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John rinn

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https://www.readbyqxmd.com/read/27626181/linc00520-is-induced-by-src-stat3-and-pi3k-and-plays-a-functional-role-in-breast-cancer
#1
Whitney S Henry, David G Hendrickson, Francisco Beca, Benjamin Glass, Marianne Lindahl-Allen, Lizhi He, Zhe Ji, Kevin Struhl, Andrew H Beck, John L Rinn, Alex Toker
Long non-coding RNAs (lncRNAs) have been implicated in normal cellular homeostasis as well as pathophysiological conditions, including cancer. Here we performed global gene expression profiling of mammary epithelial cells transformed by oncogenic v-Src, and identified a large subset of uncharacterized lncRNAs potentially involved in breast cancer development. Specifically, our analysis revealed a novel lncRNA, LINC00520 that is upregulated upon ectopic expression of oncogenic v-Src, in a manner that is dependent on the transcription factor STAT3...
September 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27595844/in-vivo-ebola-virus-infection-leads-to-a-strong-innate-response-in-circulating-immune-cells
#2
Ignacio S Caballero, Anna N Honko, Stephen K Gire, Sarah M Winnicki, Marta Melé, Chiara Gerhardinger, Aaron E Lin, John L Rinn, Pardis C Sabeti, Lisa E Hensley, John H Connor
BACKGROUND: Ebola virus is the causative agent of a severe syndrome in humans with a fatality rate that can approach 90 %. During infection, the host immune response is thought to become dysregulated, but the mechanisms through which this happens are not entirely understood. In this study, we analyze RNA sequencing data to determine the host response to Ebola virus infection in circulating immune cells. RESULTS: Approximately half of the 100 genes with the strongest early increases in expression were interferon-stimulated genes, such as ISG15, OAS1, IFIT2, HERC5, MX1 and DHX58...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27525555/the-long-non-coding-rna-morrbid-regulates-bim-and-short-lived-myeloid-cell-lifespan
#3
Jonathan J Kotzin, Sean P Spencer, Sam J McCright, Dinesh B Uthaya Kumar, Magalie A Collet, Walter K Mowel, Ellen N Elliott, Asli Uyar, Michelle A Makiya, Margaret C Dunagin, Christian C D Harman, Anthony T Virtue, Stella Zhu, Will Bailis, Judith Stein, Cynthia Hughes, Arjun Raj, E John Wherry, Loyal A Goff, Amy D Klion, John L Rinn, Adam Williams, Richard A Flavell, Jorge Henao-Mejia
Neutrophils, eosinophils and 'classical' monocytes collectively account for about 70% of human blood leukocytes and are among the shortest-lived cells in the body. Precise regulation of the lifespan of these myeloid cells is critical to maintain protective immune responses and minimize the deleterious consequences of prolonged inflammation. However, how the lifespan of these cells is strictly controlled remains largely unknown. Here we identify a long non-coding RNA that we termed Morrbid, which tightly controls the survival of neutrophils, eosinophils and classical monocytes in response to pro-survival cytokines in mice...
August 15, 2016: Nature
https://www.readbyqxmd.com/read/27524623/in%C3%A2-vivo-characterization-of-linc-p21-reveals-functional-cis-regulatory-dna-elements
#4
Abigail F Groff, Diana B Sanchez-Gomez, Marcela M L Soruco, Chiara Gerhardinger, A Rasim Barutcu, Eric Li, Lara Elcavage, Olivia Plana, Lluvia V Sanchez, James C Lee, Martin Sauvageau, John L Rinn
The Linc-p21 locus, encoding a long non-coding RNA, plays an important role in p53 signaling, cell-cycle regulation, and tumor suppression. However, despite extensive study, confusion exists regarding its mechanism of action: is activity driven by the transcript acting in trans, in cis, or by an underlying functional enhancer? Here, using a knockout mouse model and a massively parallel enhancer assay, we delineate the functional elements at this locus. We observe that, even in tissues with no detectable Linc-p21 transcript, deletion of the locus significantly affects local gene expression, including of the cell-cycle regulator Cdkn1a...
