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  • Cell Research
    Yang Zhang 1 Xiao Ou Zhang 2 Zheng Wu 1 Shaofeng Zhang 1 Hai Bin Wang 3 Junhui Ge 3 Xuhua Lu 3 Li Yang 2 and Ling Ling Chen 1 1 State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology 320 Yueyang Road Shanghai 200031 China 2 Key Laboratory of Computational Biology CAS MPG Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yueyang Road Shanghai 200031 China 3 Changzheng Hospital Second Military Medical University 415 Fengyang Road Shanghai 200003 China Correspondence Ling Ling Chen E mail linglingchen sibcb ac cn The human 8q24 gene desert contains multiple enhancers that form tissue specific long range chromatin loops with the MYC oncogene but how chromatin looping at the MYC locus is regulated remains poorly understood Here we demonstrate that a long noncoding RNA lncRNA CCAT1 L is transcribed specifically in human colorectal cancers from a locus 515 kb upstream of MYC This lncRNA plays a role in MYC transcriptional regulation and promotes long range chromatin looping Importantly the CCAT1 L locus is located within a strong super enhancer and is spatially close to MYC Knockdown of CCAT1 L reduced long range

    Original URL path: http://www.cell-research.com/arts.asp?id=1920 (2016-02-14)
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  • Cell Research
    Adhikari 1 4 Zechen Chong 1 Ting Zhang 1 Cai Xia Guo 1 Tie shan Tang 5 Bing Tao Zhu 6 Xing Zhi Xu 6 Niels Mailand 7 Yun Gui Yang 1 4 Yijun Qi 2 3 and Jannie M Rendtlew Danielsen 1 7 1 Laboratory of Genome Variations and Precision Biomedicine Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China 2 Tsinghua Peking Center for Life Sciences Beijing 100084 China 3 Center for Plant Biology School of Life Sciences Tsinghua University Beijing 100084 China 4 University of Chinese Academy of Sciences Beijing 100049 China 5 State Key Laboratory of Biomembrane and Membrane Biotechnology Institute of Zoology Chinese Academy of Sciences Beijing 100101 China 6 Beijing Key Laboratory of DNA Damage Response College of Life Sciences Capital Normal University Beijing 100048 China 7 The Novo Nordisk Foundation Center for Protein Research Ubiquitin Signalling Group Faculty of Health Sciences Copenhagen Denmark Correspondence Yijun Qi E mail qiyijun tsinghua edu cn Yun Gui Yang E mail ygyang big ac cn DNA double strand breaks DSBs are highly cytotoxic lesions and pose a major threat to genome stability if not properly repaired We and others have previously shown that a class of DSB induced small RNAs diRNAs is produced from sequences around DSB sites DiRNAs are associated with Argonaute Ago proteins and play an important role in DSB repair though the mechanism through which they act remains unclear Here we report that the role of diRNAs in DSB repair is restricted to repair by homologous recombination HR and that it specifically relies on the effector protein Ago2 in mammalian cells Interestingly we show that Ago2 forms a complex with Rad51 and that the interaction is enhanced in cells treated with ionizing radiation We demonstrate that Rad51 accumulation at DSB sites and

