Abstract：
:Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment of the corepressor complex by transcription factors to specific regions of the genome is mediated by Sin3 as well as 10 distinct polypeptides that comprise the corepressor complex. Here we report the solution structure of a novel CCCH zinc finger (ZnF) motif in the SAP30 polypeptide, a key component of the corepressor complex. The structure represents a novel fold comprising two beta-strands and two alpha-helices with the zinc organizing center showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface that is dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 ZnF motif indicated a strong preference for nucleic acid substrates. We propose that the SAP30 ZnF functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 corepressor complex. Our results also call into question the common assumption about the exclusion of DNA-binding core subunits within chromatin-modifying/remodeling complexes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
He Y,Imhoff R,Sahu A,Radhakrishnan Idoi
10.1093/nar/gkp051subject
Has Abstractpub_date
2009-04-01 00:00:00pages
2142-52issue
7eissn
0305-1048issn
1362-4962pii
gkp051journal_volume
37pub_type
杂志文章abstract：:Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1146
更新日期：2018-01-25 00:00:00
abstract：:Eukaryotic RNases H from Saccharomyces cerevisiae , Schizosaccharomyces pombe and Crithidia fasciculata , unlike the related Escherichia coli RNase HI, contain a non-RNase H domain with a common motif. Previously we showed that S.cerevisiae RNase H1 binds to duplex RNAs (either RNA-DNA hybrids or double-stranded RNA) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1834
更新日期：1998-04-01 00:00:00
abstract：:The S-adenosylmethionine (AdoMet) analog sinefungin is a natural product antibiotic that inhibits nucleic acid methyltransferases and arrests the growth of unicellular eukarya and eukaryal viruses. The basis for the particular sensitivity of fungi and protozoa to sinefungin is not known. Here we report the isolation a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm817
更新日期：2007-01-01 00:00:00
abstract：:The type I insulin-like growth factor receptor (IGF-IR) is an integral component in the control of cell proliferation, differentiation and apoptosis. The IGF-IR mRNA contains an extraordinarily long (1038 nt) 5'-untranslated region (5'-UTR), and we have characterized a diverse series of proteins interacting with this ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki603
更新日期：2005-05-24 00:00:00
abstract：:Specific DNA restriction endonuclease fragments can be identified after electrophoresis in agarose gels by hybridization in the gel (in situ) to radioactive homologous RNA. RNA-DNA hybrids are detected by autoradiography of the gel. Comparison of band patterns of the autoradiogram and the ethidium bromide stained gel ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.10.1911
更新日期：1975-10-01 00:00:00
abstract：:We report for the first time an analysis of the ATPase activity of human DNA topoisomerase (topo) IIbeta. We show that topo IIbeta is a DNA-dependent ATPase that appears to fit Michaelis-Menten kinetics. The ATPase activity is stimulated 44-fold by DNA. The k(cat) for ATP hydrolysis by human DNA topo IIbeta in the pre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf677
更新日期：2002-12-15 00:00:00
abstract：:The nucleotide sequence for human argininosuccinate synthetase cDNA was determined by analysis of six clones isolated from a single experiment. The sequence covered 1623 nucleotides including 76 bases of poly(A) and contained a 1236 nucleotide open reading frame encoding a protein of 46,434 daltons. In one cDNA isolat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.18.6505
更新日期：1983-09-24 00:00:00
abstract：:Methylation of miRNAs at the 2'-hydroxyl group on the ribose at 3'-end (2'-O-methylation, 2'Ome) is critical for miRNA function in plants and Drosophila. Whether this methylation phenomenon exists for mammalian miRNA remains unknown. Through LC-MS/MS analysis, we discover that majority of miR-21-5p isolated from human...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa504
更新日期：2020-07-27 00:00:00
abstract：:Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa068
更新日期：2020-04-17 00:00:00
abstract：:MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4563
更新日期：1993-09-25 00:00:00
abstract：:A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.11.4683
更新日期：1986-06-11 00:00:00
abstract：:In the battle against viruses, antiviral peptides (AVPs) had demonstrated the immense potential. Presently, more than 15 peptide-based drugs are in various stages of clinical trials. Emerging and re-emerging viruses further emphasize the efforts to accelerate antiviral drug discovery efforts. Despite, huge importance ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks450
