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On the Role of Pacific-Atlantic SST Contrast and Associated Caribbean Sea Convection in August-October US Regional Rainfall Variability 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2020, 47 (11)
作者:  Kim, Dongmin;  Lee, Sang-Ki;  Lopez, Hosmay;  Foltz, Gregory R.;  Misra, Vasubandhu;  Kumar, Arun
收藏  |  浏览/下载:7/0  |  提交时间:2020/05/20
Pacific-Atlantic SST interaction  Atlantic Warm pool  Caribbean Sea  U  S  precipitation  
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance 期刊论文
NATURE, 2020, 582 (7811) : 283-+
作者:  Raj, Dipak K.;  Das Mohapatra, Alok;  Jnawali, Anup;  Zuromski, Jenna;  Jha, Ambrish;  Cham-Kpu, Gerald;  Sherman, Brett;  Rudlaff, Rachel M.;  Nixon, Christina E.;  Hilton, Nicholas;  Oleinikov, Andrew V.;  Chesnokov, Olga;  Merritt, Jordan;  Pond-Tor, Sunthorn
收藏  |  浏览/下载:19/0  |  提交时间:2020/07/03

Mobile genetic elements threaten genome integrity in all organisms. RDE-3 (also known as MUT-2) is a ribonucleotidyltransferase that is required for transposon silencing and RNA interference in Caenorhabditis elegans(1-4). When tethered to RNAs in heterologous expression systems, RDE-3 can add long stretches of alternating non-templated uridine (U) and guanosine (G) ribonucleotides to the 3 '  termini of these RNAs (designated poly(UG) or pUG tails)(5). Here we show that, in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNA interference, as well as to transposon RNAs. RNA fragments attached to pUG tails with more than 16 perfectly alternating 3 '  U and G nucleotides become gene-silencing agents. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases, which use pUG-tailed RNAs (pUG RNAs) as templates to synthesize small interfering RNAs (siRNAs). Our results show that cycles of pUG RNA-templated siRNA synthesis and siRNA-directed pUG RNA biogenesis underlie double-stranded-RNA-directed transgenerational epigenetic inheritance in the C. elegans germline. We speculate that this pUG RNA-siRNA silencing loop enables parents to inoculate progeny against the expression of unwanted or parasitic genetic elements.


In Caenorhabditis elegans, the ribonucleotidyltransferase RDE-3 adds alternating uridine and guanosine ribonucleotides to the 3 '  termini of RNAs, a key step in RNA interference and thus epigenetic inheritance in the C. elegans germline.


  
Molecular architecture of the human 17S U2 snRNP 期刊论文
NATURE, 2020, 583 (7815) : 310-+
作者:  Muench, David E.;  Olsson, Andre;  Ferchen, Kyle;  Pham, Giang;  Serafin, Rachel A.;  Chutipongtanate, Somchai;  Dwivedi, Pankaj;  Song, Baobao;  Hay, Stuart;  Chetal, Kashish;  Trump-Durbin, Lisa R.;  Mookerjee-Basu, Jayati;  Zhang, Kejian;  Yu, Jennifer C.
收藏  |  浏览/下载:18/0  |  提交时间:2020/07/03

The U2 small nuclear ribonucleoprotein (snRNP) has an essential role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first step of splicing'  . Stable addition of U2 during early spliceosome formation requiresthe DEAD-box ATPase PRP5(2-7). Yeast U2 small nuclear RNA (snRNA) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-interacting stem-loop (BSL)(8), but whether the human U2 snRNA folds in a similar manner is unknown. The U2 SF3B1 protein, a common mutational target in haematopoietic cancers(9), contains a HEAT domain (SF3B1(HEAT)) with an open conformation in isolated SF3b(10), but a closed conformation in spliceosomes(11), which is required for stable interaction between U2 and the branch site. Here we report a 3D cryo-electron microscopy structure ofthe human 17S U2 snRNP at a core resolution of 4.1 angstrom and combine it with protein crosslinking data to determine the molecular architecture of this snRNP. Our structure reveals that SF3B1(HEAT) interacts with PRP5 and TAT-SF1, and maintains its open conformation in U2 snRNP, and that U2 snRNA forms a BSL that is sandwiched between PRP5, TAT-SF1 and SF3B1(HEAT). Thus, substantial remodelling of the BSL and displacement of BSL-interacting proteins must occur to allow formation of the U2-branch-site helix. Our studies provide a structural explanation of why TAT-SF1 must be displaced before the stable addition of U2 to the spliceosome, and identify RNP rearrangements facilitated by PRP5 that are required for stable interaction between U2 and the branch site.


