Biogenesis of RNase P RNA from an intron requires co-assembly with cognate protein subunits.


:RNase P RNA (RPR), the catalytic subunit of the essential RNase P ribonucleoprotein, removes the 5' leader from precursor tRNAs. The ancestral eukaryotic RPR is a Pol III transcript generated with mature termini. In the branch of the arthropod lineage that led to the insects and crustaceans, however, a new allele arose in which RPR is embedded in an intron of a Pol II transcript and requires processing from intron sequences for maturation. We demonstrate here that the Drosophila intronic-RPR precursor is trimmed to the mature form by the ubiquitous nuclease Rat1/Xrn2 (5') and the RNA exosome (3'). Processing is regulated by a subset of RNase P proteins (Rpps) that protects the nascent RPR from degradation, the typical fate of excised introns. Our results indicate that the biogenesis of RPR in vivo entails interaction of Rpps with the nascent RNA to form the RNase P holoenzyme and suggests that a new pathway arose in arthropods by coopting ancient mechanisms common to processing of other noncoding RNAs.


Nucleic Acids Res


Nucleic acids research


Palsule G,Gopalan V,Simcox A




Has Abstract


2019-09-19 00:00:00














  • Human nucleotide excision repair in vitro: repair of pyrimidine dimers, psoralen and cisplatin adducts by HeLa cell-free extract.

    abstract::We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sibghatullah,Husain I,Carlton W,Sancar A

    更新日期:1989-06-26 00:00:00

  • Activation of interferon-regulated, dsRNA-dependent enzymes by human immunodeficiency virus-1 leader RNA.

    abstract::Human immunodeficiency virus-1 (HIV-1) leader RNA, which contains double-stranded regions due to inverted repeats, was shown to activate the dsRNA-dependent enzymes associated with the interferon system. HIV-1 leader RNA produced in vitro using SP6 RNA polymerase was characterized using probes for antisense and sense-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: SenGupta DN,Silverman RH

    更新日期:1989-02-11 00:00:00

  • All three RNA recognition motifs and the hinge region of HuC play distinct roles in the regulation of alternative splicing.

    abstract::The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hinman MN,Zhou HL,Sharma A,Lou H

    更新日期:2013-05-01 00:00:00

  • Differential effects of hnRNP D/AUF1 isoforms on HIV-1 gene expression.

    abstract::Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lund N,Milev MP,Wong R,Sanmuganantham T,Woolaway K,Chabot B,Abou Elela S,Mouland AJ,Cochrane A

    更新日期:2012-04-01 00:00:00

  • Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

    abstract::We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a ph...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Burnham DR,Nijholt B,De Vlaminck I,Quan J,Yusufzai T,Dekker C

    更新日期:2017-05-05 00:00:00

  • R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.

    abstract::R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Antonov AV,Schmidt EE,Dietmann S,Krestyaninova M,Hermjakob H

    更新日期:2010-07-01 00:00:00

  • Phylogenetic relationships and altered genome structures among Tetrahymena mitochondrial DNAs.

    abstract::Tetrahymena thermophila mitochondrial DNA is a linear molecule with two tRNAs, large subunit beta (LSU beta) rRNA (21S rRNA) and LSU alpha rRNA (5.8S-like RNA) encoded near each terminus. The DNA sequence of approximately 550 bp of this region was determined in six species of Tetrahymena. In three species the LSU beta...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Morin GB,Cech TR

    更新日期:1988-01-11 00:00:00

  • A mostly traditional approach improves alignment of bisulfite-converted DNA.

    abstract::Cytosines in genomic DNA are sometimes methylated. This affects many biological processes and diseases. The standard way of measuring methylation is to use bisulfite, which converts unmethylated cytosines to thymines, then sequence the DNA and compare it to a reference genome sequence. We describe a method for the cri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Frith MC,Mori R,Asai K

    更新日期:2012-07-01 00:00:00

  • Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site.