    Original URL path: http://www.cell-research.com/arts.asp?id=1921 (2016-02-14)
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  • Cell Research
    4 and Dihua Yu 1 3 1 Department of Molecular and Cellular Oncology The University of Texas MD Anderson Cancer Center 1515 Holcombe Boulevard Houston TX 77030 USA 2 Department of Molecular Biology and Genetics Faculty of Science Bilkent University Ankara Turkey 06800 3 Cancer Biology Program Graduate School of Biomedical Sciences Houston TX 77030 USA 4 The Methodist Cancer Center Houston TX 77030 USA 5 Goodman Cancer Center McGill University Montreal Quebec H3A 1A3 Canada 6 Department of Breast Medical Oncology The University of Texas MD Anderson Cancer Center Houston TX 77030 USA Correspondence Dihua Yu Tel 713 792 3636 Fax 713 792 4544 E mail dyu mdanderson org Combinatorial targeted therapies are more effective in treating cancer by blocking by pass mechanisms or inducing synthetic lethality However their clinical application is hampered by resistance and toxicity To meet this important challenge we developed and tested a novel concept of biomarker guided sequential applications of various targeted therapies using ErbB2 overexpressing PTEN low highly aggressive breast cancer as our model Strikingly sustained activation of ErbB2 and downstream pathways drives trastuzumab resistance in both PTEN low trastuzumab resistant breast cancers from patients and mammary tumors with intratumoral heterogeneity from genetically engineered mice Although lapatinib initially inhibited trastuzumab resistant mouse tumors tumors by passed the inhibition by activating the PI3K mTOR signaling network as shown by the quantitative protein arrays Interestingly activation of the mTOR pathway was also observed in neoadjuvant lapatinib treated patients manifesting lapatinib resistance Trastuzumab lapatinib resistance was effectively overcome by sequential application of a PI3K mTOR dual kinase inhibitor BEZ235 with no significant toxicity However our p RTK array analysis demonstrated that BEZ235 treatment led to increased ErbB2 expression and phosphorylation in genetically engineered mouse tumors and in 3 D but not 2 D culture leading to

    Original URL path: http://www.cell-research.com/arts.asp?id=1922 (2016-02-14)
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  • Cell Research
    Tatsuo Fukagawa 4 Wei Yang 2 and Weidong Wang 1 1 Laboratory of Genetics National Institute on Aging National Institutes of Health Baltimore MD 21224 USA 2 Laboratory of Molecular Biology National Institute of Diabetes and Digestive and Kidney Diseases National Institute of Health Bethesda MD 20892 USA 3 Biochemistry Core Facility National Heart Lung and Blood Institute National Institutes of Health Bethesda MD 20892 USA 4 Department of Molecular Genetics National Institute of Genetics and the Graduate University for Advanced Studies Mishima 411 8540 Japan Correspondence Weidong Wang Tel 1 410 558 8334 Fax 1 410 558 8331 E mail wangw grc nia nih gov Histone fold proteins typically assemble in multiprotein complexes to bind duplex DNA However one histone fold complex MHF associates with Fanconi anemia FA protein FANCM to form a branched DNA remodeling complex that senses and repairs stalled replication forks and activates FA DNA damage response network How the FANCM MHF complex recognizes branched DNA is unclear Here we solved the crystal structure of MHF and its complex with the MHF interaction domain referred to as MID of FANCM and performed structure guided mutagenesis We found that the MID MHF complex consists of one histone H3 H4 like MHF heterotetramer wrapped by a single polypeptide of MID We identified a zinc atom liganding structure at the central interface between MID and MHF that is critical for stabilization of the complex Notably the DNA binding surface of MHF was altered by MID in both electrostatic charges and allosteric conformation This leads to a switch in the DNA binding preference from duplex DNA by MHF alone to branched DNA by the MID MHF complex Mutations that disrupt either the composite DNA binding surface or the protein protein interface of the MID MHF complex impaired activation of the

    Original URL path: http://www.cell-research.com/arts.asp?id=1923 (2016-02-14)
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  • Cell Research
    3 Tong Wang 1 Lei Yuan 1 Zhi Sheng Zheng 1 Perry J Blackshear 4 and Zhen Ge Luo 1 1 Institute of Neuroscience and State Key Laboratory of Neuroscience Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 2 School of Life Sciences Shanghai University Shanghai 200444 China 3 School of Life Science and Technology ShanghaiTech University Shanghai 200031 China 4 Laboratory of Signal Transduction National Institute of Environmental Health Sciences Research Triangle Park NC 27709 USA Correspondence Zhen Ge Luo E mail zgluo ion ac cn Axon development requires membrane addition from the intracellular supply which has been shown to be mediated by Rab10 positive plasmalemmal precursor vesicles PPVs However the molecular mechanisms underlying the membrane trafficking processes of PPVs remain unclear Here we show that myristoylated alanine rich C kinase substrate MARCKS mediates membrane targeting of Rab10 positive PPVs and this regulation is critical for axon development We found that the GTP locked active form of Rab10 binds to membrane associated MARCKS whose affinity depends on the phosphorylation status of the MARCKS effector domain Either genetic silencing of MARCKS or disruption of its interaction with Rab10 inhibited axon growth of cortical neurons impaired docking