August 23, 2016: Cell Reports
https://www.readbyqxmd.com/read/27259198/-cat-s-cradling-the-3d-genome-by-the-act-of-lncrna-transcription
#5
REVIEW
Marta Melé, John L Rinn
There is growing evidence that transcription and nuclear organization are tightly linked. Yet, whether transcription of thousands of long noncoding RNAs (lncRNAs) could play a role in this packaging process remains elusive. Although some lncRNAs have been found to have clear roles in nuclear architecture (e.g., FIRRE, NEAT1, XIST, and others), the vast majority remain poorly understood. In this Perspective, we highlight how the act of transcription can affect nuclear architecture. We synthesize several recent findings into a proposed model where the transcription of lncRNAs can serve as guide-posts for shaping genome organization...
June 2, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27197224/basset-learning-the-regulatory-code-of-the-accessible-genome-with-deep-convolutional-neural-networks
#6
David R Kelley, Jasper Snoek, John L Rinn
The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many noncoding variants statistically associated with human disease, nearly all such variants have unknown mechanisms. Here, we address this challenge using an approach based on a recent machine learning advance-deep convolutional neural networks (CNNs). We introduce the open source package Basset to apply CNNs to learn the functional activity of DNA sequences from genomics data. We trained Basset on a compendium of accessible genomic sites mapped in 164 cell types by DNase-seq, and demonstrate greater predictive accuracy than previous methods...
July 2016: Genome Research
https://www.readbyqxmd.com/read/27078102/a-distant-trophoblast-specific-enhancer-controls-hla-g-expression-at-the-maternal-fetal-interface
#7
Leonardo M R Ferreira, Torsten B Meissner, Tarjei S Mikkelsen, William Mallard, Charles W O'Donnell, Tamara Tilburgs, Hannah A B Gomes, Raymond Camahort, Richard I Sherwood, David K Gifford, John L Rinn, Chad A Cowan, Jack L Strominger
HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta...
May 10, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27058446/biallelic-mutations-in-pde10a-lead-to-loss-of-striatal-pde10a-and-a-hyperkinetic-movement-disorder-with-onset-in-infancy
#8
Christine P Diggle, Stacey J Sukoff Rizzo, Michael Popiolek, Reetta Hinttala, Jan-Philip Schülke, Manju A Kurian, Ian M Carr, Alexander F Markham, David T Bonthron, Christopher Watson, Saghira Malik Sharif, Veronica Reinhart, Larry C James, Michelle A Vanase-Frawley, Erik Charych, Melanie Allen, John Harms, Christopher J Schmidt, Joanne Ng, Karen Pysden, Christine Strick, Päivi Vieira, Katariina Mankinen, Hannaleena Kokkonen, Matti Kallioinen, Raija Sormunen, Juha O Rinne, Jarkko Johansson, Kati Alakurtti, Laura Huilaja, Tiina Hurskainen, Kaisa Tasanen, Eija Anttila, Tiago Reis Marques, Oliver Howes, Marius Politis, Somayyeh Fahiminiya, Khanh Q Nguyen, Jacek Majewski, Johanna Uusimaa, Eamonn Sheridan, Nicholas J Brandon
Deficits in the basal ganglia pathways modulating cortical motor activity underlie both Parkinson disease (PD) and Huntington disease (HD). Phosphodiesterase 10A (PDE10A) is enriched in the striatum, and animal data suggest that it is a key regulator of this circuitry. Here, we report on germline PDE10A mutations in eight individuals from two families affected by a hyperkinetic movement disorder due to homozygous mutations c.320A>G (p.Tyr107Cys) and c.346G>C (p.Ala116Pro). Both mutations lead to a reduction in PDE10A levels in recombinant cellular systems, and critically, positron-emission-tomography (PET) studies with a specific PDE10A ligand confirmed that the p...
