Abstract:
:Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as 'Olfactores conserved non-coding elements'.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sanges R,Hadzhiev Y,Gueroult-Bellone M,Roure A,Ferg M,Meola N,Amore G,Basu S,Brown ER,De Simone M,Petrera F,Licastro D,Strähle U,Banfi S,Lemaire P,Birney E,Müller F,Stupka Edoi
10.1093/nar/gkt030subject
Has Abstractpub_date
2013-04-01 00:00:00pages
3600-18issue
6eissn
0305-1048issn
1362-4962pii
gkt030journal_volume
41pub_type
杂志文章abstract::All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8269
更新日期:1984-11-12 00:00:00
abstract::A circular denaturation and restriction map of mitochondrial DNA from Neurospora crassa is presented. The map shows the position of all twelve fragments produced by restriction endonuclease Eco R I and the position of the largest Hin III fragment along the previously established map of AT-rich sequences. The two wild ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.11.3101
更新日期:1976-11-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3757
更新日期:1980-09-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm738
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.98
更新日期:2001-01-01 00:00:00
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journal_title:Nucleic acids research
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doi:10.1093/nar/15.20.8439
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.7007
更新日期:1990-12-11 00:00:00
abstract::The transcriptional activity of a human transposon-like family of repeats, called the THE-1 family, has been studied in cell culture and in human tissue. Both strands of THE-1 are present in several discrete length poly A plus RNAs. Primer extension studies and the structures of cDNA clones show that these THE-1 trans...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.13.5199
更新日期:1987-07-10 00:00:00
abstract::Transcription of ribosomal RNA genes is generally accepted to correlate with cell growth. Using primary cultures of adult bovine aortic endothelial (ABAE) cells, we have shown that transcription of rDNA in confluent cells falls to 5% of the transcription level in growing cells. Protein kinase NII appears to be a limit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.16.6625
更新日期:1989-08-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3638
更新日期:1995-09-25 00:00:00
abstract::In Eukaryotes, DNA is wound around the histone octamer forming the basic chromatin unit, the nucleosome. Atomic structures have been obtained from crystallography and single particle cryo-electron microscopy (cryoEM) of identical engineered particles. But native nucleosomes are dynamical entities with diverse DNA sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky670
更新日期:2018-09-28 00:00:00
abstract::Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.7.1362
更新日期:1997-04-01 00:00:00
abstract::Guanine-rich DNA sequences can form G-quadruplexes stabilized by stacked G-G-G-G tetrads in monovalent cation-containing solution. The length and number of individual G-tracts and the length and sequence context of linker residues define the diverse topologies adopted by G-quadruplexes. The review highlights recent so...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkm711
更新日期:2007-01-01 00:00:00
abstract::A direct correlation exists between the level of histone H4 hyperacetylation induced by sodium butyrate and the extent to which nucleosomes lose their compact shape and become elongated (62.0% of the particles have a length/width ratio over 1.6; overall mean in the length/width ratio = 1.83 +/- 0.48) when bound to ele...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.9.2739
更新日期:1990-05-11 00:00:00
abstract::A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.5013
更新日期:1998-11-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa131
更新日期:2020-05-07 00:00:00
abstract::The single nucleotide polymorphisms (SNPs) in conserved protein regions have been thought to be strong candidates that alter protein functions. Thus, we have developed SNP@Domain, a web resource, to identify SNPs within human protein domains. We annotated SNPs from dbSNP with protein structure-based as well as sequenc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl323
更新日期:2006-07-01 00:00:00
abstract::The mutations of 76 haemophilia B patients representing the whole population registered with the Malmö haemophilia centre (42) and referrals from the UK, were characterised. RFLP haplotype analysis of the defective genes indicated that 51 single base pair substitutions were definitely of independent origin and 27 of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.11.3227
更新日期:1990-06-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.24.7305
更新日期:1990-12-25 00:00:00
abstract::Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm088
更新日期:2007-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1060
更新日期:2018-01-04 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.21.6353
更新日期:1990-11-11 00:00:00
abstract::Lysinomicin, a naturally-occurring pseudodisaccharide, inhibits translation in prokaryotes. We report that lysinomicin (and three related compounds) are able to inhibit the self-splicing of group I introns, thus identifying pseudodisaccharides as a novel class of group I intron splicing inhibitors. Lysinomicin inhibit...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1994-11-25 00:00:00
abstract::The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.5.1053
更新日期:1981-03-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.12.2913
更新日期:1993-06-25 00:00:00
abstract::The immunoglobulin heavy chain intronic transcriptional enhancer (E mu) is part of a complex cis-regulatory DNA region which has notably been shown to modulate V(D)J rearrangements of associated variable gene segments. We have used recombination substrates comprised of the E mu enhancer together with various lengths o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.5.792
更新日期:1994-03-11 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
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doi:10.1093/nar/gki087
更新日期:2005-01-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.1169
更新日期:1988-02-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni012
更新日期:2005-01-13 00:00:00
abstract::Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3316
更新日期:2000-09-01 00:00:00