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DNA-repair enzyme turns to translation 期刊论文
NATURE, 2020, 579 (7798) : 198-199
作者:  Bian, Zhilei;  Gong, Yandong;  Huang, Tao;  Lee, Christopher Z. W.;  Bian, Lihong;  Bai, Zhijie;  Shi, Hui;  Zeng, Yang;  Liu, Chen;  He, Jian;  Zhou, Jie;  Li, Xianlong;  Li, Zongcheng;  Ni, Yanli;  Ma, Chunyu;  Cui, Lei;  Zhang, Rui;  Chan, Jerry K. Y.;  Ng, Lai Guan;  Lan, Yu;  Ginhoux, Florent;  Liu, Bing
收藏  |  浏览/下载:12/0  |  提交时间:2020/07/03

A key DNA-repair enzyme has a surprising role during the early steps in the assembly of ribosomes - the molecular machines that translate the genetic code into protein.


  
Mutations that prevent caspase cleavage of RIPK1 cause autoinflammatory disease 期刊论文
NATURE, 2020, 577 (7788) : 103-+
作者:  Lalaoui, Najoua;  Boyden, Steven E.;  Oda, Hirotsugu;  Wood, Geryl M.;  Stone, Deborah L.;  Chau, Diep;  Liu, Lin;  Stoffels, Monique;  Kratina, Tobias;  Lawlor, Kate E.;  Zaal, Kristien J. M.;  Hoffmann, Patrycja M.;  Etemadi, Nima;  Shield-Artin, Kristy;  Biben, Christine;  Tsai, Wanxia Li;  Blake, Mary D.;  Kuehn, Hye Sun;  Yang, Dan;  Anderton, Holly;  Silke, Natasha;  Wachsmuth, Laurens;  Zheng, Lixin;  Moura, Natalia Sampaio;  Beck, David B.;  Gutierrez-Cruz, Gustavo;  Ombrello, Amanda K.;  Pinto-Patarroyo, Gineth P.;  Kueh, Andrew J.;  Herold, Marco J.;  Hall, Cathrine;  Wang, Hongying;  Chae, Jae Jin;  Dmitrieva, Natalia I.;  McKenzie, Mark;  Light, Amanda;  Barham, Beverly K.;  Jones, Anne;  Romeo, Tina M.;  Zhou, Qing;  Aksentijevich, Ivona;  Mullikin, James C.;  Gross, Andrew J.;  Shum, Anthony K.;  Hawkins, Edwin D.;  Masters, Seth L.;  Lenardo, Michael J.;  Boehm, Manfred;  Rosenzweig, Sergio D.;  Pasparakis, Manolis;  Voss, Anne K.;  Gadina, Massimo;  Kastner, Daniel L.;  Silke, John
收藏  |  浏览/下载:23/0  |  提交时间:2020/07/03

RIPK1 is a key regulator of innate immune signalling pathways. To ensure an optimal inflammatory response, RIPK1 is regulated post-translationally by well-characterized ubiquitylation and phosphorylation events, as well as by caspase-8-mediated cleavage1-7. The physiological relevance of this cleavage event remains unclear, although it is thought to inhibit activation of RIPK3 and necroptosis8. Here we show that the heterozygous missense mutations D324N, D324H and D324Y prevent caspase cleavage of RIPK1 in humans and result in an early-onset periodic fever syndrome and severe intermittent lymphadenopathy-a condition we term '  cleavage-resistant RIPK1-induced autoinflammatory syndrome'  . To define the mechanism for this disease, we generated a cleavage-resistant Ripk1(D325A) mutant mouse strain. Whereas Ripk1(-/-) mice died postnatally from systemic inflammation, Ripk1(D325A/D325A) mice died during embryogenesis. Embryonic lethality was completely prevented by the combined loss of Casp8 and Ripk3, but not by loss of Ripk3 or Mlkl alone. Loss of RIPK1 kinase activity also prevented Ripk1(D325A/D325A) embryonic lethality, although the mice died before weaning from multi-organ inflammation in a RIPK3-dependent manner. Consistently, Ripk1(D325A/D325A) and Ripk1(D325A/+) cells were hypersensitive to RIPK3-dependent TNF-induced apoptosis and necroptosis. Heterozygous Ripk1(D325A/+) mice were viable and grossly normal, but were hyper-responsive to inflammatory stimuli in vivo. Our results demonstrate the importance of caspase-mediated RIPK1 cleavage during embryonic development and show that caspase cleavage of RIPK1 not only inhibits necroptosis but also maintains inflammatory homeostasis throughout life.