April 7, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27009974/function-and-evolution-of-local-repeats-in-the-firre-locus
#9
Ezgi Hacisuleyman, Chinmay J Shukla, Catherine L Weiner, John L Rinn
More than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other repeats, such as local repeats that occur in multiple instances within a given locus in the genome but not elsewhere. Here, we systematically characterize local repeats in the genomic locus of the Firre long noncoding RNA (lncRNA). We find a conserved function for the RRD repeat as a ribonucleic nuclear retention signal that is sufficient to retain an otherwise cytoplasmic mRNA in the nucleus...
March 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/26975529/integrative-analyses-reveal-a-long-noncoding-rna-mediated-sponge-regulatory-network-in-prostate-cancer
#10
Zhou Du, Tong Sun, Ezgi Hacisuleyman, Teng Fei, Xiaodong Wang, Myles Brown, John L Rinn, Mary Gwo-Shu Lee, Yiwen Chen, Philip W Kantoff, X Shirley Liu
Mounting evidence suggests that long noncoding RNAs (lncRNAs) can function as microRNA sponges and compete for microRNA binding to protein-coding transcripts. However, the prevalence, functional significance and targets of lncRNA-mediated sponge regulation of cancer are mostly unknown. Here we identify a lncRNA-mediated sponge regulatory network that affects the expression of many protein-coding prostate cancer driver genes, by integrating analysis of sequence features and gene expression profiles of both lncRNAs and protein-coding genes in tumours...
March 15, 2016: Nature Communications
https://www.readbyqxmd.com/read/26883116/widespread-rna-binding-by-chromatin-associated-proteins
#11
David G Hendrickson, David R Kelley, Danielle Tenen, Bradley Bernstein, John L Rinn
BACKGROUND: Recent evidence suggests that RNA interaction can regulate the activity and localization of chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. RESULTS: Here, we perform formaldehyde RNA immunoprecipitation (fRIP-Seq) to survey the RNA associated with a panel of 24 chromatin regulators and traditional RNA binding proteins...
2016: Genome Biology
https://www.readbyqxmd.com/read/26832224/transcriptional-silencing-of-long-noncoding-rna-gng12-as1-uncouples-its-transcriptional-and-product-related-functions
#12
Lovorka Stojic, Malwina Niemczyk, Arturo Orjalo, Yoko Ito, Anna Elisabeth Maria Ruijter, Santiago Uribe-Lewis, Nimesh Joseph, Stephen Weston, Suraj Menon, Duncan T Odom, John Rinn, Fanni Gergely, Adele Murrell
Long noncoding RNAs (lncRNAs) regulate gene expression via their RNA product or through transcriptional interference, yet a strategy to differentiate these two processes is lacking. To address this, we used multiple small interfering RNAs (siRNAs) to silence GNG12-AS1, a nuclear lncRNA transcribed in an antisense orientation to the tumour-suppressor DIRAS3. Here we show that while most siRNAs silence GNG12-AS1 post-transcriptionally, siRNA complementary to exon 1 of GNG12-AS1 suppresses its transcription by recruiting Argonaute 2 and inhibiting RNA polymerase II binding...
February 2, 2016: Nature Communications
https://www.readbyqxmd.com/read/26659182/the-histone-chaperone-caf-1-safeguards-somatic-cell-identity
#13
Sihem Cheloufi, Ulrich Elling, Barbara Hopfgartner, Youngsook L Jung, Jernej Murn, Maria Ninova, Maria Hubmann, Aimee I Badeaux, Cheen Euong Ang, Danielle Tenen, Daniel J Wesche, Nadezhda Abazova, Max Hogue, Nilgun Tasdemir, Justin Brumbaugh, Philipp Rathert, Julian Jude, Francesco Ferrari, Andres Blanco, Michaela Fellner, Daniel Wenzel, Marietta Zinner, Simon E Vidal, Oliver Bell, Matthias Stadtfeld, Howard Y Chang, Genevieve Almouzni, Scott W Lowe, John Rinn, Marius Wernig, Alexei Aravin, Yang Shi, Peter J Park, Josef M Penninger, Johannes Zuber, Konrad Hochedlinger
Cellular differentiation involves profound remodelling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNA interference (RNAi) screens targeting chromatin factors during transcription-factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPS cells). Subunits of the chromatin assembly factor-1 (CAF-1) complex, including Chaf1a and Chaf1b, emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance...
