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The Ascano Laboratory

The Ascano Laboratory Publications

2020

Kim B , Arcos S , Rothamel K , Ascano M , Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes Nature protocols. 2020 Dec 2; 16 (1). 516-531
Rothamel K , Arcos S , Kim B , Reasoner C , Mukherjee N , Ascano M , ELAVL1 Primarily Couples mRNA Stability with the 3’UTRs of Interferon Stimulated Genes bioRxiv. 2020 Aug 24; https://doi.org/10.1101/2020.08.24.263418 (2020.08.24.263418).
Wiser C , Kim B , Vincent J , Ascano M , Small molecule inhibition of human cGAS reduces total cGAMP output and cytokine expression in cells Scientific reports. 2020 May 05; 10 (1). 7604
Kim B , Arcos S , Rothamel K , Jian J , Rose KL , McDonald WH , Bian Y , Reasoner S , Barrows NJ , Bradrick S , Garcia-Blanco MA , Ascano M , Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP Molecular cell. 2020 May 06; 78 (4). 624-640.e7

2019

Shae D , Becker KW , Christov P , Yun DS , Lytton-Jean AKR , Sevimli S , Ascano M , Kelley M , Johnson DB , Balko JM , Wilson JT , Endosomolytic polymersomes increase the activity of cyclic dinucleotide STING agonists to enhance cancer immunotherapy Nature nanotechnology. 2019 Jan 21; 14 (3). 269-278
Barrows NJ , Anglero-Rodriguez Y , Kim B , Jamison SF , Le Sommer C , McGee CE , Pearson JL , Dimopoulos G , Ascano M , Bradrick SS , Garcia-Blanco MA , Dual roles for the ER membrane protein complex in flavivirus infection: viral entry and protein biogenesis Scientific reports. 2019 Jul 04; 9 (1). 9711

2018

Mok-Lin E , Ascano M , Serganov A , Rosenwaks Z , Tuschl T , Williams Z , Premature recruitment of oocyte pool and increased mTOR activity in Fmr1 knockout mice and reversal of phenotype with rapamycin Scientific reports. 2018 Jan 12; 8 (1). 588

2017

Vincent J , Adura C , Gao P , Luz A , Lama L , Asano Y , Okamoto R , Imaeda T , Aida J , Rothamel K , Gogakos T , Steinberg J , Reasoner S , Aso K , Tuschl T , Patel DJ , Glickman JF , Ascano M , Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. Nature communications. 2017 Sep 29; 8 (1). 750

2016

Kashima R , Roy S , Ascano M , Martinez-Cerdeno V , Ariza-Torres J , Kim S , Louie J , Lu Y , Leyton P , Bloch KD , Kornberg TB , Hagerman PJ , Hagerman R , Lagna G , Hata A , Augmented noncanonical BMP type II receptor signaling mediates the synaptic abnormality of fragile X syndrome. Science signaling. 2016 Jun 7; 9 (431). ra58

2015

Kavanaugh G , Zhao R , Guo Y , Mohni KN , Glick G , Lacy ME , Hutson MS , Ascano M , Cortez D , Enhancer of Rudimentary Homolog Affects the Replication Stress Response through Regulation of RNA Processing. Molecular and cellular biology. 2015 Sep 1; 35 (17). 2979-90
Kim B , Sasaki Y , Egawa T , Restriction of Nonpermissive RUNX3 Protein Expression in T Lymphocytes by the Kozak Sequence. Journal of immunology (Baltimore, Md. : 1950). 2015 Aug 15; 195 (4). 1517-23

2014

Spitzer Jessica , Hafner Markus , Landthaler Markus , Ascano Manuel , Farazi Thalia , Wardle Greg , Nusbaum Jeff , Khorshid Mohsen , Burger Lukas , Zavolan Mihaela , Tuschl Thomas , Transcriptome-Wide Identification of Protein-Binding Sites on RNA by PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) 2014 May 19; 2
Gerstberger S , Hafner M , Ascano M , Tuschl T , Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease. Advances in experimental medicine and biology. 2014 ; 825 1-55
Gao P , Zillinger T , Wang W , Ascano M , Dai P , Hartmann G , Tuschl T , Deng L , Barchet W , Patel DJ , Binding-Pocket and Lid-Region Substitutions Render Human STING Sensitive to the Species-Specific Drug DMXAA. Cell reports. 2014 Sep 3;
Ericson JA , Duffau P , Yasuda K , Ortiz-Lopez A , Rothamel K , Rifkin IR , Monach PA , , Gene expression during the generation and activation of mouse neutrophils: implication of novel functional and regulatory pathways. PloS one. 2014 ; 9 (10). e108553
Mostafavi S , Ortiz-Lopez A , Bogue MA , Hattori K , Pop C , Koller D , Mathis D , Benoist C , Immunological Genome Consortium , Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains. Journal of immunology (Baltimore, Md. : 1950). 2014 Nov 1; 193 (9). 4485-96
Raj T , Rothamel K , Mostafavi S , Ye C , Lee MN , Replogle JM , Feng T , Lee M , Asinovski N , Frohlich I , Imboywa S , Von Korff A , Okada Y , Patsopoulos NA , Davis S , McCabe C , Paik HI , Srivastava GP , Raychaudhuri S , Hafler DA , Koller D , Regev A , Hacohen N , Mathis D , Benoist C , Stranger BE , De Jager PL , Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science (New York, N.Y.). 2014 May 2; 344 (6183). 519-23
Raj T , Ryan KJ , Replogle JM , Chibnik LB , Rosenkrantz L , Tang A , Rothamel K , Stranger BE , Bennett DA , Evans DA , De Jager PL , Bradshaw EM , CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer’s disease susceptibility. Human molecular genetics. 2014 May 15; 23 (10). 2729-36
Spitzer J , Hafner M , Landthaler M , Ascano M , Farazi T , Wardle G , Nusbaum J , Khorshid M , Burger L , Zavolan M , Tuschl T , PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. Methods in enzymology. 2014 ; 539 113-61
Wittkowski KM , Sonakya V , Bigio B , Tonn MK , Shic F , Ascano M , Nasca C , Gold-Von Simson G , A novel computational biostatistics approach implies impaired dephosphorylation of growth factor receptors as associated with severity of autism. Translational psychiatry. 2014 ; 4 e354

