Abstract：
:H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address these questions, we have analyzed the contribution of dKDM5/LID, the main H3K4me3 demethylase in Drosophila, to the regulation of the pattern of H3K4me3. ChIP-seq results show that, at developmental genes, dKDM5/LID localizes at TSS and regulates H3K4me3. dKDM5/LID target genes are highly transcribed and enriched in active RNApol II and H3K36me3, suggesting a positive contribution to transcription. Expression-profiling show that, though weakly, dKDM5/LID target genes are significantly downregulated upon dKDM5/LID depletion. Furthermore, dKDM5/LID depletion results in decreased RNApol II occupancy, particularly by the promoter-proximal Pol llo(ser5) form. Our results also show that ASH2, an evolutionarily conserved factor that locates at TSS and is required for H3K4me3, binds and positively regulates dKDM5/LID target genes. However, dKDM5/LID and ASH2 do not bind simultaneously and recognize different chromatin states, enriched in H3K4me3 and not, respectively. These results indicate that, at developmental genes, dKDM5/LID and ASH2 coordinately regulate H3K4me3 at TSS and that this dynamic regulation contributes to transcription.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lloret-Llinares M,Pérez-Lluch S,Rossell D,Morán T,Ponsa-Cobas J,Auer H,Corominas M,Azorín Fdoi
10.1093/nar/gks773subject
Has Abstractpub_date
2012-10-01 00:00:00pages
9493-505issue
19eissn
0305-1048issn
1362-4962pii
gks773journal_volume
40pub_type
杂志文章abstract：:A dinucleoside monophosphate, 6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil-phosphoryl- (3'-5')-6,2'-anhydro-6-oxy-1-beta-D-arabinofuranosyluracil (I) was synthesized by the condensation reaction using DCC from 5'-monomethoxytrityl derivative(VII) and 3'-acetyl-5'-phosphate(X) of the monomer units. Yield was ca. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.3.479
更新日期：1974-03-01 00:00:00
abstract：:The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.18.3666
更新日期：2000-09-15 00:00:00
abstract：:Microsatellites are widely used as genetic markers because they are co-dominant, multiallelic, easily scored and highly polymorphic. A major drawback of microsatellite markers is the time and cost required to characterise them. We have developed a novel technique to reduce this cost by producing a microsatellite-rich ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.21.4369
更新日期：1996-11-01 00:00:00
abstract：:The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.11.3919
更新日期：1977-11-01 00:00:00
abstract：:The cDNA encoding Chinese hamster O6-alkylguanine-DNA-alkyltransferase (ATase) has been isolated from a library prepared from RNA isolated from V79 lung fibroblasts which had an upregulated level of this repair activity following stepwise selection with a chloroethylating agent (1, 2). Expression of the cDNA in E. col...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.8.1891
更新日期：1992-04-25 00:00:00
abstract：:Initial steps in the synthesis of functional tRNAs require 5'- and 3'-processing of precursor tRNAs (pre-tRNAs), which in yeast mitochondria are achieved by two endonucleases, RNase P and RNase Z. In this study, using a combination of detergent-free Blue Native Gel Electrophoresis, proteomics and in vitro testing of p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr941
更新日期：2012-02-01 00:00:00
abstract：:The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz574
更新日期：2019-08-22 00:00:00
abstract：:Little is known about the function of most non-coding RNAs (ncRNAs). The majority of long ncRNAs (lncRNAs) is expressed at very low levels and it is a matter of intense debate whether these can be of functional relevance. Here, we identified lncRNAs regulating the viability of lung cancer cells in a high-throughput RN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx076
更新日期：2017-05-19 00:00:00
abstract：:The rat beta-casein gene is a member of a small gene family, encoding the principal milk proteins. In order to understand the mechanisms by which its stage- and tissue-specific expression are regulated, initially, a 14 kb genomic clone containing the entire 7.5 kb rat beta-casein gene with 3.5 kb of 5' and 3.0 kb of 3...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.3.1027
更新日期：1988-02-11 00:00:00
abstract：:Molecular beacons (MBs) have the potential to provide a powerful tool for rapid RNA detection in living cells, as well as monitoring the dynamics of RNA expression in response to external stimuli. To exploit this potential, it is necessary to distinguish true signal from background signal due to non-specific interacti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq050