December 10, 2015: Nature
https://www.readbyqxmd.com/read/26637795/mechanisms-of-long-non-coding-rnas-in-mammalian-nervous-system-development-plasticity-disease-and-evolution
#14
REVIEW
James A Briggs, Ernst J Wolvetang, John S Mattick, John L Rinn, Guy Barry
Only relatively recently has it become clear that mammalian genomes encode tens of thousands of long non-coding RNAs (lncRNAs). A striking 40% of these are expressed specifically in the brain, where they show precisely regulated temporal and spatial expression patterns. This begs the question, what is the functional role of these many lncRNA transcripts in the brain? Here we canvass a growing number of mechanistic studies that have elucidated central roles for lncRNAs in the regulation of nervous system development and function...
December 2, 2015: Neuron
https://www.readbyqxmd.com/read/26582791/silent-pericentromeric-repeats-speak-out
#15
COMMENT
Scott T Younger, John L Rinn
No abstract text is available yet for this article.
December 8, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/26551807/measurements-of-elliptic-and-triangular-flow-in-high-multiplicity-3he-au-collisions-at-%C3%A2-s-nn-200-gev
#16
A Adare, S Afanasiev, C Aidala, N N Ajitanand, Y Akiba, R Akimoto, H Al-Bataineh, J Alexander, M Alfred, H Al-Ta'ani, K R Andrews, A Angerami, K Aoki, N Apadula, L Aphecetche, E Appelt, Y Aramaki, R Armendariz, S H Aronson, J Asai, H Asano, E C Aschenauer, E T Atomssa, R Averbeck, T C Awes, B Azmoun, V Babintsev, M Bai, G Baksay, L Baksay, A Baldisseri, N S Bandara, B Bannier, K N Barish, P D Barnes, B Bassalleck, A T Basye, S Bathe, S Batsouli, V Baublis, C Baumann, A Bazilevsky, M Beaumier, S Beckman, S Belikov, R Belmont, J Ben-Benjamin, R Bennett, A Berdnikov, Y Berdnikov, J H Bhom, A A Bickley, D S Blau, J G Boissevain, J S Bok, H Borel, K Boyle, M L Brooks, D Broxmeyer, J Bryslawskyj, H Buesching, V Bumazhnov, G Bunce, S Butsyk, C M Camacho, S Campbell, A Caringi, P Castera, B S Chang, W C Chang, J-L Charvet, C-H Chen, S Chernichenko, C Y Chi, J Chiba, M Chiu, I J Choi, J B Choi, R K Choudhury, P Christiansen, T Chujo, P Chung, A Churyn, O Chvala, V Cianciolo, Z Citron, C R Cleven, B A Cole, M P Comets, Z Conesa del Valle, M Connors, P Constantin, M Csanád, T Csörgő, T Dahms, S Dairaku, I Danchev, D Danley, K Das, A Datta, M S Daugherity, G David, M K Dayananda, M B Deaton, K DeBlasio, K Dehmelt, H Delagrange, A Denisov, D d'Enterria, A Deshpande, E J Desmond, K V Dharmawardane, O Dietzsch, A Dion, P B Diss, J H Do, M Donadelli, L D'Orazio, O Drapier, A Drees, K A Drees, A K Dubey, J M Durham, A Durum, D Dutta, V Dzhordzhadze, S Edwards, Y V Efremenko, J Egdemir, F Ellinghaus, W S Emam, T Engelmore, A Enokizono, H En'yo, S Esumi, K O Eyser, B Fadem, N Feege, D E Fields, M Finger, M Finger, F Fleuret, S L Fokin, Z Fraenkel, J E Frantz, A Franz, A D Frawley, K Fujiwara, Y