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  • 1
    Publication Date: 2008-02-01
    Description: Ca2+/calmodulin-dependent regulation of voltage-gated CaV1-2 Ca2+ channels shows extraordinary modes of spatial Ca2+ decoding and channel modulation, vital for many biological functions. A single calmodulin (CaM) molecule associates constitutively with the channel's carboxy-terminal tail, and Ca2+ binding to the C-terminal and N-terminal lobes of CaM can each induce distinct channel regulations. As expected from close channel proximity, the C-lobe responds to the roughly 100-microM Ca2+ pulses driven by the associated channel, a behaviour defined as 'local Ca2+ selectivity'. Conversely, all previous observations have indicated that the N-lobe somehow senses the far weaker signals from distant Ca2+ sources. This 'global Ca2+ selectivity' satisfies a general signalling requirement, enabling a resident molecule to remotely sense cellular Ca2+ activity, which would otherwise be overshadowed by Ca2+ entry through the host channel. Here we show that the spatial Ca2+ selectivity of N-lobe CaM regulation is not invariably global but can be switched by a novel Ca2+/CaM-binding site within the amino terminus of channels (NSCaTE, for N-terminal spatial Ca2+ transforming element). Native CaV2.2 channels lack this element and show N-lobe regulation with a global selectivity. On the introduction of NSCaTE into these channels, spatial Ca2+ selectivity transforms from a global to local profile. Given this effect, we examined CaV1.2/CaV1.3 channels, which naturally contain NSCaTE, and found that their N-lobe selectivity is indeed local. Disruption of this element produces a global selectivity, confirming the native function of NSCaTE. Thus, differences in spatial selectivity between advanced CaV1 and CaV2 channel isoforms are explained by the presence or absence of NSCaTE. Beyond functional effects, the position of NSCaTE on the channel's amino terminus indicates that CaM can bridge the amino terminus and carboxy terminus of channels. Finally, the modularity of NSCaTE offers practical means for understanding the basis of global Ca2+ selectivity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262256/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4262256/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dick, Ivy E -- Tadross, Michael R -- Liang, Haoya -- Tay, Lai Hock -- Yang, Wanjun -- Yue, David T -- P30 DC005211/DC/NIDCD NIH HHS/ -- R01 MH065531/MH/NIMH NIH HHS/ -- R37 HL076795/HL/NHLBI NIH HHS/ -- T32 DC000023/DC/NIDCD NIH HHS/ -- England -- Nature. 2008 Feb 14;451(7180):830-4. doi: 10.1038/nature06529. Epub 2008 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Calcium Signals Laboratory, Departments of Biomedical Engineering and Neuroscience, The Johns Hopkins University School of Medicine, Ross Building, Room 713, 720 Rutland Avenue, Baltimore, Maryland 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235447" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcium/*metabolism ; Calcium Channels/chemistry/genetics/*metabolism ; *Calcium Signaling ; Calmodulin/*metabolism ; Cell Line ; Evolution, Molecular ; Humans ; Molecular Sequence Data ; Substrate Specificity
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 1990-09-21
    Description: Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, W -- Hendrickson, W A -- Crouch, R J -- Satow, Y -- GM 34102/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1990 Sep 21;249(4975):1398-405.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2169648" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Computer Graphics ; *Endoribonucleases/genetics ; Escherichia coli/enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Recombinant Proteins ; Ribonuclease H ; *Selenium ; *Selenomethionine ; Sequence Homology, Nucleic Acid ; X-Ray Diffraction/methods
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2011-11-08
    Description: The embryonic pyruvate kinase M2 (PKM2) isoform is highly expressed in human cancer. In contrast to the established role of PKM2 in aerobic glycolysis or the Warburg effect, its non-metabolic functions remain elusive. Here we demonstrate, in human cancer cells, that epidermal growth factor receptor (EGFR) activation induces translocation of PKM2, but not PKM1, into the nucleus, where K433 of PKM2 binds to c-Src-phosphorylated Y333 of beta-catenin. This interaction is required for both proteins to be recruited to the CCND1 promoter, leading to HDAC3 removal from the promoter, histone H3 acetylation and cyclin D1 expression. PKM2-dependent beta-catenin transactivation is instrumental in EGFR-promoted tumour cell proliferation and brain tumour development. In addition, positive correlations have been identified between c-Src activity, beta-catenin Y333 phosphorylation and PKM2 nuclear accumulation in human glioblastoma specimens. Furthermore, levels of beta-catenin phosphorylation and nuclear PKM2 