  
Impaired cell fate through gain-of-function mutations in a chromatin reader 期刊论文
NATURE, 2020, 577 (7788) : 121-+
作者:  Wan, Liling;  Chong, Shasha;  Xuan, Fan;  Liang, Angela;  Cui, Xiaodong;  Gates, Leah;  Carroll, Thomas S.;  Li, Yuanyuan;  Feng, Lijuan;  Chen, Guochao;  Wang, Shu-Ping;  Ortiz, Michael V.;  Daley, Sara K.;  Wang, Xiaolu;  Xuan, Hongwen;  Kentsis, Alex;  Muir, Tom W.;  Roeder, Robert G.;  Li, Haitao;  Li, Wei;  Tjian, Robert;  Wen, Hong;  Allis, C. David
收藏  |  浏览/下载:10/0  |  提交时间:2020/07/03

Modifications of histone proteins have essential roles in normal development and human disease. Recognition of modified histones by '  reader'  proteins is a key mechanism that mediates the function of histone modifications, but how the dysregulation of these readers might contribute to disease remains poorly understood. We previously identified the ENL protein as a reader of histone acetylation via its YEATS domain, linking it to the expression of cancer-driving genes in acute leukaemia1. Recurrent hotspot mutations have been found in the ENL YEATS domain in Wilms tumour2,3, the most common type of paediatric kidney cancer. Here we show, using human and mouse cells, that these mutations impair cell-fate regulation by conferring gain-of-function in chromatin recruitment and transcriptional control. ENL mutants induce gene-expression changes that favour a premalignant cell fate, and, in an assay for nephrogenesis using murine cells, result in undifferentiated structures resembling those observed in human Wilms tumour. Mechanistically, although bound to largely similar genomic loci as the wild-type protein, ENL mutants exhibit increased occupancy at a subset of targets, leading to a marked increase in the recruitment and activity of transcription elongation machinery that enforces active transcription from target loci. Furthermore, ectopically expressed ENL mutants exhibit greater self-association and form discrete and dynamic nuclear puncta that are characteristic of biomolecular hubs consisting of local high concentrations of regulatory factors. Such mutation-driven ENL self-association is functionally linked to enhanced chromatin occupancy and gene activation. Collectively, our findings show that hotspot mutations in a chromatinreader domain drive self-reinforced recruitment, derailing normal cell-fate control during development and leading to an oncogenic outcome.


  
Monumental architecture at Aguada Fenix and the rise of Maya civilization 期刊论文
NATURE, 2020
作者:  Bedding, Timothy R.;  Murphy, Simon J.;  Hey, Daniel R.;  Huber, Daniel;  Li, Tanda;  Smalley, Barry;  Stello, Dennis;  White, Timothy R.;  Ball, Warrick H.;  Chaplin, William J.;  Colman, Isabel L.;  Fuller, Jim;  Gaidos, Eric;  Harbeck, Daniel R.;  Hermes, J. J.;  Holdsworth, Daniel L.;  Li, Gang;  Li, Yaguang;  Mann, Andrew W.;  Reese, Daniel R.;  Sekaran, Sanjay;  Yu, Jie;  Antoci, Victoria;  Bergmann, Christoph;  Brown, Timothy M.;  Howard, Andrew W.;  Ireland, Michael J.;  Isaacson, Howard;  Jenkins, Jon M.;  Kjeldsen, Hans;  McCully, Curtis;  Rabus, Markus;  Rains, Adam D.;  Ricker, George R.;  Tinney, Christopher G.;  Vanderspek, Roland K.
收藏  |  浏览/下载:30/0  |  提交时间:2020/07/03