Fukao, T Fusayasu, S Gadrat, C Gal, P Gallus, P Garg, I Garishvili, H Ge, F Giordano, A Glenn, H Gong, X Gong, M Gonin, J Gosset, Y Goto, R Granier de Cassagnac, N Grau, S V Greene, G Grim, M Grosse Perdekamp, Y Gu, T Gunji, L Guo, H-Å Gustafsson, T Hachiya, A Hadj Henni, C Haegemann, J S Haggerty, K I Hahn, H Hamagaki, J Hamblen, H F Hamilton, R Han, S Y Han, J Hanks, H Harada, C Harper, E P Hartouni, K Haruna, S Hasegawa, T O S Haseler, K Hashimoto, E Haslum, R Hayano, X He, M Heffner, T K Hemmick, T Hester, H Hiejima, J C Hill, R Hobbs, M Hohlmann, R S Hollis, W Holzmann, K Homma, B Hong, T Horaguchi, Y Hori, D Hornback, T Hoshino, N Hotvedt, J Huang, S Huang, T Ichihara, R Ichimiya, H Iinuma, Y Ikeda, K Imai, J Imrek, M Inaba, Y Inoue, A Iordanova, D Isenhower, L Isenhower, M Ishihara, T Isobe, M Issah, A Isupov, D Ivanishchev, Y Iwanaga, B V Jacak, M Jezghani, J Jia, X Jiang, J Jin, O Jinnouchi, D John, B M Johnson, T Jones, K S Joo, D Jouan, D S Jumper, F Kajihara, S Kametani, N Kamihara, J Kamin, S Kanda, M Kaneta, S Kaneti, B H Kang, J H Kang, J S Kang, H Kanou, J Kapustinsky, K Karatsu, M Kasai, D Kawall, M Kawashima, A V Kazantsev, T Kempel, J A Key, V Khachatryan, A Khanzadeev, K M Kijima, J Kikuchi, A Kim, B I Kim, C Kim, D H Kim, D J Kim, E Kim, E-J Kim, G W Kim, M Kim, S H Kim, Y-J Kim, Y K Kim, B Kimelman, E Kinney, K Kiriluk, Á Kiss, E Kistenev, R Kitamura, A Kiyomichi, J Klatsky, J Klay, C Klein-Boesing, D Kleinjan, P Kline, T Koblesky, L Kochenda, V Kochetkov, B Komkov, M Konno, J Koster, D Kotchetkov, D Kotov, A Kozlov, A Král, A Kravitz, J Kubart, G J Kunde, N Kurihara, K Kurita, M Kurosawa, M J Kweon, Y Kwon, G S Kyle, R Lacey, Y S Lai, J G Lajoie, D Layton, A Lebedev, D M Lee, J Lee, K B Lee, K S Lee, M K Lee, S Lee, S H Lee, S R Lee, T Lee, M J Leitch, M A L Leite, B Lenzi, X Li, P Lichtenwalner, P Liebing, S H Lim, L A Linden Levy, T Liška, A Litvinenko, H Liu, M X Liu, B Love, D Lynch, C F Maguire, Y I Makdisi, M Makek, A Malakhov, M D Malik, A Manion, V I Manko, E Mannel, Y Mao, L Mašek, H Masui, F Matathias, M McCumber, P L McGaughey, D McGlinchey, C McKinney, N Means, A Meles, M Mendoza, B Meredith, Y Miake, T Mibe, A C Mignerey, P Mikeš, K Miki, T E Miller, A Milov, S Mioduszewski, D K Mishra, M Mishra, J T Mitchell, M Mitrovski, Y Miyachi, S Miyasaka, S Mizuno, A K Mohanty, P Montuenga, H J Moon, T Moon, Y Morino, A Morreale, D P Morrison, S Motschwiller, T V Moukhanova, D Mukhopadhyay, T Murakami, J Murata, A Mwai, S Nagamiya, K Nagashima, Y Nagata, J L Nagle, M Naglis, M I Nagy, I Nakagawa, H Nakagomi, Y Nakamiya, K R Nakamura, T Nakamura, K Nakano, S Nam, C Nattrass, P K Netrakanti, J Newby, M Nguyen, M Nihashi, T Niida, S Nishimura, B E Norman, R Nouicer, T Novak, N Novitzky, A S Nyanin, C Oakley, E O'Brien, S X Oda, C A Ogilvie, H Ohnishi, M Oka, K Okada, O O Omiwade, Y Onuki, J D Orjuela Koop, J D Osborn, A