have been correlated with grades of glioma malignancy and prognosis. These findings reveal that EGF induces beta-catenin transactivation via a mechanism distinct from that induced by Wnt/Wingless and highlight the essential non-metabolic functions of PKM2 in EGFR-promoted beta-catenin transactivation, cell proliferation and tumorigenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235705/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235705/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Weiwei -- Xia, Yan -- Ji, Haitao -- Zheng, Yanhua -- Liang, Ji -- Huang, Wenhua -- Gao, Xiang -- Aldape, Kenneth -- Lu, Zhimin -- 5 P50 CA127001-03/CA/NCI NIH HHS/ -- 5R01CA109035/CA/NCI NIH HHS/ -- CA16672/CA/NCI NIH HHS/ -- R01 CA109035/CA/NCI NIH HHS/ -- R01 CA109035-05/CA/NCI NIH HHS/ -- England -- Nature. 2011 Dec 1;480(7375):118-22. doi: 10.1038/nature10598.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22056988" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line, Tumor ; Cyclin D1/metabolism ; *Gene Expression Regulation, Neoplastic ; HEK293 Cells ; Humans ; Mice ; NIH 3T3 Cells ; Neoplasms/physiopathology ; Nuclear Proteins/*metabolism ; Phosphorylation ; Protein Binding ; Protein Transport ; Protein-Tyrosine Kinases/metabolism ; Pyruvate Kinase/*metabolism ; Receptor, Epidermal Growth Factor/*metabolism ; beta Catenin/*metabolism ; src-Family Kinases
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-03-31
    Description: Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers for responses to targeted agents. Here, to uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we screened a panel of several hundred cancer cell lines--which represent much of the tissue-type and genetic diversity of human cancers--with 130 drugs under clinical and preclinical investigation. In aggregate, we found that mutated cancer genes were associated with cellular response to most currently available cancer drugs. Classic oncogene addiction paradigms were modified by additional tissue-specific or expression biomarkers, and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. Unexpected relationships were revealed, including the marked sensitivity of Ewing's sarcoma cells harbouring the EWS (also known as EWSR1)-FLI1 gene translocation to poly(ADP-ribose) polymerase (PARP) inhibitors. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349233/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349233/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Garnett, Mathew J -- Edelman, Elena J -- Heidorn, Sonja J -- Greenman, Chris D -- Dastur, Anahita -- Lau, King Wai -- Greninger, Patricia -- Thompson, I Richard -- Luo, Xi -- Soares, Jorge -- Liu, Qingsong -- Iorio, Francesco -- Surdez, Didier -- Chen, Li -- Milano, Randy J -- Bignell, Graham R -- Tam, Ah T -- Davies, Helen -- Stevenson, Jesse A -- Barthorpe, Syd -- Lutz, Stephen R -- Kogera, Fiona -- Lawrence, Karl -- McLaren-Douglas, Anne -- Mitropoulos, Xeni -- Mironenko, Tatiana -- Thi, Helen -- Richardson, Laura -- Zhou, Wenjun -- Jewitt, Frances -- Zhang, Tinghu -- O'Brien, Patrick -- Boisvert, Jessica L -- Price, Stacey -- Hur, Wooyoung -- Yang, Wanjuan -- Deng, Xianming -- Butler, Adam -- Choi, Hwan Geun -- Chang, Jae Won -- Baselga, Jose -- Stamenkovic, Ivan -- Engelman, Jeffrey A -- Sharma, Sreenath V -- Delattre, Olivier -- Saez-Rodriguez, Julio -- Gray, Nathanael S -- Settleman, Jeffrey -- Futreal, P Andrew -- Haber, Daniel A -- Stratton, Michael R -- Ramaswamy, Sridhar -- McDermott, Ultan -- Benes, Cyril H -- 086357/Wellcome Trust/United Kingdom -- 1U54HG006097-01/HG/NHGRI NIH HHS/ -- P41GM079575-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 28;483(7391):570-5. doi: 10.1038/nature11005.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22460902" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Cell Survival/drug effects ; Drug Resistance, Neoplasm/drug effects/*genetics ; *Drug Screening Assays, Antitumor ; Gene Expression Regulation, Neoplastic/genetics ; Genes, Neoplasm/*genetics ; Genetic Markers/*genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Indoles/pharmacology ; Neoplasms/*drug therapy/*genetics/pathology ; Oncogene Proteins, Fusion/genetics ; Pharmacogenetics ; Phthalazines/pharmacology ; Piperazines/pharmacology ; Poly(ADP-ribose) Polymerase Inhibitors ; Proto-Oncogene Protein c-fli-1/genetics ; RNA-Binding Protein EWS/genetics ; Sarcoma, Ewing/drug therapy/genetics/pathology
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  • 5
    Publication Date: 2013-03-29