Archaeologists have traditionally thought that the development of Maya civilization was gradual, assuming that small villages began to emerge during the Middle Preclassic period (1000-350 bc  dates are calibrated throughout) along with the use of ceramics and the adoption of sedentism(1). Recent finds of early ceremonial complexes are beginning to challenge this model. Here we describe an airborne lidar survey and excavations of the previously unknown site of Aguada Fenix (Tabasco, Mexico) with an artificial plateau, which measures 1,400 m in length and 10 to 15 m in height and has 9 causeways radiating out from it. We dated this construction to between 1000 and 800 bc using a Bayesian analysis of radiocarbon dates. To our knowledge, this is the oldest monumental construction ever found in the Maya area and the largest in the entire pre-Hispanic history of the region. Although the site exhibits some similarities to the earlier Olmec centre of San Lorenzo, the community of Aguada Fenix probably did not have marked social inequality comparable to that of San Lorenzo. Aguada Fenix and other ceremonial complexes of the same period suggest the importance of communal work in the initial development of Maya civilization.


Lidar survey of the Maya lowlands uncovers the monumental site of Aguada Fenix, which dates to around 1000-800 bc and points to the role of communal construction in the development of Maya civilization.


  
Origin of complexity in haemoglobin evolution 期刊论文
NATURE, 2020
作者:  Cheema, Suraj S.;  Kwon, Daewoong;  Shanker, Nirmaan;  dos Reis, Roberto;  Hsu, Shang-Lin;  Xiao, Jun;  Zhang, Haigang;  Wagner, Ryan;  Datar, Adhiraj;  McCarter, Margaret R.;  Serrao, Claudy R.;  Yadav, Ajay K.;  Karbasian, Golnaz;  Hsu, Cheng-Hsiang;  Tan, Ava J.;  Wang, Li-Chen;  Thakare, Vishal;  Zhang, Xiang;  Mehta, Apurva;  Karapetrova, Evguenia;  Chopdekar, Rajesh, V;  Shafer, Padraic;  Arenholz, Elke;  Hu, Chenming;  Proksch, Roger;  Ramesh, Ramamoorthy;  Ciston, Jim;  Salahuddin, Sayeef
收藏  |  浏览/下载:50/0  |  提交时间:2020/07/03

Most proteins associate into multimeric complexes with specific architectures(1,2), which often have functional properties such as cooperative ligand binding or allosteric regulation(3). No detailed knowledge is available about how any multimer and its functions arose during evolution. Here we use ancestral protein reconstruction and biophysical assays to elucidate the origins of vertebrate haemoglobin, a heterotetramer of paralogous alpha- and beta-subunits that mediates respiratory oxygen transport and exchange by cooperatively binding oxygen with moderate affinity. We show that modern haemoglobin evolved from an ancient monomer and characterize the historical '  missing link'  through which the modern tetramer evolved-a noncooperative homodimer with high oxygen affinity that existed before the gene duplication that generated distinct alpha- and beta-subunits. Reintroducing just two post-duplication historical substitutions into the ancestral protein is sufficient to cause strong tetramerization by creating favourable contacts with more ancient residues on the opposing subunit. These surface substitutions markedly reduce oxygen affinity and even confer cooperativity, because an ancient linkage between the oxygen binding site and the multimerization interface was already an intrinsic feature of the protein'  s structure. Our findings establish that evolution can produce new complex molecular structures and functions via simple genetic mechanisms that recruit existing biophysical features into higher-level architectures.


Experimental analysis of reconstructed ancestral globins reveals that haemoglobin'  s complex tetrameric structure and oxygen-binding functions evolved by simple genetic and biophysical mechanisms.