    Original URL path: http://www.cell-research.com/arts.asp?id=1924 (2016-02-14)
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  • Cell Research
    12 Xuefu Rd Pukou District Nanjing Jiangsu 210061 China 2 Department of Developmental Biology University of Texas Southwestern Medical Center at Dallas Dallas TX 75390 USA 3 Zhejiang Provincial Key Lab for Technology and Application of Model Organism School of Life Sciences Wenzhou Medical College Wenzhou Zhejiang 325035 China Correspondence Jin Jiang Tel 01 2146455914 E mail jin jiang utsouthwestern edu Qing Zhang Tel 86 25 58641597 E mail zhangqing nju edu cn Hedgehog Hh signaling plays vital roles in animal development and tissue homeostasis and its misregulation causes congenital diseases and several types of cancer Suppressor of Fused Su fu is a conserved inhibitory component of the Hh signaling pathway but how it is regulated remains poorly understood Here we demonstrate that in Drosophila Hh signaling promotes downregulation of Su fu through its target protein HIB Hh induced BTB protein Interestingly although HIB mediated downregulation of Su fu depends on the E3 ubiquitin ligase Cul3 HIB does not directly regulate Su fu protein stability Through an RNAi based candidate gene screen we identify the spliceosome factor Crooked neck Crn as a regulator of Su fu level Epistasis analysis indicates that HIB downregulates Su fu through Crn Furthermore we provide

    Original URL path: http://www.cell-research.com/arts.asp?id=1925 (2016-02-14)
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  • Cell Research
    College of Life Sciences Beijing Normal University Beijing 100875 China Correspondence Rongwen Xi E mail xirongwen nibs ac cn Quiescent multipotent gastric stem cells GSSCs in the copper cell region of adult Drosophila midgut can produce all epithelial cell lineages found in the region including acid secreting copper cells interstitial cells and enteroendocrine cells but mechanisms controlling their quiescence and the ternary lineage differentiation are unknown By using cell ablation or damage induced regeneration assays combined with cell lineage tracing and genetic analysis here we demonstrate that Delta Dl expressing cells in the copper cell region are the authentic GSSCs that can self renew and continuously regenerate the gastric epithelium after a sustained damage Lineage tracing analysis reveals that the committed GSSC daughter with activated Notch will invariably differentiate into either a copper cell or an interstitial cell but not the enteroendocrine cell lineage and loss of function and gain of function studies revealed that Notch signaling is both necessary and sufficient for copper cell interstitial cell differentiation We also demonstrate that elevated epidermal growth factor receptor EGFR signaling which is achieved by the activation of ligand Vein from the surrounding muscle cells and ligand Spitz from progenitor cells mediates

    Original URL path: http://www.cell-research.com/arts.asp?id=1926 (2016-02-14)
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  • Cell Research
    1 Pengfei Yuan 1 Yuexin Zhou 1 Changzu Cai 1 Qingpeng Ren 1 Dingqiao Wen 1 3 Coco Chu 3 Hai Qi 2 and Wensheng Wei 1 1 State Key Laboratory of Protein and Plant Gene Research College of Life Sciences Peking University Beijing 100871 China 2 Tsinghua Peking Center for Life Sciences Laboratory of Dynamic Immunobiology School of Medicine Tsinghua University Beijing 100084 China 3 Current address Department of Computer Science Rice University Houston TX 77005 USA Correspondence Wensheng Wei Tel 86 10 62757227 E mail wswei pku edu cn The most striking feature of a transcription activator like effector TALE is the presence of a central DNA binding region composed of tandem repeats of about 34 amino acids1 Two hypervariable residues at positions 12 and 13 repeat variable diresidues or RVDs in each repeat bind to DNA and this modular DNA binding feature of TALE repeats has inspired the development of custom designed TALE repeats for gene editing2 3 4 5 The nucleotide recognition preference of the commonly used RVDs has been experimentally or computationally determined2 5 For instance RVD NN has a high preference for both G and A The rare RVDs NK and NH have better

    Original URL path: http://www.cell-research.com/arts.asp?id=1927 (2016-02-14)
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