amino Acid Sequence KW - Animals KW - Base Sequence KW - Blotting, Northern KW - Blotting, Southern KW - Cloning, Molecular KW - DNA KW - Drosophila melanogaster KW - Gene expression KW - Gene Library KW - genes KW - HUMANS KW - Molecular Sequence Data KW - Molecular Weight KW - Oligonucleotide Probes KW - Poly A KW - Ribonucleoproteins KW - Ribonucleoproteins, Small Nuclear KW - RNA KW - RNA, Messenger KW - Sequence Homology, Nucleic Acid KW - Xenopus AB -

A genomic clone encoding the Drosophila U1 small nuclear ribonucleoprotein particle 70K protein was isolated by hybridization with a human U1 small nuclear ribonucleoprotein particle 70K protein cDNA. Southern blot and in situ hybridizations showed that this U1 70K gene is unique in the Drosophila genome, residing at cytological position 27D1,2. Polyadenylated transcripts of 1.9 and 3.1 kilobases were observed. While the 1.9-kilobase mRNA is always more abundant, the ratio of these two transcripts is developmentally regulated. Analysis of cDNA and genomic sequences indicated that these two RNAs encode an identical protein with a predicted molecular weight of 52,879. Comparison of the U1 70K proteins predicted from Drosophila, human, and Xenopus cDNAs revealed 68% amino acid identity in the most amino-terminal 214 amino acids, which include a sequence motif common to many proteins which bind RNA. The carboxy-terminal half is less well conserved but is highly charged and contains distinctive arginine-rich regions in all three species. These arginine-rich regions contain stretches of arginine-serine dipeptides like those found in transformer, transformer-2, and suppressor-of-white-apricot proteins, all of which have been identified as regulators of mRNA splicing in Drosophila melanogaster.

VL - 10 CP - 6 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 - 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 - The U1 small nuclear RNA-protein complex selectively binds a 5' splice site in vitro. JF - Cell Y1 - 1983 A1 - Mount, S M A1 - Pettersson, I A1 - Hinterberger, M A1 - Karmas, A A1 - Steitz, J A KW - Base Sequence KW - DNA-Directed RNA Polymerases KW - HUMANS KW - Nucleoproteins KW - Ribonuclease T1 KW - Ribonucleoproteins KW - Ribonucleoproteins, Small Nuclear KW - RNA KW - RNA Splicing KW - T-Phages AB -

The ability of purified U1 small nuclear RNA-protein complexes (U1 snRNPs) to bind in vitro to two RNAs transcribed from recombinant DNA clones by bacteriophage T7 RNA polymerase has been studied. A transcript which contains sequences corresponding to the small intron and flanking exons of the major mouse beta-globin gene is bound in marked preference to an RNA devoid of splice site sequences. The site of U1 snRNP binding to the globin RNA has been defined by T1 ribonuclease digestion of the RNA-U1 snRNP complex. A 15-17-nucleotide region, including the 5' splice site, remains undigested and complexed with the snRNP such that it can be co-precipitated by antibodies directed against the U1 snRNP. Partial proteinase K digestion of the U1 snRNP abolishes interaction with the globin RNA, indicating that the snRNP proteins contribute significantly to RNA binding. No RNA cleavage, splicing, or recognition of the 3' splice site by U1 snRNPs has been detected. Our results are discussed in terms of the probable role of U1 snRNPs in the messenger RNA splicing of eucaryotic cell nuclei.

VL - 33 CP - 2 ER - TY - JOUR T1 - Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing. JF - Nucleic Acids Res Y1 - 1981 A1 - Mount, S M A1 - Steitz, J A KW - Animals KW - Antibodies KW - Autoimmune Diseases KW - Base Sequence KW - Cells, Cultured KW - Cloning, Molecular KW - Drosophila melanogaster KW - HUMANS KW - Lupus Erythematosus, Systemic KW - Nucleic Acid Conformation KW - Nucleic Acid Hybridization KW - Ribonuclease T1 KW - Ribonucleoproteins KW - RNA KW - RNA, Small Nuclear AB -

U1 RNA from cultured Drosophila melanogaster cells (Kc) was identified by its ability to be recognized, as an RNP, by anti-(U1)RNP antibodies from human lupus patients. Its sequence was deduced largely from direct analysis of the RNA molecule and then confirmed by DNA sequence determinations on a genomic clone isolated by hybridization to Drosophila U1 RNA. The Drosophila U1 RNA sequence exhibits 72% agreement with human U1 RNA. Nucleotides 3-11, which are complementary to the entire consensus sequence for donor (5') splice junctions in hnRNA, and to part of the acceptor (3') consensus, are exactly conserved. However, nucleotides 14-21, postulated to interact only with acceptor junctions, differ. Comparison of the Drosophila U1 sequence with vertebrate U1 sequences allows a particular secondary structure model to be preferred over others. These results are consistent with the hypothesis that U1 snRNPs are involved in splicing, but suggest specific modifications of the model detailing molecular interactions between U1 RNA and hnRNA during the splicing reaction.

VL - 9 CP - 23 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 -