    Description: Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m)A(m)), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ling, Hong-Qing -- Zhao, Shancen -- Liu, Dongcheng -- Wang, Junyi -- Sun, Hua -- Zhang, Chi -- Fan, Huajie -- Li, Dong -- Dong, Lingli -- Tao, Yong -- Gao, Chuan -- Wu, Huilan -- Li, Yiwen -- Cui, Yan -- Guo, Xiaosen -- Zheng, Shusong -- Wang, Biao -- Yu, Kang -- Liang, Qinsi -- Yang, Wenlong -- Lou, Xueyuan -- Chen, Jie -- Feng, Mingji -- Jian, Jianbo -- Zhang, Xiaofei -- Luo, Guangbin -- Jiang, Ying -- Liu, Junjie -- Wang, Zhaobao -- Sha, Yuhui -- Zhang, Bairu -- Wu, Huajun -- Tang, Dingzhong -- Shen, Qianhua -- Xue, Pengya -- Zou, Shenhao -- Wang, Xiujie -- Liu, Xin -- Wang, Famin -- Yang, Yanping -- An, Xueli -- Dong, Zhenying -- Zhang, Kunpu -- Zhang, Xiangqi -- Luo, Ming-Cheng -- Dvorak, Jan -- Tong, Yiping -- Wang, Jian -- Yang, Huanming -- Li, Zhensheng -- Wang, Daowen -- Zhang, Aimin -- Wang, Jun -- England -- Nature. 2013 Apr 4;496(7443):87-90. doi: 10.1038/nature11997. Epub 2013 Mar 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23535596" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Brachypodium/genetics ; Crops, Agricultural/classification/genetics ; Diploidy ; Genetic Markers/genetics ; Genome, Plant/*genetics ; Molecular Sequence Data ; Oryza/genetics ; Phylogeny ; Sorghum/genetics ; Synteny/genetics ; Triticum/classification/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2011-03-23
    Description: The genome is extensively transcribed into long intergenic noncoding RNAs (lincRNAs), many of which are implicated in gene silencing. Potential roles of lincRNAs in gene activation are much less understood. Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control. Some locus control elements and enhancers transcribe lincRNAs, hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3' to 5'of the cluster. Here we identify HOTTIP, a lincRNA transcribed from the 5' tip of the HOXA locus that coordinates the activation of several 5' HOXA genes in vivo. Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670758/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670758/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Kevin C -- Yang, Yul W -- Liu, Bo -- Sanyal, Amartya -- Corces-Zimmerman, Ryan -- Chen, Yong -- Lajoie, Bryan R -- Protacio, Angeline -- Flynn, Ryan A -- Gupta, Rajnish A -- Wysocka, Joanna -- Lei, Ming -- Dekker, Job -- Helms, Jill A -- Chang, Howard Y -- HG003143/HG/NHGRI NIH HHS/ -- R01 HG003143/HG/NHGRI NIH HHS/ -- R01 HG003143-06/HG/NHGRI NIH HHS/ -- R01 HG003143-06S1/HG/NHGRI NIH HHS/ -- R01 HG003143-06S2/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Apr 7;472(7341):120-4. doi: 10.1038/nature09819. Epub 2011 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21423168" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cells, Cultured ; Chromatin/*genetics/metabolism ; DNA, Intergenic/genetics ; Embryo, Mammalian/metabolism ; Fibroblasts/metabolism ; Gene Expression Regulation, Developmental/*genetics ; Gene Knockdown Techniques ; Genes, Homeobox/*genetics ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/chemistry/metabolism ; Humans ; Lysine/metabolism ; Methylation ; Mice ; Molecular Sequence Data ; Multigene Family/genetics ; Organ Specificity ; RNA, Untranslated/*genetics ; Transcription, Genetic
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  • 7
    Publication Date: 2015-12-15
    Description: Release of promoter-proximal paused RNA polymerase II (Pol II) during early elongation is a critical step in transcriptional regulation in metazoan cells. Paused Pol II release is thought to require the kinase activity of cyclin-dependent kinase 9 (CDK9) for the phosphorylation of DRB sensitivity-inducing factor, negative elongation factor, and C-terminal domain (CTD) serine-2 of Pol II. We found that Pol II-associated factor 1 (PAF1) is a critical regulator of paused Pol II release, that positive transcription elongation factor b (P-TEFb) directly regulates the initial recruitment of PAF1 complex (PAF1C) to genes, and that the subsequent recruitment of CDK12 is dependent on PAF1C. These findings reveal cooperativity among P-TEFb, PAF1C, and CDK12 in pausing release and Pol II CTD phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Ming -- Yang, Wenjing -- Ni, Ting -- Tang, Zhanyun -- Nakadai, Tomoyoshi -- Zhu, Jun -- Roeder, Robert G -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Dec 11;350(6266):1383-6. doi: 10.1126/science.aad2338.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. ; Systems Biology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA. ; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China. ; Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. roeder@rockefeller.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26659056" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor ; Cyclin-Dependent Kinase 9/metabolism ; Cyclin-Dependent Kinases/metabolism ; *Gene Expression Regulation ; Humans ; Nuclear Proteins/genetics/*metabolism ; Phosphorylation ; Positive Transcriptional Elongation Factor B/metabolism ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; RNA Polymerase II/chemistry/genetics/*metabolism ; *Transcription Elongation, Genetic ; Transcription Factors/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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