更新日期：2010-05-01 00:00:00
abstract：:In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.14.3433
更新日期：1998-07-15 00:00:00
abstract：:Real-time PCR is being used increasingly as the method of choice for mRNA quantification, allowing rapid analysis of gene expression from low quantities of starting template. Despite a wide range of approaches, the same principles underlie all data analysis, with standard approaches broadly classified as either absolu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng073
更新日期：2003-07-15 00:00:00
abstract：:We have cloned and mapped the sequences extending 38 kb 3' of the c-myc gene. This region is found to be highly repetitive in nature and hybridizes extensively with a BLUR 8 Alu probe. Unique sequence probes derived from this region were used to map the chromosomal breakpoints of a number of lymphoma cell lines with t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.10.4037
更新日期：1986-05-27 00:00:00
abstract：:A precursor of modified nucleoside Q isolated from E. coli methyl-deficient tRNA was determined to be 7-(aminomethyl)-7-deazaguanosine. The structure was deduced by means of its chromatographic and electrophoretic mobilities, and UV and mass spectra, in addition to comparison with the synthesized authentic compound. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.7.2289
更新日期：1978-07-01 00:00:00
abstract：:Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv469
更新日期：2015-06-23 00:00:00
abstract：:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.13.2672
更新日期：1997-07-01 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：:MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. Only few databases report protein-polysaccharide interactions and, to the best of our knowledge, there is no other database of extracellular interactions. MatrixDB takes ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq830
更新日期：2011-01-01 00:00:00
abstract：:The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.23.9823
更新日期：1989-12-11 00:00:00
abstract：:In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA-eEF1A-GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv376
更新日期：2015-05-19 00:00:00
abstract：:Use of the polymerase chain reaction (PCR) to amplify variable numbers of tandem repeat (VNTR) loci has become widely used in genetic typing. Unfortunately, preferential amplification of small allelic products relative to large allelic products may result in incorrect or ambiguous typing in a heterozygous sample. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.15.3050
更新日期：1995-08-11 00:00:00
abstract：:The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.11.3099
更新日期：1991-06-11 00:00:00
abstract：:Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1366
更新日期：2015-01-01 00:00:00
abstract：:For the first time mosaic nucleic acids composed of 50% RNA and 50% DNA can be obtained as transcripts with T7 RNA polymerase. Two NTPs could be replaced simultaneously in a transcription reaction. This means more than 40 deoxynucleotides were inserted in one transcript. Previously, a maximum of two deoxynucleotides c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.11.1845
更新日期：1995-06-11 00:00:00
abstract：:DNA polymerase delta (Pol δ) is responsible for the elongation and maturation of Okazaki fragments in eukaryotic cells. Proliferating cell nuclear antigen (PCNA) recruits Pol δ to the DNA and serves as a processivity factor. Here, we show that PCNA also stimulates the catalytic rate of Saccharomyces cerevisiae Pol δ b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1321
更新日期：2019-02-28 00:00:00
abstract：:Redefinition of UAG, UAA and UGA to specify a standard amino acid occurs in response to recoding signals present in a minority of mRNAs. This 'read-through' is in competition with termination and is utilized for gene expression. One of the recoding signals known to stimulate read-through is a hexanucleotide sequence o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.9.2011
更新日期：2002-05-01 00:00:00
abstract：:We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl170
更新日期：2006-07-01 00:00:00
abstract：:An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.3.833
更新日期：1988-02-11 00:00:00
abstract：:The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq834
更新日期：2011-01-01 00:00:00
abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm947
更新日期：2007-01-01 00:00:00
