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The Phloem-Delivered RNA Pool Contains Small.noncoding RNAs and Interferes with Translation

PLANT PHYSIOLOGY 2009年第1期150卷 378-387页

作者： Zhang, Shoudong Sun, Li Kragler, Friedrich Univ Vienna Dept Biochem Max F Perutz Labs A-1030 Vienna Austria

In plants, the vascular tissue contains the enucleated sieve tubes facilitating long-distance transport of nutrients, hormones, and proteins. In addition, several mRNAs and small interfering RNAs/microRNAs were shown to be delivered via sieve tubes whose content is embodied by the phloem sap (PS). A number of these phloem transcripts are transported from source to sink tissues and function at targeted tissues. To gain additional insights into phloem-delivered RNAs and their potential role in signaling, we isolated and characterized PS RNA molecules distinct from microRNAs/small interfering RNAs with a size ranging from 30 to 90 bases. We detected a high number of full-length and phloem-specific fragments of.noncoding RNAs such as tRNAs, ribosomal RNAs, and spliceosomal RNAs in the PS of pumpkin (Cucurbita maxima). In vitro assays show that small quantities of PS RNA molecules efficiently inhibit translation in an unspecific manner. Proof of concept that PS-specific tRNA fragments may interfere with ribosomal activity was obtained with artificially produced tRNA fragments. The results are discussed in terms of a functional role for long distance delivered.noncoding PS RNAs.

关键词： .noncoding contains quantities long-distance tRNAs inhibit enucleated interfering transport system sink tissues sieve tubes ribosomal activity PS RNAs

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Regulation of histone H4 Lys16 acetylation by predicted alternative secondary structures in roX.noncoding RNAs

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MOLECULAR AND CELLULAR BIOLOGY 2008年第16期28卷 4952-4962页

作者： Park, Seung-Won Kuroda, Mitzi I. Park, Yongkyu Univ Med & Dent New Jersey New Jersey Med Sch Dept Cell Biol & Mol Med Newark NJ 07103 USA Brigham & Womens Hosp Harvard Partners Ctr Genet & Genom Boston MA 02115 USA Harvard Univ Sch Med Dept Genet Boston MA 02115 USA

Despite differences in size and sequence, the two.noncoding roX1 and roX2 RNAs are functionally redundant for dosage compensation of the Drosophila melanogaster male X chromosome. Consistent with functional conservation, we found that roX RNAs of distant Drosophila species could complement D. melanogaster roX mutants despite low homology. Deletion of a conserved predicted stem-loop structure in roX2, containing a short GUb (GUUNUACG box) in its 3' stem, resulted in a defect in histone H4K16 acetylation on the X chromosome in spite of apparently normal localization of the MSL complex. Two copies of the GUb sequence, newly termed the "roX box," were functionally redundant in roX2, as mutants in a single roX box had no phenotype, but double mutants showed reduced H4K16 acetylation. Interestingly, mutation of two of three roX boxes in the 3' end of roX1 RNA also reduced H4K16 acetylation. Finally, fusion of roX1 sequences containing a roX box restored function to a roX2 deletion RNA lacking its cognate roX box. These results support a model in which the functional redundancy between roX1 and roX2 RNAs is based, at least in part, on short GUUNUACG sequences that regulate the activity of the MSL complex.

关键词： .noncoding RNAs dosage predicted despite acetylation Medical School MSL complex stem-loop secondary structures Drosophila species functionally redundant roX RNA melanogaster roX GUb roX box

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Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution

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PLOS COMPUTATIONAL BIOLOGY 2009年第3期5卷 e1000299-e1000299页

作者： He, Xin Ling, Xu Sinha, Saurabh Univ Illinois Dept Comp Sci Urbana IL 61801 USA

Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved.noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs) and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i) the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii) binding sites in distal bound sequences (relative to transcription start sites) tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context.

关键词： .noncoding predicting probabilistic uses modules cross-species cis-regulatory sequence alignment sequence evolution TFBSs CRMs Statistical Alignment CRM sequences model of CRM

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Signatures of Purifying and Local Positive Selection in Human miRNAs

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AMERICAN JOURNAL OF HUMAN GENETICS 2009年第3期84卷 316-327页

作者： Quach, Helene Barreiro, Luis B. Laval, Guillaume Zidane, Nora Patin, Etienne Kidd, Kenneth K. Kidd, Judith R. Bouchier, Christiane Veuille, Michel Antoniewski, Christophe Quintana-Murci, Lluis CNRS Inst Pasteur URA3012 F-75015 Paris France Yale Univ Sch Med Dept Genet New Haven CT 06510 USA Museum Natl Hist Nat Equipe Genet Popolat Ecole Prat Hautes Etud UMR 5202 F-75005 Paris France CNRS Inst Pasteur Genet & Epigenet Drosophila URA 2578 F-75015 Paris France