  
Hydrogen peroxide sensor HPCA1 is an LRR receptor kinase in Arabidopsis 期刊论文
NATURE, 2020, 578 (7796) : 577-+
作者:  Bogomilov, M.;  Tsenov, R.;  Vankova-Kirilova, G.;  Song, Y. P.;  Tang, J. Y.;  Li, Z. H.;  Bertoni, R.;  Bonesini, M.;  Chignoli, F.;  Mazza, R.;  Palladino, V;  de Bari, A.;  Orestano, D.;  Tortora, L.;  Kuno, Y.;  Sakamoto, H.;  Sato, A.;  Ishimoto, S.;  Chung, M.;  Sung, C. K.;  Filthaut, F.;  Jokovic, D.;  Maletic, D.;  Savic, M.;  Jovancevic, N.;  Nikolov, J.;  Vretenar, M.;  Ramberger, S.;  Asfandiyarov, R.;  Blondel, A.;  Drielsma, F.;  Karadzhov, Y.;  Boyd, S.;  Greis, J. R.;  Lord, T.;  Pidcott, C.;  Taylor, I;  Charnley, G.;  Collomb, N.;  Dumbell, K.;  Gallagher, A.;  Grant, A.;  Griffiths, S.;  Hartnett, T.;  Martlew, B.;  Moss, A.;  Muir, A.;  Mullacrane, I;  Oates, A.;  Owens, P.;  Stokes, G.;  Warburton, P.;  White, C.;  Adams, D.;  Bayliss, V;  Boehm, J.;  Bradshaw, T. W.;  Brown, C.;  Courthold, M.;  Govans, J.;  Hills, M.;  Lagrange, J-B;  Macwaters, C.;  Nichols, A.;  Preece, R.;  Ricciardi, S.;  Rogers, C.;  Stanley, T.;  Tarrant, J.;  Tucker, M.;  Watson, S.;  Wilson, A.;  Bayes, R.;  Nugent, J. C.;  Soler, F. J. P.;  Chatzitheodoridis, G. T.;  Dick, A. J.;  Ronald, K.;  Whyte, C. G.;  Young, A. R.;  Gamet, R.;  Cooke, P.;  Blackmore, V. J.;  Colling, D.;  Dobbs, A.;  Dornan, P.;  Franchini, P.;  Hunt, C.;  Jurj, P. B.;  Kurup, A.;  Long, K.;  Martyniak, J.;  Middleton, S.;  Pasternak, J.;  Uchida, M. A.;  Cobb, J. H.;  Booth, C. N.;  Hodgson, P.;  Langlands, J.;  Overton, E.;  Pec, V;  Smith, P. J.;  Wilbur, S.;  Ellis, M.;  Gardener, R. B. S.;  Kyberd, P.;  Nebrensky, J. J.;  DeMello, A.;  Gourlay, S.;  Lambert, A.;  Li, D.;  Luo, T.;  Prestemon, S.;  Virostek, S.;  Palmer, M.;  Witte, H.;  Adey, D.;  Bross, A. D.;  Bowring, D.;  Liu, A.;  Neuffer, D.;  Popovic, M.;  Rubinov, P.;  Freemire, B.;  Hanlet, P.;  Kaplan, D. M.;  Mohayai, T. A.;  Rajaram, D.;  Snopok, P.;  Torun, Y.;  Cremaldi, L. M.;  Sanders, D. A.;  Summers, D. J.;  Coney, L. R.;  Hanson, G. G.;  Heidt, C.
收藏  |  浏览/下载:33/0  |  提交时间:2020/07/03

Hydrogen peroxide (H2O2) is a major reactive oxygen species in unicellular and multicellular organisms, and is produced extracellularly in response to external stresses and internal cues(1-4). H2O2 enters cells through aquaporin membrane proteins and covalently modifies cytoplasmic proteins to regulate signalling and cellular processes. However, whether sensors for H2O2 also exist on the cell surface remains unknown. In plant cells, H2O2 triggers an influx of Ca2+ ions, which is thought to be involved in H2O2 sensing and signalling. Here, by using forward genetic screens based on Ca2+ imaging, we isolated hydrogen-peroxide-induced Ca(2+)increases (hpca) mutants in Arabidopsis, and identified HPCA1 as a leucine-rich-repeat receptor kinase belonging to a previously uncharacterized subfamily that features two extra pairs of cysteine residues in the extracellular domain. HPCA1 is localized to the plasma membrane and is activated by H2O2 via covalent modification of extracellular cysteine residues, which leads to autophosphorylation of HPCA1. HPCA1 mediates H2O2-induced activation of Ca2+ channels in guard cells and is required for stomatal closure. Our findings help to identify how the perception of extracellular H2O2 is integrated with responses to various external stresses and internal cues in plants, and have implications for the design of crops with enhanced fitness.


