Abstract：
:Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the human and mouse mRNA foldings and found a pronounced periodic pattern of nucleotide involvement in mRNA secondary structure. We show that this pattern is created by the structure of the genetic code, and the dinucleotide relative abundances are important for the maintenance of mRNA secondary structure. Although synonymous codon usage contributes to this pattern, it is intrinsic to the structure of the genetic code and manifests itself even in the absence of synonymous codon usage bias at the 4-fold degenerate sites. While all codon sites are important for the maintenance of mRNA secondary structure, degeneracy of the code allows regulation of stability and periodicity of mRNA secondary structure. We demonstrate that the third degenerate codon sites contribute most strongly to mRNA stability. These results convincingly support the hypothesis that redundancies in the genetic code allow transcripts to satisfy requirements for both protein structure and RNA structure. Our data show that selection may be operating on synonymous codons to maintain a more stable and ordered mRNA secondary structure, which is likely to be important for transcript stability and translation. We also demonstrate that functional domains of the mRNA [5'-untranslated region (5'-UTR), CDS and 3'-UTR] preferentially fold onto themselves, while the start codon and stop codon regions are characterized by relaxed secondary structures, which may facilitate initiation and termination of translation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Shabalina SA,Ogurtsov AY,Spiridonov NAdoi
10.1093/nar/gkl287subject
Has Abstractpub_date
2006-05-08 00:00:00pages
2428-37issue
8eissn
0305-1048issn
1362-4962pii
34/8/2428journal_volume
34pub_type
杂志文章abstract：:Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2547
更新日期：1978-07-01 00:00:00
abstract：:The three dimensional crystal structure of T5 5'-3' exonuclease was compared with that of two other members of the 5'-3' exonuclease family: T4 ribonuclease H and the N-terminal domain of Thermus aquaticus DNA polymerase I. Though these structures were largely similar, some regions of these enzymes show evidence of si...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4224
更新日期：1997-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.25.7097
更新日期：1991-12-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1008
更新日期：2015-01-01 00:00:00
abstract：:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of chromatin interactio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx885
更新日期：2017-12-15 00:00:00
abstract：:With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw332
更新日期：2016-07-08 00:00:00
abstract：:In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1133
更新日期：2015-12-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.18.3778
更新日期：1995-09-25 00:00:00
abstract：:Diadenosine 5',5'"-P1,P4-tetraphosphate (Ap4A) has been detected in cysts and developing embryos of the brine shrimp Artemia in amounts 10(4)-10(6) times lower than that of the guanine analogue, Gp4G. The unexpectedly high level of Ap4A in dormant cysts of 2.37 pmol/10(6) cells can be reduced to 0.03 pmol/10(6) cells ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1609
更新日期：1984-02-10 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq723
更新日期：2011-01-01 00:00:00
abstract：:THY Pol-2 intein, from Thermococcus hydrothermalis, belongs to the same allelic family as TLI Pol-2 (PI-TLII), Tfu Pol-2 (PI-TFUII) and TspTY Pol-3 mini-intein, all inserted at the pol-c site of archaeal DNA polymerase genes. This new intein was cloned, expressed in Escherichia coli and purified. The intein is a speci...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.21.4391
更新日期：2000-11-01 00:00:00
abstract：:Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1114
更新日期：2017-02-28 00:00:00
abstract：:The development of complex methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where optima are sought in a multidimensional parameter space through step-by-step optimizations. The difficulty of miniaturizing reactions under the microliter volumes usually handled in multiwe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa079
更新日期：2020-04-17 00:00:00
abstract：:Numerous examples exist of how disrupting the actions of physiological regulators of blood cell development yields hematologic malignancies. The master regulator of hematopoietic stem/progenitor cells GATA-2 was cloned almost 20 years ago, and elegant genetic analyses demonstrated its essential function to promote hem...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
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更新日期：2012-07-01 00:00:00
abstract：:Human telomerase is a ribonucleoprotein which uses its internal RNA moiety as a template for telomeric DNA synthesis. This enzyme is up-regulated in most malignant tumors and is therefore considered as a possible cancer target. Here we examined the effects of differently modified oligomers on telomeraseactivity from H...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.4.1152
更新日期：1999-02-15 00:00:00
abstract：:Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv903
更新日期：2016-01-29 00:00:00
abstract：:Chicken globin double-stranded cDNA was synthesised from anaemic adult reticulocyte alpha- and beta-globin mRNA and ligated into the Hind III site of pBR322 using synthetic Hind III decamers. Transformation of E. coli x1776 resulted in the production of a number of alpha- and beta-cDNA clones. One of the alpha-type cl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.6.1187
更新日期：1980-03-25 00:00:00
abstract：:A DNA methylase has been purified 270-fold from HeLa cell nuclei by chromatography on DEAE-cellulose, phosphocellulose, and hydroxyapatite. The enzyme transfers methyl groups from S-adenosyl-L-methionine to cytosine residues in DNA. The sole product of the reaction has been identified as 5-methylcytosine. The enzyme i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.10.1669
更新日期：1975-10-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.10.2086
更新日期：1999-05-15 00:00:00
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更新日期：1988-04-11 00:00:00
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journal_title：Nucleic acids research
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更新日期：2015-02-27 00:00:00
abstract：:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along ...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2008-07-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2015-12-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2009-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2005-01-20 00:00:00
abstract：:PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.304
更新日期：1998-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：1986-07-11 00:00:00
abstract：:The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw716
更新日期：2016-10-14 00:00:00
abstract：:From a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties. The planning of such an in vitro selection experiment requires some consideration regarding how much DNA template or RNA transcript should be used initially. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.17.3437
更新日期：1996-09-01 00:00:00
abstract：:DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn055
更新日期：2008-04-01 00:00:00
