Abstract:
:RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and inter-molecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Xayaphoummine A,Viasnoff V,Harlepp S,Isambert Hdoi
10.1093/nar/gkl1036subject
Has Abstractpub_date
2007-01-01 00:00:00pages
614-22issue
2eissn
0305-1048issn
1362-4962pii
gkl1036journal_volume
35pub_type
杂志文章abstract::The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.20.3910
更新日期:2000-10-15 00:00:00
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
doi:10.1093/nar/25.24.5085
更新日期:1997-12-15 00:00:00
abstract::Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki087
更新日期:2005-01-01 00:00:00
abstract::We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem-loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV)...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr237
更新日期:2011-09-01 00:00:00
abstract::A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal-background segmentation and define...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.15.e75
更新日期:2001-08-01 00:00:00
abstract::Sug1 and Sug2 are two of six ATPases in the 19S regulatory particle of the 26S proteasome. We have shown previously that these proteins play a non-proteolytic role in the transcription of the GAL genes in yeast. In this study, we probe the requirement for these factors in stress-induced transcription in yeast. It is k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl012
更新日期:2006-03-03 00:00:00
abstract::IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl958
更新日期:2007-01-01 00:00:00
abstract::The repetitive fraction of the genome of the eukaryotic slime mould Physarum polycephalum is dominated by the Tp1 family of highly repetitive retrotransposon-like sequences. Tp1 elements consist of two terminal direct repeats of 277bp which flank an internal domain of 8.3kb. They are the major sequence component in th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.2.279
更新日期:1991-01-25 00:00:00
abstract::The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh184
更新日期:2004-01-16 00:00:00
abstract::The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is an open online resource, which maintains an up-to-date catalog of genome and metagenome projects in the context of a comprehensive list of associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Proje...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky977
更新日期:2019-01-08 00:00:00
abstract::The nucleotide sequences of the Streptomyces transposable element IS110 and its insertion site in the DNA of a derivative of the temperate phage luminal diameter C31 were determined. The element is inserted about 460 bp from the right-hand end of luminal diameter C31 DNA, in a region of apparently non-coding DNA. The ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.7053
更新日期:1987-09-11 00:00:00
abstract::Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.10.2521
更新日期:1976-10-01 00:00:00
abstract::We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh363
更新日期:2004-07-01 00:00:00
abstract::Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz838
更新日期:2019-11-18 00:00:00
abstract::Invertebrate RNA viruses are targets of the host RNA interference (RNAi) pathway, which limits virus infection by degrading viral RNA substrates. Several insect RNA viruses encode suppressor proteins to counteract this antiviral response. We recently demonstrated that the dsDNA virus Invertebrate iridescent virus 6 (I...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku910
更新日期:2014-10-29 00:00:00
abstract::Members of the Tc1/mariner superfamily of transposable elements isolated from vertebrates are transpositionally inactive due to the accumulation of mutations in their transposase genes. A novel open reading frame-trapping method was used to isolate uninterrupted transposase coding regions from the genome of the frog s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg910
更新日期:2003-12-01 00:00:00
abstract::LINE-1 (L1) is a highly successful autonomous non-LTR retrotransposon and a major force shaping mammalian genomes. Although there are about 600 000 L1 copies covering 23% of the rat genome, full-length rat L1s (L1Rn) with intact open reading frames (ORFs) representing functional master copies for retrotransposition ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1045
更新日期:2008-02-01 00:00:00
abstract::Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky098
更新日期:2018-04-20 00:00:00
abstract::The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku690
更新日期:2014-09-01 00:00:00
abstract::Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa915
更新日期:2021-01-08 00:00:00
abstract::Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zone...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq936
更新日期:2011-01-01 00:00:00
abstract::Telomerase activity, not detectable in somatic cells but frequently activated during carcinogenesis, confers immortality to tumors. Mechanisms governing expression of the catalytic subunit hTERT, the limiting factor for telomerase activity, still remain unclear. We previously proposed a model in which the binding of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq827
更新日期:2011-02-01 00:00:00
abstract::The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks420
更新日期:2012-07-01 00:00:00
abstract::Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm210
更新日期:2007-01-01 00:00:00
abstract::Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.7.1023
更新日期:1975-07-01 00:00:00
abstract::A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.12.3681
更新日期:1982-06-25 00:00:00
abstract::The iProClass database provides comprehensive, value-added descriptions of proteins and serves as a framework for data integration in a distributed networking environment. The protein information in iProClass includes family relationships as well as structural and functional classifications and features. The current v...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg044
更新日期:2003-01-01 00:00:00
abstract::DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku613
更新日期:2014-01-01 00:00:00
abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1239
更新日期:2010-04-01 00:00:00
abstract::Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa174
更新日期:2020-05-07 00:00:00