Abstract：
:RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from microarray data with a so far unreached accuracy. Based on such measurements of RNA half-lives for human B-cells and mouse fibroblasts, we identified conserved regulatory principles for a large number of biological processes. We show that different regulatory patterns between functionally similar proteins are characterized by differences in the half-life of the corresponding transcripts and can be identified by measuring RNA half-life. We identify more than 100 protein families which show such differential regulatory patterns in both species. Additionally, we provide strong evidence that the activity of protein complexes consisting of subunits with overall long transcript half-lives can be regulated by transcriptional regulation of individual key subunits with short-lived transcripts. Based on this observation, we predict more than 100 key regulatory subunits for human complexes of which 28% could be confirmed in mice (P < 10(-9)). Therefore, this atlas of transcript half-lives provides new fundamental insights into many cellular processes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Friedel CC,Dölken L,Ruzsics Z,Koszinowski UH,Zimmer Rdoi
10.1093/nar/gkp542subject
Has Abstractpub_date
2009-09-01 00:00:00pages
e115issue
17eissn
0305-1048issn
1362-4962pii
gkp542journal_volume
37pub_type
杂志文章abstract：:LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Currently, it contains entries for 19,604 UniProt proteins (HS: 13,342; AT: 6262). Each database entry contains the experimentally der...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq927
更新日期：2011-01-01 00:00:00
abstract：:PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. The mission of PubChem is to deliver free and easy access to all deposited data, and to provide intuitive data analysis tools. The PubChem BioAssay database currently contains 500,000 des...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1132
更新日期：2012-01-01 00:00:00
abstract：:Stem cell fate decisions are controlled by a molecular network in which transcription factors and miRNAs are of key importance. To systemically investigate their impact on neural stem cell (NSC) maintenance and neuronal commitment, we performed a high-throughput mRNA and miRNA profiling and isolated functional interac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt070
更新日期：2013-04-01 00:00:00
abstract：:An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regula...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq032
更新日期：2010-06-01 00:00:00
abstract：:Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.3.778
更新日期：1998-02-01 00:00:00
abstract：:We have established a sensitive, monoclonal antibody (Mab)-based procedure permitting the selective enrichment of sequences containing the miscoding alkylation product O6-ethylguanine (O6-EtGua) from mammalian DNA. H5 rat hepatoma cells were reacted with the N-nitroso carcinogen N-ethyl-N-nitrosourea in vitro, to give...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.16.4467
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abstract：:U1-snRNA is an integral part of the U1 ribonucleoprotein pivotal for pre-mRNA splicing. Toll-like receptor (TLR) signaling has recently been associated with immunoregulatory capacities of U1-snRNA. Using lung A549 epithelial/carcinoma cells, we report for the first time on interferon regulatory factor (IRF)-3 activati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp525
更新日期：2009-08-01 00:00:00
abstract：:The abundance and complexity of total poly(A)+RNA of human normal unstimulated lymphocytes, PHA-stimulated and leukemic lymphocytes were examined using the cDNA-poly(A)+ RNA hybridization technique. It was found that in both PHA-stimulated and leukemic lymphocytes the complexity of total poly(A)+RNA is strongly reduce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.24.7013
更新日期：1981-12-21 00:00:00
abstract：:T-region transfer from wild-type Agrobacterium strains is thought to be an orientated process, starting at the right border repeat and terminating at the left border repeat of the T-region. Here we demonstrate that a right border repeat in the inverted orientation relative to the onc-genes can also mediate transfer of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.21.10225
更新日期：1988-11-11 00:00:00
abstract：:In plants, small interfering RNAs (siRNAs) can trigger a silencing signal that may spread within a tissue to adjacent cells or even systemically to other organs. Movement of the signal is initially limited to a few cells, but in some cases the signal can be amplified and travel over larger distances. How far silencing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1240
更新日期：2011-04-01 00:00:00
abstract：:This is a study of the effect of total and partial deuteration of solvent on critical temperatures and profiles of all four reactions occurring in poly(A) x n poly(U) (n = 1 or 2) aqueous systems. The study was done at observational times not longer than hydrogen exchange times at base pairs in helically ordered struc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.18.4283
更新日期：1980-09-25 00:00:00
abstract：:Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.23.10985
更新日期：1988-12-09 00:00:00
abstract：:We have investigated the mechanism of the electrophoresis-driven chromatin aggregation which had been described by Weintraub (1984, Cell 38, 17-27) as a putative mean for propagation of genetic repression in eukaryotes. We show that the oligonucleosome aggregates are assembled de novo at the starting zone of DNP elect...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.24.7397
更新日期：1990-12-25 00:00:00
abstract：:A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.12.4857
更新日期：1987-06-25 00:00:00
abstract：:Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr444
更新日期：2011-10-01 00:00:00
abstract：:An updated list of DNA sequences cloned from the human genome over the past year (1991) is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic probes comprising both gene and pseudogene sequences. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.suppl.2181
更新日期：1992-05-11 00:00:00
abstract：:The repAC operon of plasmid RSF1010 consists of the genes for proteins E, F, RepA (DNA helicase), and RepC (origin-binding initiator protein) and is transcriptionally initiated by a promoter called P4. We have studied the expression of the repAC operon in vivo by using fusions to the lacZ reporter gene. The results sh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.21.6215
更新日期：1990-11-11 00:00:00
abstract：:We have constructed a complete, five-enzyme restriction map of the genome of the archaeon Halobacterium sp. GRB, based on a set of 84 overlapping cosmid clones. Fewer than 30 kbp, in three gaps, remain uncloned. The genome consists of five replicons: a chromosome (2038 kbp) and four plasmids (305, 90, 37, and 1.8 kbp)...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.8.1476
更新日期：1994-04-25 00:00:00
abstract：:The Moloney murine leukemia virus (MLV) is a prototype gammaretrovirus requiring nuclear disassembly before DNA integration. In the nucleus, integration site selection towards promoter/enhancer elements is mediated by the host factor bromo- and extraterminal domain (BET) proteins (bromodomain (Brd) proteins 2, 3 and 4...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1157
更新日期：2019-02-20 00:00:00
abstract：:Cis-elements (-933 to -641) upstream of the human M creatine kinase gene cap site contain an enhancer that confers developmental and tissue-specific expression to the chloramphenicol acetyltransferase gene in C2C12 myogenic cells transfected in culture. Division of the enhancer at -770 into a 5' fragment that includes...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.9.2313
更新日期：1992-05-11 00:00:00
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journal_title：Nucleic acids research
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更新日期：1981-12-11 00:00:00
abstract：:MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and va...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm216
更新日期：2007-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx654
更新日期：2017-09-29 00:00:00
abstract：:Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf062
更新日期：2002-06-15 00:00:00
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pub_type： 杂志文章
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更新日期：1997-10-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki481
更新日期：2005-07-01 00:00:00
abstract：:MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...
journal_title：Nucleic acids research
pub_type： 杂志文章
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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/gkt272
更新日期：2013-06-01 00:00:00
abstract：:Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.12.2607
更新日期：2001-06-15 00:00:00
abstract：:Abasic sites are common DNA lesions resulting from spontaneous depurination and excision of damaged nucleobases by DNA repair enzymes. However, the influence of the local sequence context on the structure of the abasic site and ultimately, its recognition and repair, remains elusive. In the present study, duplex DNAs ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm622
更新日期：2008-01-01 00:00:00