    abstract::The repetitive zinc finger domain of transcription factor IIIA binds 5S DNA and 5S RNA with similar affinity. Site directed mutagenesis of the Xenopus borealis somatic 5S RNA gene has been used to produce a series of derivatives of 5S RNA containing local sequence substitutions or sequence deletions. Gel mobility shif...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bogenhagen DF,Sands MS

    更新日期:1992-06-11 00:00:00

  • Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding.

    abstract::Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin alpha-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin-ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interact...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: García-Ortega L,Alvarez-García E,Gavilanes JG,Martínez-del-Pozo A,Joseph S

    更新日期:2010-07-01 00:00:00

  • A computer program package for storing and retrieving DNA/RNA and protein sequence data.

    abstract::A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Isono K

    更新日期:1984-01-11 00:00:00

  • Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.

    abstract::Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Penno C,Kumari R,Baranov PV,van Sinderen D,Atkins JF

    更新日期:2017-09-29 00:00:00

  • In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.

    abstract::Hammerhead ribozymes were transcribed from a dsDNA template containing four random nucleotides between stems II and III, which replace the naturally occurring GAA nucleotides. In vitro selection was used to select hammerhead ribozymes capable of in cis cleavage using denaturing polyacrylamide gels for the isolation of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Thomson JB,Sigurdsson ST,Zeuch A,Eckstein F

    更新日期:1996-11-15 00:00:00

  • Inferring the regulatory network behind a gene expression experiment.

    abstract::Transcription factors (TFs) and miRNAs are the most important dynamic regulators in the control of gene expression in multicellular organisms. These regulatory elements play crucial roles in development, cell cycling and cell signaling, and they have also been associated with many diseases. The Regulatory Network Anal...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bleda M,Medina I,Alonso R,De Maria A,Salavert F,Dopazo J

    更新日期:2012-07-01 00:00:00

  • Alternative-splicing-based bicistronic vectors for ratio-controlled protein expression and application to recombinant antibody production.

    abstract::In the last decade polycistronic vectors have become essential tools for both basic science and gene therapy applications. In order to co-express heterologous polypeptides, different systems have been developed from Internal Ribosome Entry Site (IRES) based vectors to the use of the 2A peptide. Unfortunately, these me...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fallot S,Ben Naya R,Hieblot C,Mondon P,Lacazette E,Bouayadi K,Kharrat A,Touriol C,Prats H

    更新日期:2009-11-01 00:00:00

  • REV1 and polymerase ζ facilitate homologous recombination repair.

    abstract::REV1 and DNA Polymerase ζ (REV3 and REV7) play important roles in translesion DNA synthesis (TLS) in which DNA replication bypasses blocking lesions. REV1 and Polζ have also been implicated in promoting repair of DNA double-stranded breaks (DSBs). However, the mechanism by which these two TLS polymerases increase tole...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sharma S,Hicks JK,Chute CL,Brennan JR,Ahn JY,Glover TW,Canman CE

    更新日期:2012-01-01 00:00:00

  • Ku heterodimer binds to both ends of the Werner protein and functional interaction occurs at the Werner N-terminus.

    abstract::The human Werner syndrome protein, WRN, is a member of the RecQ helicase family and contains 3'-->5' helicase and 3'-->5' exonuclease activities. Recently, we showed that the exonuclease activity of WRN is greatly stimulated by the human Ku heterodimer protein. We have now mapped this interaction physically and functi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Karmakar P,Snowden CM,Ramsden DA,Bohr VA

    更新日期:2002-08-15 00:00:00

  • Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis.

    abstract::The integrase (IN) protein of human immunodeficiency virus type 1 (HIV-1) catalyzes site-specific cleavage of 2 bases from the viral long terminal repeat (LTR) sequence yet it binds DNA with little DNA sequence specificity. We have previously demonstrated that the C-terminal half of IN (amino acids 154-288) possesses ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Woerner AM,Marcus-Sekura CJ

    更新日期:1993-07-25 00:00:00

  • Does the 'non-coding' strand code?