HPCA1, a member of a previously uncharacterized subfamily of leucine-rich-repeat receptor-like kinases, is the hydrogen-peroxide sensor at the plasma membrane in Arabidopsis.


  
Patterns of somatic structural variation in human cancer genomes 期刊论文
NATURE, 2020, 578 (7793) : 112-+
作者:  Wan, Liling;  Chong, Shasha;  Xuan, Fan;  Liang, Angela;  Cui, Xiaodong;  Gates, Leah;  Carroll, Thomas S.;  Li, Yuanyuan;  Feng, Lijuan;  Chen, Guochao;  Wang, Shu-Ping;  Ortiz, Michael V.;  Daley, Sara K.;  Wang, Xiaolu;  Xuan, Hongwen;  Kentsis, Alex;  Muir, Tom W.;  Roeder, Robert G.;  Li, Haitao;  Li, Wei;  Tjian, Robert;  Wen, Hong;  Allis, C. David
收藏  |  浏览/下载:36/0  |  提交时间:2020/07/03

A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes(1-7). Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types(8). Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions-as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and-in liver cancerfrequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.


  
Tripled yield in direct-drive laser fusion through statistical modelling 期刊论文
NATURE, 2019, 565 (7741) : 581-+
作者:  Gopalaswamy, V.;  Betti, R.;  Knauer, J. P.;  Luciani, N.;  Patel, D.;  Woo, K. M.;  Bose, A.;  Igumenshchev, I. V.;  Campbell, E. M.;  Anderson, K. S.;  Bauer, K. A.;  Bonino, M. J.;  Cao, D.;  Christopherson, A. R.;  Collins, G. W.;  Collins, T. J. B.;  Davies, J. R.;  Delettrez, J. A.;  Edgell, D. H.;  Epstein, R.;  Forrest, C. J.;  Froula, D. H.;  Glebov, V. Y.;  Goncharov, V. N.;  Harding, D. R.;  Hu, S. X.;  Jacobs-Perkins, D. W.;  Janezic, R. T.;  Kelly, J. H.;  Mannion, O. M.;  Maximov, A.;  Marshall, F. J.;  Michel, D. T.;  Miller, S.;  Morse, S. F. B.;  Palastro, J.;  Peebles, J.;  Radha, P. B.;  Regan, S. P.;  Sampat, S.;  Sangster, T. C.;  Sefkow, A. B.;  Seka, W.;  Shah, R. C.;  Shmyada, W. T.;  Shvydky, A.;  Stoeckl, C.;  Solodov, A. A.;  Theobald, W.;  Zuegel, J. D.;  Johnson, M. Gatu;  Petrasso, R. D.;  Li, C. K.;  Frenje, J. A.
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (vol 483, pg 603, 2012) 期刊论文
NATURE, 2019, 565 (7738) : E5-E6
作者:  Barretina, Jordi;  Caponigro, Giordano;  Stransky, Nicolas;  Venkatesan, Kavitha;  Margolin, Adam A.;  Kim, Sungjoon;  Wilson, Christopher J.;  Lehar, Joseph;  Kryukov, Gregory V.;  Sonkin, Dmitriy;  Reddy, Anupama;  Liu, Manway;  Murray, Lauren;  Berger, Michael F.;  Monahan, John E.;  Morais, Paula;  Meltzer, Jodi;  Korejwa, Adam;  Jane-Valbuena, Judit;  Mapa, Felipa A.;  