MicroRNAs (miRNAs) are.noncoding RNAs involved in posttranscriptional gene repression, and their role in diverse physiological processes is increasingly recognized. Yet, few efforts have been devoted to evolutionary studies of human miRNAs. Knowledge about the way in which natural selection has targeted miRNAs should provide insight into their functional relevance as well as their mechanisms of action. Here we used miRNAs as a model system for investigating the influence of natural selection on gene regulation by characterizing the full spectrum of naturally occurring sequence variation of 117 human miRNAs from different populations worldwide. We found that purifying selection has globally constrained the diversity of miRNA-containing regions and has Strongly targeted the mature miRNA. This observation emphasizes that mutations in these molecules are likely to be deleterious, and therefore they can have severe phenotypic consequences on human health. More importantly, we obtained evidence of population-specific events of positive selection acting on a number of miRNA-containing regions. Notably, our analysis revealed that positive selection has targeted a "small-RNA-rich island" on chromosome 14, harboring both miRNAs and small nucleolar RNAs, in Europeans and East Asians. These observations support the notion that the tuning of gene expression contributes to the processes by which populations adapt to specific environments. These findings will fuel future investigations exploring how genetic and functional variation of miRNAs under selection affects the repression of their mRNA targets, increasing our understanding of the role of gene regulation in population adaptation and human disease.

关键词： .noncoding Naturally occurring MicroRNAs signatures gene regulation sequence variation purifying selection Centre National Characterizing Institut Pasteur mature miRNA human miRNAs Local Positive Selection miRNA-containing

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Understanding the degradation of hominid gene control

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PLOS COMPUTATIONAL BIOLOGY 2006年第3期2卷 198-198页

作者： Keightley, Peter D. Lercher, Martin J. Eyre-Walker, Adam Univ Edinburgh Edinburgh Midlothian Scotland Univ Bath Bath BA2 7AY Avon England Univ Sussex Brighton BN1 9RH E Sussex England

By comparing 500-bp blocks in mice and rats, we found that mean nucleotide divergence within 2 kb of the start and stop codons of protein-coding genes is substantially lower than that of introns, and decreases when approaching the coding sequence [1]. If nucleotide changes within introns are largely free from selection, this implies that.noncoding blocks close to genes evolved under selective constraints, presumably because they contain gene expression control regions.

关键词： .noncoding BLOCKS hominids murids Understanding the Degradation Hominid Gene Control Bush and Lahn

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Inhibition of cell growth and shoot development by a specific nucleotide sequence in a.noncoding viroid RNA

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PLANT CELL 2003年第6期15卷 1360-1374页

作者： Qi, YJ Ding, B Ohio State Univ Dept Plant Biol Columbus OH 43210 USA Ohio State Univ Ctr Plant Biotechnol Columbus OH 43210 USA

Viroids are small.noncoding and infectious RNAs that replicate autonomously and move systemically throughout an infected plant. The RNAs of the family Pospiviroidae contain a central conserved region (CCR) that has long been thought to be involved in replication. Here, we report that the CCR of Potato spindle tuber viroid (PSTVd) also plays a role in pathogenicity. A U257A change in the CCR converted the intermediate strain PSTVd(Int) to a lethal strain that caused severe growth stunting and premature death of infected plants. PSTVd with nucleotide U257 changed to C or G did not cause such symptoms. The pathogenic effect of the U257A substitution was abolished by a C259U substitution in the same RNA. Analyses of the pathogenic effects of the U257A substitution in three other PSTVd variants established A257 as a new pathogenicity determinant that functions independently and synergistically with the classic pathogenicity domain. The U257A substitution did not alter PSTVd secondary structure, replication levels, or tissue tropism. The stunted growth of PSTVd(Int)U257A-infected tomato plants resulted from restricted cell expansion but not cell division or differentiation. This was correlated positively with the downregulated expression of an expansin gene, LeExp2. Our results demonstrate that specific nucleotides in a.noncoding, pathogenic RNA have a profound effect in altering distinct cellular responses, which then lead to well-defined alterations in plant growth and developmental patterns. The feasibility of correlating viroid RNA sequence/structure with the altered expression of specific host genes, cellular processes, and developmental patterns makes viroid infection a valuable system in which to investigate host factors for symptom expression and perhaps also to characterize the mechanisms of RNA regulation of gene expression in plants.

关键词： .noncoding nucleotide sequence inhibition of cell shoot PSTVd variants infected plants viroids Potato spindle tuber pathogenicity domain infected tomato

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Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences

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JOURNAL OF HEREDITY 2001年第6期92卷 481-489页

作者： Chen, FC Vallender, EJ Wang, H Tzeng, CS Li, WH Univ Chicago Dept Ecol & Evolut Chicago IL 60637 USA Univ Chicago Comm Genet Chicago IL 60637 USA Natl Tsing Hua Univ Dept Life Sci Hsinchu Taiwan

To study the genomic divergence between human and chimpanzee, large-scale genomic sequence alignments were performed. The genomic sequences of human and chimpanzee were first masked with the RepeatMasker and the repeats were excluded before alignments. The repeats were then reinserted into the alignments of nonrepetitive segments and entire sequences were aligned again. A total of 2.3 million base pairs (Mb) of genomic sequences, including repeats, were aligned and the average nucleotide divergence was estimated to be 1.22%. The Jukes-Cantor (JC) distances (nucleotide divergences) in nonrepetitive (1.44 Mb) and repetitive sequences (0.86 Mb) are 1.14% and 1.34%, respectively, suggesting a slightly higher average rate in repetitive sequences. Annotated coding and.noncoding regions of homologous chimpanzee genes were also retrieved from GenBank and compared. The average synonymous and nonsynonymous divergences in 88 coding genes are 1.48% and 0.55%, respectively. The JC distances in intron, 5' flanking, 3' flanking, promoter, and pseudogene regions are 1.47%,1.41%,1.68%, 0.75%, and 1.39%, respectively. It is not clear why the genetic distances in most of these regions are somewhat higher than those in genomic sequences. One possible explanation is that some of the genes may be located in regions with higher mutation rates.

