Abstract:
:CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK12 is also frequently co-amplified with the HER2 (ERBB2) oncogene. The mechanisms underlying functions of CDK12 in general and in cancer remain poorly defined. Based on global analysis of mRNA transcripts in normal and breast cancer cell lines with and without CDK12 amplification, we demonstrate that CDK12 primarily regulates alternative last exon (ALE) splicing, a specialized subtype of alternative mRNA splicing, that is both gene- and cell type-specific. These are unusual properties for spliceosome regulatory factors, which typically regulate multiple forms of alternative splicing in a global manner. In breast cancer cells, regulation by CDK12 modulates ALE splicing of the DNA damage response activator ATM and a DNAJB6 isoform that influences cell invasion and tumorigenesis in xenografts. We found that there is a direct correlation between CDK12 levels, DNAJB6 isoform levels and the migration capacity and invasiveness of breast tumor cells. This suggests that CDK12 gene amplification can contribute to the pathogenesis of the cancer.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Tien JF,Mazloomian A,Cheng SG,Hughes CS,Chow CCT,Canapi LT,Oloumi A,Trigo-Gonzalez G,Bashashati A,Xu J,Chang VC,Shah SP,Aparicio S,Morin GBdoi
10.1093/nar/gkx187subject
Has Abstractpub_date
2017-06-20 00:00:00pages
6698-6716issue
11eissn
0305-1048issn
1362-4962pii
3073990journal_volume
45pub_type
杂志文章abstract::High mobility group protein B1 (HMGB1) binds to the internucleosomal linker DNA in chromatin and abuts the nucleosome. Bending and untwisting of the linker DNA results in transmission of strain to the nucleosome core, disrupting histone/DNA contacts. An interaction between H3 and HMGB1 has been reported. Here we confi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt950
更新日期:2014-01-01 00:00:00
abstract::Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH deg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm865
更新日期:2007-01-01 00:00:00
abstract::Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several viruses through direct interactions with viral RNA. NF90 and NF45 dimerize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks696
更新日期:2012-10-01 00:00:00
abstract::Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks259
更新日期:2012-07-01 00:00:00
abstract::Spermine-DNA complexes have been examined by small-angle and wide-angle X-ray scattering as well as by circular dichroism studies. Condensed complexes are building up below a critical ionic strength. We have found that at one and the same ionic strength condensed complexes having two different supramolecular structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.5.1297
更新日期:1979-11-10 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::In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.10.4083
更新日期:1984-05-25 00:00:00
abstract::Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq590
更新日期:2010-11-01 00:00:00
abstract::The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1068
更新日期:2015-01-01 00:00:00
abstract::Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20-30 translation rounds during 6-8 h in wheat germ extract at 25°C). Three distinct types of the conformation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1270
更新日期:2015-01-01 00:00:00
abstract::We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf647
更新日期:2002-12-01 00:00:00
abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1072
更新日期:2017-01-04 00:00:00
abstract::Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku349
更新日期:2014-06-01 00:00:00
abstract::A U3 snoRNA gene isolated from a Chlamydomonas reinhardtii (CRE:) genomic library contains putative pol III-specific transcription signals similar to those of RNA polymerase III-specific small nuclear (sn)RNA genes of higher plants. The 222 nt long CRE: U3 snoRNA was immunoprecipitated by anti-gamma-mpppN antisera, bu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.15.2959
更新日期:2000-08-01 00:00:00
abstract::A simple and rapid procedure to isolate clones carrying sequences from a specific region of the polytene chromosome of Drosophila is demonstrated. The procedure involves microdissection of the region of interest, amplification of the DNA by PCR using a primer designed to prime the synthesis nonspecifically, labeling o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.3.599
更新日期:1990-02-11 00:00:00
abstract::The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new feat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1019
更新日期:2018-01-04 00:00:00
abstract::The U1 snRNP-specific protein C contains an N-terminal zinc finger-like CH motif which is required for the binding of the U1C protein to the U1 snRNP particle. Recently a similar motif was reported to be essential for in vivo homodimerization of the yeast splicing factor PRP9. In the present study we demonstrate that ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.23.4864
更新日期:1995-12-11 00:00:00
abstract::We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.12.4471
更新日期:1989-06-26 00:00:00
abstract::Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.3057
更新日期:1978-08-01 00:00:00
abstract::In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting element...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks164
更新日期:2012-06-01 00:00:00
abstract::Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and appli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky356
更新日期:2018-07-02 00:00:00
abstract::The DNA topoisomerase from Agrobacterium tumefaciens has been purified to apparent homogeneity. The enzyme is a single polypeptide of about 100,000 in molecular weight. No apparent separation of the nicking and sealing activities could be obtained in attempts to separate the two activities by a variety of methods, inc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.4.909
更新日期:1981-02-25 00:00:00
abstract::Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3631
更新日期:1999-09-15 00:00:00
abstract::Human prostatic acid phosphatase (PAcP) is a prostate epithelium-specific differentiation antigen. Cellular PAcP functions as a neutral protein tyrosine phosphatase and is involved in regulating androgen-promoted prostate cancer cell proliferation. Despite the fact that the promoter of the PAcP gene has been cloned, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh677
更新日期:2004-07-07 00:00:00
abstract::Besides orthologs of other eukaryotic mismatch-repair (MMR) proteins, plants encode MSH7, a paralog of MSH6. The Arabidopsis thaliana recognition heterodimers AtMSH2*MSH6 (AtMutSalpha) and AtMSH2*MSH3 (AtMutSbeta) were previously found to bind the same subsets of mismatches as their counterparts in other eukaryotes--r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg780
更新日期:2003-10-15 00:00:00
abstract::We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.1935
更新日期:2002-05-01 00:00:00
abstract::The promoter region of the mouse CCAAT-Enhancer Binding Protein (C/EBP alpha) gene is capable of directing high levels of expression of reporter constructs in various cell lines, albeit even in cells that do not express their endogenous C/EBP alpha gene. To understand the molecular mechanisms underlying this ubiquitou...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1735
更新日期:1993-04-25 00:00:00
abstract::A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.13.3136
更新日期:1998-07-01 00:00:00
abstract::Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.10.3723
更新日期:1985-05-24 00:00:00