Oskarsson, M Ouchida, K Ozawa, R Pak, D Pal, A P T Palounek, V Pantuev, V Papavassiliou, B H Park, I H Park, J Park, J S Park, S Park, S K Park, W J Park, S F Pate, L Patel, M Patel, H Pei, J-C Peng, H Pereira, D V Perepelitsa, G D N Perera, V Peresedov, D Yu Peressounko, J Perry, R Petti, C Pinkenburg, R Pinson, R P Pisani, M Proissl, M L Purschke, A K Purwar, H Qu, J Rak, A Rakotozafindrabe, B J Ramson, I Ravinovich, K F Read, S Rembeczki, M Reuter, K Reygers, D Reynolds, V Riabov, Y Riabov, E Richardson, T Rinn, D Roach, G Roche, S D Rolnick, A Romana, M Rosati, C A Rosen, S S E Rosendahl, P Rosnet, Z Rowan, J G Rubin, P Rukoyatkin, P Ružička, V L Rykov, B Sahlmueller, N Saito, T Sakaguchi, S Sakai, K Sakashita, H Sakata, H Sako, V Samsonov, S Sano, M Sarsour, S Sato, T Sato, M Savastio, S Sawada, B Schaefer, B K Schmoll, K Sedgwick, J Seele, R Seidl, A Yu Semenov, V Semenov, A Sen, R Seto, P Sett, A Sexton, D Sharma, I Shein, A Shevel, T-A Shibata, K Shigaki, H H Shim, M Shimomura, K Shoji, P Shukla, A Sickles, C L Silva, D Silvermyr, C Silvestre, K S Sim, B K Singh, C P Singh, V Singh, S Skutnik, M Slunečka, M Snowball, T Sodre, A Soldatov, R A Soltz, W E Sondheim, S P Sorensen, I V Sourikova, F Staley, P W Stankus, E Stenlund, M Stepanov, A Ster, S P Stoll, T Sugitate, C Suire, A Sukhanov, T Sumita, J Sun, J Sziklai, T Tabaru, S Takagi, E M Takagui, A Takahara, A Taketani, R Tanabe, Y Tanaka, S Taneja, K Tanida, M J Tannenbaum, S Tarafdar, A Taranenko, P Tarján, E Tennant, H Themann, D Thomas, T L Thomas, R Tieulent, A Timilsina, T Todoroki, M Togawa, A Toia, J Tojo, L Tomášek, M Tomášek, Y Tomita, H Torii, C L Towell, R Towell, R S Towell, V-N Tram, I Tserruya, Y Tsuchimoto, K Utsunomiya, C Vale, H Valle, H W van Hecke, E Vazquez-Zambrano, A Veicht, J Velkovska, R Vértesi, A A Vinogradov, M Virius, A Vossen, V Vrba, E Vznuzdaev, M Wagner, D Walker, X R Wang, D Watanabe, K Watanabe, Y Watanabe, Y S Watanabe, F Wei, R Wei, J Wessels, A S White, S N White, D Winter, C L Woody, R M Wright, M Wysocki, B Xia, W Xie, L Xue, S Yalcin, Y L Yamaguchi, K Yamaura, R Yang, A Yanovich, Z Yasin, J Ying, S Yokkaichi, J H Yoo, J S Yoo, I Yoon, Z You, G R Young, I Younus, H Yu, I E Yushmanov, W A Zajc, O Zaudtke, A Zelenski, C Zhang, S Zhou, J Zimamyi, L Zolin, L Zou
We present the first measurement of elliptic (v(2)) and triangular (v(3)) flow in high-multiplicity (3)He+Au collisions at √(s(NN))=200  GeV. Two-particle correlations, where the particles have a large separation in pseudorapidity, are compared in (3)He+Au and in p+p collisions and indicate that collective effects dominate the second and third Fourier components for the correlations observed in the (3)He+Au system. The collective behavior is quantified in terms of elliptic v(2) and triangular v(3) anisotropy coefficients measured with respect to their corresponding event planes...