    abstract::The hypothesis that DNA strands complementary to the coding strand contain in phase coding sequences has been investigated. Statistical analysis of the 50 genes of bacteriophage T7 shows no significant correlation between patterns of codon usage on the coding and non-coding strands. In Bacillus and yeast genes the cor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sharp PM

    更新日期:1985-02-25 00:00:00

  • Use of an engineered ribozyme to produce a circular human exon.

    abstract::We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mikheeva S,Hakim-Zargar M,Carlson D,Jarrell K

    更新日期:1997-12-15 00:00:00

  • The major transcription initiation site of the SV40 late promoter is a potent thyroid hormone response element.

    abstract::Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily, which act as transcription factors upon binding to specific DNA sequences called thyroid hormone (T3) response elements (TREs). Such elements are found in the upstream regulatory region of promoters as well as in intragenic sequen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Desvergne B,Favez T

    更新日期:1997-05-01 00:00:00

  • Sequence of the pS2 mRNA induced by estrogen in the human breast cancer cell line MCF-7.

    abstract::We present the complete sequence of an mRNA which is induced by estrogen in the human breast cancer cell line MCF-7 [pS2 mRNA, Masiakowski et al., Nucleic Acids Res. 10, 7895-7903 (1982)]. Primer extension and cloning of double-stranded cDNA (ds-cDNA) into a vector designed to make full-length cDNA were used to determ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jakowlew SB,Breathnach R,Jeltsch JM,Masiakowski P,Chambon P

    更新日期:1984-03-26 00:00:00

  • Two-dimensional conformation-dependent electrophoresis (2D-CDE) to separate DNA fragments containing unmatched bulge from complex DNA samples.

    abstract::DNA fragments containing mispaired and modified bases, bulges, lesions and specific sequences have altered conformation. Methods for separating complex samples of DNA fragments based on conformation but independent of length have many applications, including (i) separation of mismatched or unmatched DNA fragments from...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gunnarsson GH,Thormar HG,Gudmundsson B,Akesson L,Jonsson JJ

    更新日期:2004-02-03 00:00:00

  • Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells.

    abstract::The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Choi JH,Gaddameedhi S,Kim SY,Hu J,Kemp MG,Sancar A

    更新日期:2014-02-01 00:00:00

  • A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm.

    abstract::Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Taniguchi J,Pandian GN,Hidaka T,Hashiya K,Bando T,Kim KK,Sugiyama H

    更新日期:2017-09-19 00:00:00

  • PRODORIC2: the bacterial gene regulation database in 2018.

    abstract::Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Eckweiler D,Dudek CA,Hartlich J,Brötje D,Jahn D

    更新日期:2018-01-04 00:00:00

  • X-inactivation: quantitative predictions of protein interactions in the Xist network.

    abstract::The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and mai...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Agostini F,Cirillo D,Bolognesi B,Tartaglia GG

    更新日期:2013-01-07 00:00:00

  • A G-tract element in apoptotic agents-induced alternative splicing.

    abstract::Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hai Y,Cao W,Liu G,Hong SP,Elela SA,Klinck R,Chu J,Xie J

    更新日期:2008-06-01 00:00:00

  • Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.

    abstract::CSP41 is a ubiquitous chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase (SDR) superfamily. To help elucidate the role of CSP41 in chloroplast gene regulation, the mechanisms that determine its substrate recognition and catalytic activity were investigated. A divalent metal is required f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bollenbach TJ,Stern DB

    更新日期:2003-08-01 00:00:00

  • A systemic transcriptome analysis reveals the regulation of neural stem cell maintenance by an E2F1-miRNA feedback loop.

    abstract::Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a high-throughput mRNA and miRNA profiling and isolated functional interac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Palm T,Hemmer K,Winter J,Fricke IB,Tarbashevich K,Sadeghi Shakib F,Rudolph IM,Hillje AL,De Luca P,Bahnassawy L,Madel R,Viel T,De Siervi A,Jacobs AH,Diederichs S,Schwamborn JC

    更新日期:2013-04-01 00:00:00