Thibault, Joseph;  Bric-Furlong, Eva;  Raman, Pichai;  Shipway, Aaron;  Engels, Ingo H.;  Cheng, Jill;  Yu, Guoying K.;  Yu, Jianjun;  Aspesi, Peter, Jr.;  de Silva, Melanie;  Jagtap, Kalpana;  Jones, Michael D.;  Wang, Li;  Hatton, Charles;  Palescandolo, Emanuele;  Gupta, Supriya;  Mahan, Scott;  Sougnez, Carrie;  Onofrio, Robert C.;  Liefeld, Ted;  MacConaill, Laura;  Winckler, Wendy;  Reich, Michael;  Li, Nanxin;  Mesirov, Jill P.;  Gabriel, Stacey B.;  Getz, Gad;  Ardlie, Kristin;  Chan, Vivien;  Myer, Vic E.;  Weber, Barbara L.;  Porter, Jeff;  Warmuth, Markus;  Finan, Peter;  Harris, Jennifer L.;  Meyerson, Matthew;  Golub, Todd R.;  Morrissey, Michael P.;  Sellers, William R.;  Schlegel, Robert;  Garraway, Levi A.
收藏  |  浏览/下载:22/0  |  提交时间:2019/11/27
Challenging local realism with human choices 期刊论文
NATURE, 2018, 557 (7704) : 212-+
作者:  Abellan, C.;  Acin, A.;  Alarcon, A.;  Alibart, O.;  Andersen, C. K.;  Andreoli, F.;  Beckert, A.;  Beduini, F. A.;  Bendersky, A.;  Bentivegna, M.;  Bierhorst, P.;  Burchardt, D.;  Cabello, A.;  Carine, J.;  Carrasco, S.;  Carvacho, G.;  Cavalcanti, D.;  Chaves, R.;  Cortes-Vega, J.;  Cuevas, A.;  Delgado, A.;  de Riedmatten, H.;  Eichler, C.;  Farrera, P.;  Fuenzalida, J.;  Garcia-Matos, M.;  Garthoff, R.;  Gasparinetti, S.;  Gerrits, T.;  Jouneghani, F. Ghafari;  Glancy, S.;  Gomez, E. S.;  Gonzalez, P.;  Guan, J-Y;  Handsteiner, J.;  Heinsoo, J.;  Heinze, G.;  Hirschmann, A.;  Jimenez, O.;  Kaiser, F.;  Knill, E.;  Knoll, L. T.;  Krinner, S.;  Kurpiers, P.;  Larotonda, M. A.;  Larsson, J-A;  Lenhard, A.;  Li, H.;  Li, M-H;  Lima, G.;  Liu, B.;  Liu, Y.;  Lopez Grande, I. H.;  Lunghi, T.;  Ma, X.;  Magana-Loaiza, O. S.;  Magnard, P.;  Magnoni, A.;  Marti-Prieto, M.;  Martinez, D.;  Mataloni, P.;  Mattar, A.;  Mazzera, M.;  Mirin, R. P.;  Mitchell, M. W.;  Nam, S.;  Oppliger, M.;  Pan, J-W;  Patel, R. B.;  Pryde, G. J.;  Rauch, D.;  Redeker, K.;  Rielander, D.;  Ringbauer, M.;  Roberson, T.;  Rosenfeld, W.;  Salathe, Y.;  Santodonato, L.;  Sauder, G.;  Scheidl, T.;  Schmiegelow, C. T.;  Sciarrino, F.;  Seri, A.;  Shalm, L. K.;  Shi, S-C;  Slussarenko, S.;  Stevens, M. J.;  Tanzilli, S.;  Toledo, F.;  Tura, J.;  Ursin, R.;  Vergyris, P.;  Verma, V. B.;  Walter, T.;  Wallraff, A.;  Wang, Z.;  Weinfurter, H.;  Weston, M. M.;  White, A. G.;  Wu, C.;  Xavier, G. B.;  You, L.;  Yuan, X.;  Zeilinger, A.;  Zhang, Q.;  Zhang, W.;  Zhong, J.
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/27