October 2, 2015: Physical Review Letters
https://www.readbyqxmd.com/read/26501951/a-comparison-of-genetically-matched-cell-lines-reveals-the-equivalence-of-human-ipscs-and-escs
#17
Jiho Choi, Soohyun Lee, William Mallard, Kendell Clement, Guidantonio Malagoli Tagliazucchi, Hotae Lim, In Young Choi, Francesco Ferrari, Alexander M Tsankov, Ramona Pop, Gabsang Lee, John L Rinn, Alexander Meissner, Peter J Park, Konrad Hochedlinger
The equivalence of human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) remains controversial. Here we use genetically matched hESC and hiPSC lines to assess the contribution of cellular origin (hESC vs. hiPSC), the Sendai virus (SeV) reprogramming method and genetic background to transcriptional and DNA methylation patterns while controlling for cell line clonality and sex. We find that transcriptional and epigenetic variation originating from genetic background dominates over variation due to cellular origin or SeV infection...
November 2015: Nature Biotechnology
https://www.readbyqxmd.com/read/26430155/linking-rna-biology-to-lncrnas
#18
REVIEW
Loyal A Goff, John L Rinn
The regulatory potential of RNA has never ceased to amaze: from RNA catalysis, to RNA-mediated splicing, to RNA-based silencing of an entire chromosome during dosage compensation. More recently, thousands of long noncoding RNA (lncRNA) transcripts have been identified, the majority with unknown function. Thus, it is tempting to think that these lncRNAs represent a cadre of new factors that function through ribonucleic mechanisms. Some evidence points to several lncRNAs with tantalizing physiological contributions and thought-provoking molecular modalities...
October 2015: Genome Research
https://www.readbyqxmd.com/read/26321202/genome-wide-rna-seq-of-human-motor-neurons-implicates-selective-er-stress-activation-in-spinal-muscular-atrophy
#19
Shi-Yan Ng, Boon Seng Soh, Natalia Rodriguez-Muela, David G Hendrickson, Feodor Price, John L Rinn, Lee L Rubin
Spinal muscular atrophy (SMA) is caused by mutations in the SMN1 gene. Because this gene is expressed ubiquitously, it remains poorly understood why motor neurons (MNs) are one of the most affected cell types. To address this question, we carried out RNA sequencing studies using fixed, antibody-labeled, and purified MNs produced from control and SMA patient-derived induced pluripotent stem cells (iPSCs). We found SMA-specific changes in MNs, including hyper-activation of the ER stress pathway. Functional studies demonstrated that inhibition of ER stress improves MN survival in vitro even in MNs expressing low SMN...
November 5, 2015: Cell Stem Cell
https://www.readbyqxmd.com/read/26304948/technical-performance-of-universal-and-enhanced-intraoral-imaging-rectangular-collimators
#20
K Brandon Johnson, Sally M Mauriello, John B Ludlow, Enrique Platin
PURPOSE: The purpose of this study was to compare the number and type of technical errors between 2 rectangular collimators, time/motion effort and radiographer preference. METHODS: Subjects (n=17) were recruited to expose an 18 projection full mouth series (FMX) using Tru-Align™ (enhanced) and Rinn® (universal) collimator devices. Both FMXs were exposed using photostimulable phosphor (PSP) digital sensors on a DXTTR manikin with an intraoral x-ray unit. A 5-question survey evaluated ease of device use, time required and device preference...
August 2015: Journal of Dental Hygiene: JDH
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