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Ice retreat in Wilkes Basin of East Antarctica during a warm interglacial 期刊论文
NATURE, 2020, 583 (7817) : 554-+
作者:  T. Blackburn;  G. H. Edwards;  S. Tulaczyk;  M. Scudder;  G. Piccione;  B. Hallet;  N. McLean;  J. C. Zachos;  B. Cheney;  J. T. Babbe
收藏  |  浏览/下载:21/0  |  提交时间:2020/08/09

Uranium isotopes in subglacial precipitates from the Wilkes Basin of the East Antarctic Ice Sheet reveal ice retreat during a warm Pleistocene interglacial period about 400,000 years ago.


Efforts to improve sea level forecasting on a warming planet have focused on determining the temperature, sea level and extent of polar ice sheets during Earth'  s past interglacial warm periods(1-3). About 400,000 years ago, during the interglacial period known as Marine Isotopic Stage 11 (MIS11), the global temperature was 1 to 2 degrees Celsius greater(2)and sea level was 6 to 13 metres higher(1,3). Sea level estimates in excess of about 10 metres, however, have been discounted because these require a contribution from the East Antarctic Ice Sheet(3), which has been argued to have remained stable for millions of years before and includes MIS11(4,5). Here we show how the evolution of(234)U enrichment within the subglacial waters of East Antarctica recorded the ice sheet'  s response to MIS11 warming. Within the Wilkes Basin, subglacial chemical precipitates of opal and calcite record accumulation of(234)U (the product of rock-water contact within an isolated subglacial reservoir) up to 20 times higher than that found in marine waters. The timescales of(234)U enrichment place the inception of this reservoir at MIS11. Informed by the(234)U cycling observed in the Laurentide Ice Sheet, where(234)U accumulated during periods of ice stability(6)and was flushed to global oceans in response to deglaciation(7), we interpret our East Antarctic dataset to represent ice loss within the Wilkes Basin at MIS11. The(234)U accumulation within the Wilkes Basin is also observed in the McMurdo Dry Valleys brines(8-10), indicating(11)that the brine originated beneath the adjacent East Antarctic Ice Sheet. The marine origin of brine salts(10)and bacteria(12)implies that MIS11 ice loss was coupled with marine flooding. Collectively, these data indicate that during one of the warmest Pleistocene interglacials, the ice sheet margin at the Wilkes Basin retreated to near the precipitate location, about 700 kilometres inland from the current position of the ice margin, which-assuming current ice volumes-would have contributed about 3 to 4 metres(13)to global sea levels.


  
WHAT SCIENTISTS WANT TO KNOW ABOUT THE CORONAVIRUS OUTBREAK 期刊论文
NATURE, 2020, 577 (7792) : 605-607
作者:  Shade, Kai-Ting C.;  Conroy, Michelle E.;  Washburn, Nathaniel;  Kitaoka, Maya;  Huynh, Daniel J.;  Laprise, Emma;  Patil, Sarita U.;  Shreffler, Wayne G.;  Anthony, Robert M.
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03
Structure of nevanimibe-bound tetrameric human ACAT1 期刊论文
NATURE, 2020, 581 (7808) : 339-U214
作者:  Ma, Xiyu;  Claus, Lucas A. N.;  Leslie, Michelle E.;  Tao, Kai;  Wu, Zhiping;  Liu, Jun;  Yu, Xiao;  Li, Bo;  Zhou, Jinggeng;  Savatin, Daniel V.;  Peng, Junmin;  Tyler, Brett M.;  Heese, Antje;  Russinova, Eugenia;  He, Ping;  Shan, Libo
收藏  |  浏览/下载:28/0  |  提交时间:2020/07/03

The structure of human ACAT1 in complex with the inhibitor nevanimibe is resolved by cryo-electron microscopy.


Cholesterol is an essential component of mammalian cell membranes, constituting up to 50% of plasma membrane lipids. By contrast, it accounts for only 5% of lipids in the endoplasmic reticulum (ER)(1). The ER enzyme sterol O-acyltransferase 1 (also named acyl-coenzyme A:cholesterol acyltransferase, ACAT1) transfers a long-chain fatty acid to cholesterol to form cholesteryl esters that coalesce into cytosolic lipid droplets. Under conditions of cholesterol overload, ACAT1 maintains the low cholesterol concentration of the ER and thereby has an essential role in cholesterol homeostasis(2,3). ACAT1 has also been implicated in Alzheimer'  s disease(4), atherosclerosis(5) and cancers(6). Here we report a cryo-electron microscopy structure of human ACAT1 in complex with nevanimibe(7), an inhibitor that is in clinical trials for the treatment of congenital adrenal hyperplasia. The ACAT1 holoenzyme is a tetramer that consists of two homodimers. Each monomer contains nine transmembrane helices (TMs), six of which (TM4-TM9) form a cavity that accommodates nevanimibe and an endogenous acyl-coenzyme A. This cavity also contains a histidine that has previously been identified as essential for catalytic activity(8). Our structural data and biochemical analyses provide a physical model to explain the process of cholesterol esterification, as well as details of the interaction between nevanimibe and ACAT1, which may help to accelerate the development of ACAT1 inhibitors to treat related diseases.


  
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.