关键词： .noncoding alignments divergences excluded estimated genetic distances large-scale aligned genomic sequences Human and Chimpanzee nonrepetitive genomic divergence retrieved coding genes RepeatMasker JC distances

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Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations

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AMERICAN JOURNAL OF HUMAN GENETICS 2000年第1期66卷 216-234页

作者： Goddard, KAB Hopkins, PJ Hall, JM Witte, JS Case Western Reserve Univ Dept Epidemiol & Biostat Cleveland OH 44109 USA PPGx Inc La Jolla CA USA

Single-nucleotide polymorphisms (SNPs) may be extremely important for deciphering the impact of genetic variation on complex human diseases. The ultimate value of SNPs for linkage and association mapping studies depends in part on the distribution of SNP allele frequencies and intermarker linkage disequilibrium (LD) across populations. Limited information is available about these distributions on a genomewide scale, particularly for LD. Using 114 SNPs from 33 genes, we compared these distributions in five American populations (727 individuals) of African, European, Chinese, Hispanic, and Japanese descent. The allele frequencies were highly correlated across populations but differed by >20% for at least one pair of populations in 35% of SNPs. The correlation in LD was high for some pairs of populations but not for others (e.g., Chinese American or Japanese American vs. any other population). Regardless of population, average minor-allele frequencies were significantly higher for SNPs in.noncoding regions (20%-25%) than for SNPs in coding regions (12%-16%). Interestingly, we found that intermarker LD may be strongest with pairs of SNPs in which both markers are nonconservative substitutions, compared to pairs of SNPs where at least one marker is a conservative substitution. These results suggest that population differences and marker location within the gene may be important factors in the selection of SNPs for use in the study of complex disease with linkage or association mapping methods.

关键词： .noncoding distributions American populations single-nucleotide SNP allele allele-frequency Hispanic Chinese American average minor-allele pairs of SNPs

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Genomic sequence, splicing, and gene annotation

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AMERICAN JOURNAL OF HUMAN GENETICS 2000年第4期67卷 788-792页

作者： Mount, SM Univ Maryland Dept Cell Biol & Mol Genet College Pk MD 20742 USA

Examines the annotation of human genome sequence. Effects of nucleotides far from splice sites in splicing; Cause of inherited disease; Contribution of elements in the selection of splice sites.

关键词： .noncoding nucleotides recognized splice pre-mRNA Molecular Genetics genome annotation genomic sequence annotations conform gene finding gene annotation internal exons arbitrarily

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bic, a novel gene activated by proviral insertions in avian leukosis virus-induced lymphomas, is likely to function through its.noncoding RNA

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MOLECULAR AND CELLULAR BIOLOGY 1997年第3期17卷 1490-1502页

作者： Tam, W BenYehuda, D Hayward, WS CORNELL UNIV GRAD SCH MED SCI GRAD PROGRAM MOL BIOL NEW YORK NY 10021 USA

The bic locus is a common retroviral integration site in avian leukosis virus (ALV)-induced B-cell lymphomas originally identified by infection of chickens with ALVs of two different subgroups(Clurman and Hayward, Mel. Cell, Biol, 9:2657-2664, 1989), Based on its frequent association with c-myc activation and its preferential activation in metastatic tumors, the bic locus is thought to harbor a gene that can collaborate with c-myc in lymphomagenesis and presumably plays a role in late stages of tumor progression. In the present study, we have cloned and characterized two novel genes, bdw and bic, at the bic locus. bdw encoded a putative novel protein of 345 amino acids, However, its expression did not appear to be altered in tumor tissues, suggesting that it is not involved in oncogenesis, The bic gene consisted of two exons and was expressed as two spliced and alternatively polyadenylated transcripts at low levels in lymphoid/hematopoietic tissues. In tumors harboring bic integrations, proviruses drove bic gene expression by promoter insertion, resulting in high levels of expression of a chimeric RNA containing bic exon 2. Interestingly, bic lacked an extensive open reading frame, implying that it may function through its RNA. Computer analysis of RNA from small exon 2 of bic predicted extensive double-stranded structures, including a highly ordered RNA duplex between nucleotides 316 and 461, The possible role of bic in cell growth and differentiation is discussed in view of the emerging evidence that untranslated RNAs play a role in growth control.

关键词： .noncoding tumor progression virus-induced insertions metastatic Chickens proviral novel gene integration site Myc activation Sloan-Kettering avian leukosis lymphomagenesis bic locus common retroviral cell lymphomas bdw

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