更新日期：2012-07-01 00:00:00
abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl369
更新日期：2006-05-31 00:00:00
abstract：:The nucleotide sequence of Drosophila melanogaster tRNA 5 Lys is pGCCCGGAUAm2GCUCAGDCGGDAGAGCA psi psi GGACUsU*UUt6A*A psi CCAAGGm7GDm5CCAGGGTm psi CAm1AGUCCCUGUUCGGGCGCCA. The sU* is probably 5-methylcarboxymethyl-2-thiouridine and t6A* is a mixture of modified derivatives of t6A including t6A itself and a component ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.20.6393
更新日期：1982-10-25 00:00:00
abstract：:How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz176
更新日期：2019-06-20 00:00:00
abstract：:We have used DNase I footprinting to examine the association kinetics of GA-, GT- and CT-containing oligonucleotides with the target sequence (GGA)5GG. (CCT)5CC. These reactions are slow yielding bimolecular association rate constants between 50 and 2000 M-1s-1. We find that GT-containing oligonucleotides bind much fa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.16.3269
更新日期：1997-08-15 00:00:00
abstract：:Multicellular organismal development is controlled by a complex network of transcription factors, promoters and enhancers. Although reliable computational and experimental methods exist for enhancer detection, prediction of their target genes remains a major challenge. On the basis of available literature and ChIP-seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1081
更新日期：2011-04-01 00:00:00
abstract：:Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku269
更新日期：2014-06-01 00:00:00
abstract：:DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.22.5152
更新日期：1993-11-11 00:00:00
abstract：:Alternative splicing expands the coding capacity of metazoan genes, and it was largely genetic studies in the fruit-fly Drosophila melanogaster that established the principle that regulated alternative splicing results in tissue- and stage-specific protein isoforms with different functions in development. Alternative ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkr648
更新日期：2012-01-01 00:00:00
abstract：:Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.6.977
更新日期：1994-03-25 00:00:00
abstract：:2'-Deoxyoligonucleotides with 5-fluorocytosine residues incorporated at specific positions of the nucleotide sequence are tools of great potential in the study of the catalytic mechanism by which DNA cytosine methyltransferases methylate the 5-position of DNA cytosine residues in specific sequence contexts. Chemical s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.10.2421
更新日期：1992-05-25 00:00:00
abstract：:DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr053
更新日期：2011-05-01 00:00:00
abstract：:Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.5.1150
更新日期：1998-03-01 00:00:00
abstract：:The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reacti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.377
更新日期：2000-01-01 00:00:00
abstract：:Alternative splicing of mRNA precursors results in multiple protein variants from a single gene and is critical for diverse cellular processes and development. Xist encodes a long noncoding RNA which is a central player to induce X-chromosome inactivation in female mammals and has two major splicing variants: long and...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1227
更新日期：2018-03-16 00:00:00
abstract：:The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.11.4639
更新日期：1986-06-11 00:00:00
abstract：:The distribution of 7-methylguanine in the families of repetitive and unique sequences of rat liver chromatin DNA has been studied using the technique of DNA-DNA reassociation. Rats were injected with di[14C]methylnitrosamine and chromatin DNA was prepared 3 h later. The distribution of 7-methylguanine was found to be...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.9.3357
更新日期：1978-09-01 00:00:00
abstract：:We report the isolation of a novel human POU domain encoding gene named RDC-1. The POU domain of the RDC-1 encoded protein is highly related to the POU domain potentially encoded by the rat brain-3 sequence and to that of the Drosophila I-POU protein; outside of the POU region, RDC-1 is unrelated to any previously cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.18.4919
更新日期：1992-09-25 00:00:00
abstract：:The intron 2 of the murine thymidine kinase (TK) gene was observed to contain two DNase hypersensitive site. In vitro footprinting experiments indicated specific binding sites for nuclear proteins which were characterized within the sequence of intron 2. Two GC boxes (binding sites for transcription factor SP1) and tw...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.24.6805
更新日期：1991-12-25 00:00:00