  
APOE4 leads to blood-brain barrier dysfunction predicting cognitive decline 期刊论文
NATURE, 2020, 581 (7806) : 70-+
作者:  Doherty, Tiarnan A. S.;  Winchester, Andrew J.;  Macpherson, Stuart;  Johnstone, Duncan N.;  Pareek, Vivek;  Tennyson, Elizabeth M.;  Kosar, Sofiia;  Kosasih, Felix U.;  Anaya, Miguel;  Abdi-Jalebi, Mojtaba;  Andaji-Garmaroudi, Zahra;  Wong, E. Laine;  Madeo, Julien;  Chiang, Yu-Hsien;  Park, Ji-Sang;  Jung, Young-Kwang;  Petoukhoff, Christopher E.;  Divitini, Giorgio;  Man, Michael K. L.;  Ducati, Caterina;  Walsh, Aron;  Midgley, Paul A.;  Dani, Keshav M.;  Stranks, Samuel D.
收藏  |  浏览/下载:25/0  |  提交时间:2020/07/03

Breakdown of the blood-brain barrier in individuals carrying the epsilon 4 allele of the APOE gene, but not the epsilon 3 allele, increases with and predicts cognitive impairment and is independent of amyloid beta or tau pathology.


Vascular contributions to dementia and Alzheimer'  s disease are increasingly recognized(1-6). Recent studies have suggested that breakdown of the blood-brain barrier (BBB) is an early biomarker of human cognitive dysfunction(7), including the early clinical stages of Alzheimer'  s disease(5,8-10). The E4 variant of apolipoprotein E (APOE4), the main susceptibility gene for Alzheimer'  s disease(11-14), leads to accelerated breakdown of the BBB and degeneration of brain capillary pericytes(15-19), which maintain BBB integrity(20-22). It is unclear, however, whether the cerebrovascular effects of APOE4 contribute to cognitive impairment. Here we show that individuals bearing APOE4 (with the epsilon 3/epsilon 4 or epsilon 4/epsilon 4 alleles) are distinguished from those without APOE4 (epsilon 3/epsilon 3) by breakdown of the BBB in the hippocampus and medial temporal lobe. This finding is apparent in cognitively unimpaired APOE4 carriers and more severe in those with cognitive impairment, but is not related to amyloid-beta or tau pathology measured in cerebrospinal fluid or by positron emission tomography(23). High baseline levels of the BBB pericyte injury biomarker soluble PDGFR beta(7,8) in the cerebrospinal fluid predicted future cognitive decline in APOE4 carriers but not in non-carriers, even after controlling for amyloid-beta and tau status, and were correlated with increased activity of the BBB-degrading cyclophilin A-matrix metalloproteinase-9 pathway(19) in cerebrospinal fluid. Our findings suggest that breakdown of the BBB contributes to APOE4-associated cognitive decline independently of Alzheimer'  s disease pathology, and might be a therapeutic target in APOE4 carriers.


  
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.


  
Dating the skull from Broken Hill, Zambia, and its position in human evolution 期刊论文
NATURE, 2020, 580 (7803) : 372-+
作者:  Mergner, Julia;  Frejno, Martin;  List, Markus;  Papacek, Michael;  Chen, Xia;  Chaudhary, Ajeet;  Samaras, Patroklos;  Richter, Sandra;  Shikata, Hiromasa;  Messerer, Maxim;  Lang, Daniel;  Altmann, Stefan;  Cyprys, Philipp;  Zolg, Daniel P.;  Mathieson, Toby;  Bantscheff, Marcus
收藏  |  浏览/下载:5/0  |  提交时间:2020/07/03

The cranium from Broken Hill (Kabwe) was recovered from cave deposits in 1921, during metal ore mining in what is now Zambia(1). It is one of the best-preserved skulls of a fossil hominin, and was initially designated as the type specimen of Homo rhodesiensis, but recently it has often been included in the taxon Homo heidelbergensis(2-4). However, the original site has since been completely quarried away, and-although the cranium is often estimated to be around 500 thousand years old(5-7)-its unsystematic recovery impedes its accurate dating and placement in human evolution. Here we carried out analyses directly on the skull and found a best age estimate of 299 +/- 25 thousand years (mean +/- 2s). The result suggests that later Middle Pleistocene Africa contained multiple contemporaneous hominin lineages (that is, Homo sapiens(8,9), H. heidelbergensis/H. rhodesiensis and Homo naledi(10,11)), similar to Eurasia, where Homo neanderthalensis, the Denisovans, Homo floresiensis, Homo luzonensis and perhaps also Homo heidelbergensis and Homo erectus(12) were found contemporaneously. The age estimate also raises further questions about the mode of evolution of H. sapiens in Africa and whether H. heidelbergensis/H. rhodesiensis was a direct ancestor of our species(13,14).


  
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.


  
Direct thermal neutron detection by the 2D semiconductor (LiInP2Se6)-Li-6 (2020) (vol 577, pg 346, 2020) 期刊论文
NATURE, 2020, 579 (7799) : E9-E9
作者:  Groen, Simon C.;  Calic, Irina;  Joly-Lopez, Zoe;  Platts, Adrian E.;  Choi, Jae Young;  Natividad, Mignon;  Dorph, Katherine;  Mauck, William M., III;  Bracken, Bernadette;  Cabral, Carlo Leo U.;  Kumar, Arvind;  Torres, Rolando O.;  Satija, Rahul;  Vergara, Georgina;  Henry, Amelia;  Franks, Steven J.;  Purugganan, Michael D.
收藏  |  浏览/下载:26/0  |  提交时间:2020/07/03

An amendment to this paper has been published and can be accessed via a link at the top of the paper.