  
Large-Scale Atmospheric Circulation Patterns Associated With US Great Plains Warm Season Droughts Revealed by Self-Organizing Maps 期刊论文
JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, 2020, 125 (5)
作者:  Zhuang, Yizhou;  Fu, Rong;  Wang, Hongqing
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/02
self-organizing maps  U  S  Great Plains  drought  large-scale atmospheric pattern  
U1 snRNP regulates chromatin retention of noncoding RNAs 期刊论文
NATURE, 2020
作者:  Dehollain, J. P.;  Mukhopadhyay, U.;  Michal, V. P.;  Wang, Y.;  Wunsch, B.;  Reichl, C.;  Wegscheider, W.;  Rudner, M. S.;  Demler, E.;  Vandersypen, L. M. K.
收藏  |  浏览/下载:23/0  |  提交时间:2020/07/03

Long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable transcripts locate preferentially to chromatin, where some regulate chromatin structure, transcription and RNA processing(1-13). Although several RNA sequences responsible for nuclear localization have been identified-such as repeats in the lncRNA Xist and Alu-like elements in long RNAs14-16-how lncRNAs as a class are enriched at chromatin remains unknown. Here we describe a random, mutagenesis-coupled, high-throughput method that we name '  RNA elements for subcellular localization by sequencing'  (mutREL-seq). Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucleoprotein (snRNP) and is essential for the localization of reporter RNAs to chromatin. Across the genome, chromatin-bound lncRNAs are enriched with 5 '  splice sites and depleted of 3 '  splice sites, and exhibit high levels of U1 snRNA binding compared with cytoplasm-localized messenger RNAs. Acute depletion of U1 snRNA or of the U1 snRNP protein component SNRNP70 markedly reduces the chromatin association of hundreds of lncRNAs and unstable transcripts, without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear and genome-wide localization of the lncRNA Malat1. Moreover, U1 snRNP interacts with transcriptionally engaged RNA polymerase II. These results show that U1 snRNP acts widely to tether and mobilize lncRNAs to chromatin in a transcription-dependent manner. Our findings have uncovered a previously unknown role of U1 snRNP beyond the processing of precursor mRNA, and provide molecular insight into how lncRNAs are recruited to regulatory sites to carry out chromatin-associated functions.


Long noncoding RNAs and certain unstable transcripts tend to localize to chromatin, in a process that is shown here to depend on an RNA motif that recognizes the small nuclear ribonuclear protein U1, and to rely on transcription.


  
Germline Elongator mutations in Sonic Hedgehog medulloblastoma 期刊论文
NATURE, 2020, 580 (7803) : 396-+
作者:  Helmrich, S.;  Arias, A.;  Lochead, G.;  Wintermantel, T. M.;  Buchhold, M.;  Diehl, S.;  Whitlock, S.
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children(1,2), and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma(3). Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHH alpha subtype(4) and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U-34) position(5,6). Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems(7-9). Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.


  
DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis 期刊论文
NATURE, 2020, 579 (7798) : 291-+
作者:  Avellaneda, Mario J.;  Franke, Kamila B.;  Sunderlikova, Vanda;  Bukau, Bernd;  Mogk, Axel;  Tans, Sander J.
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

The DNA-dependent protein kinase (DNA-PK), which comprises the KU heterodimer and a catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor(1). KU binds to DNA ends, initiates cNHEJ, and recruits and activates DNA-PKcs. KU also binds to RNA, but the relevance of this interaction in mammals is unclear. Here we use mouse models to show that DNA-PK has an unexpected role in the biogenesis of ribosomal RNA (rRNA) and in haematopoiesis. The expression of kinase-dead DNA-PKcs abrogates cNHEJ(2). However, most mice that both expressed kinase-dead DNA-PKcs and lacked the tumour suppressor TP53 developed myeloid disease, whereas all other previously characterized mice deficient in both cNHEJ and TP53 expression succumbed to pro-B cell lymphoma(3). DNA-PK autophosphorylates DNA-PKcs, which is its best characterized substrate. Blocking the phosphorylation of DNA-PKcs at the T2609 cluster, but not the S2056 cluster, led to KU-dependent defects in 18S rRNA processing, compromised global protein synthesis in haematopoietic cells and caused bone marrow failure in mice. KU drives the assembly of DNA-PKcs on a wide range of cellular RNAs, including the U3 small nucleolar RNA, which is essential for processing of 18S rRNA(4). U3 activates purified DNA-PK and triggers phosphorylation of DNA-PKcs at T2609. DNA-PK, but not other cNHEJ factors, resides in nucleoli in an rRNA-dependent manner and is co-purified with the small subunit processome. Together our data show that DNA-PK has RNA-dependent, cNHEJ-independent functions during ribosome biogenesis that require the kinase activity of DNA-PKcs and its phosphorylation at the T2609 cluster.


  
Redox-switchable carboranes for uranium capture and release 期刊论文
NATURE, 2020, 577 (7792) : 652-+
作者:  Marques, Joao C.;  Li, Meng;  Schaak, Diane;  Robson, Drew N.;  Li, Jennifer M.
收藏  |  浏览/下载:31/0  |  提交时间:2020/07/03

The uranyl ion (UO22+  U(vi) oxidation state) is the most common form of uranium found in terrestrial and aquatic environments and is a central component in nuclear fuel processing and waste remediation efforts. Uranyl capture from either seawater or nuclear waste has been well studied and typically relies on extremely strong chelating/binding affinities to UO22+ using chelating polymers(1,2), porous inorganic(3-5) or carbon-based(6,7) materials, as well as homogeneous(8) compounds. By contrast, the controlled release of uranyl after capture is less established and can be difficult, expensive or destructive to the initial material(2,9). Here we show how harnessing the redox-switchable chelating and donating properties of an ortho-substituted closo-carborane (1,2-(Ph2PO)(2)-1,2-C2B10H10) cluster molecule can lead to the controlled chemical or electrochemical capture and release of UO22+ in monophasic (organic) or biphasic (organic/aqueous) model solvent systems. This is achieved by taking advantage of the increase in the ligand bite angle when the closo-carborane is reduced to the nido-carborane, resulting in C-C bond rupture and cage opening. The use of electrochemical methods for uranyl capture and release may complement existing sorbent and processing systems.


Redox-switchable chelation is demonstrated for a carborane cluster molecule, leading to controlled chemical or electrochemical capture and release of uranyl in monophasic or biphasic model solvent systems.


  
Excessive electricity intensity of Vietnam: Evidence from a comparative study of Asia-Pacific countries 期刊论文
ENERGY POLICY, 2019, 130: 409-417
作者:  Hien, P. D.
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/27
Electricity intensity  Vietnam  Asia-Pacific economies  Inverted-U model  Factor analysis  State-owned enterprises  
Snowpack Contributions and Temperature Characterization of Landfalling Atmospheric Rivers in the Western Cordillera of the United States 期刊论文
GEOPHYSICAL RESEARCH LETTERS, 2019, 46 (12) : 6663-6672
作者:  Hu, J. Michelle;  Nolin, Anne W.
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/26
atmospheric river  mountain snowpack  extreme events  precipitation  hydroclimatology  U  S  west coast