2013

Ergun A , Doran G , Costello JC , Paik HH , Collins JJ , Mathis D , Benoist C , ImmGen Consortium , Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences of the United States of America. 2013 Aug 27; 110 (35). 14324-9
Mingueneau M , Kreslavsky T , Gray D , Heng T , Cruse R , Ericson J , Bendall S , Spitzer MH , Nolan GP , Kobayashi K , von Boehmer H , Mathis D , Benoist C , , Best AJ , Knell J , Goldrath A , Joic V , Koller D , Shay T , Regev A , Cohen N , Brennan P , Brenner M , Kim F , Nageswara Rao T , Wagers A , Heng T , Ericson J , Rothamel K , Ortiz-Lopez A , Mathis D , Benoist C , Bezman NA , Sun JC , Min-Oo G , Kim CC , Lanier LL , Miller J , Brown B , Merad M , Gautier EL , Jakubzick C , Randolph GJ , Monach P , Blair DA , Dustin ML , Shinton SA , Hardy RR , Laidlaw D , Collins J , Gazit R , Rossi DJ , Malhotra N , Sylvia K , Kang J , Kreslavsky T , Fletcher A , Elpek K , Bellemare-Pelletier A , Malhotra D , Turley S , The transcriptional landscape of αβ T cell differentiation. Nature immunology. 2013 Jun ; 14 (6). 619-32
Jojic V , Shay T , Sylvia K , Zuk O , Sun X , Kang J , Regev A , Koller D , , Best AJ , Knell J , Goldrath A , Joic V , Koller D , Shay T , Regev A , Cohen N , Brennan P , Brenner M , Kim F , Rao TN , Wagers A , Heng T , Ericson J , Rothamel K , Ortiz-Lopez A , Mathis D , Benoist C , Bezman NA , Sun JC , Min-Oo G , Kim CC , Lanier LL , Miller J , Brown B , Merad M , Gautier EL , Jakubzick C , Randolph GJ , Monach P , Blair DA , Dustin ML , Shinton SA , Hardy RR , Laidlaw D , Collins J , Gazit R , Rossi DJ , Malhotra N , Sylvia K , Kang J , Kreslavsky T , Fletcher A , Elpek K , Bellemarte-Pelletier A , Malhotra D , Turley S , Identification of transcriptional regulators in the mouse immune system. Nature immunology. 2013 Jun ; 14 (6). 633-43
Shay T , Jojic V , Zuk O , Rothamel K , Puyraimond-Zemmour D , Feng T , Wakamatsu E , Benoist C , Koller D , Regev A , , Conservation and divergence in the transcriptional programs of the human and mouse immune systems. Proceedings of the National Academy of Sciences of the United States of America. 2013 Feb 19; 110 (8). 2946-51
Lee MS , Kim B , Lee SM , Cho WC , Lee WB , Kang JS , Choi UY , Lyu J , Kim YJ , Genome-wide profiling of in vivo LPS-responsive genes in splenic myeloid cells. Molecules and cells. 2013 Jun ; 35 (6). 498-513
Lee MS , Kim B , Oh GT , Kim YJ , OASL1 inhibits translation of the type I interferon-regulating transcription factor IRF7. Nature immunology. 2013 Apr ; 14 (4). 346-55
Gao P , Ascano M , Zillinger T , Wang W , Dai P , Serganov AA , Gaffney BL , Shuman S , Jones RA , Deng L , Hartmann G , Barchet W , Tuschl T , Patel DJ , Structure-function analysis of STING activation by c[G(2′,5′)pA(3′,5′)p] and targeting by antiviral DMXAA. Cell. 2013 Aug 15; 154 (4). 748-62
Nakanishi K , Ascano M , Gogakos T , Ishibe-Murakami S , Serganov AA , Briskin D , Morozov P , Tuschl T , Patel DJ , Eukaryote-specific insertion elements control human ARGONAUTE slicer activity. Cell reports. 2013 Jun 27; 3 (6). 1893-900
Gao P , Ascano M , Wu Y , Barchet W , Gaffney BL , Zillinger T , Serganov AA , Liu Y , Jones RA , Hartmann G , Tuschl T , Patel DJ , Cyclic [G(2′,5′)pA(3′,5′)p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase. Cell. 2013 May 23; 153 (5). 1094-107
Ascano M , Gerstberger S , Tuschl T , Multi-disciplinary methods to define RNA-protein interactions and regulatory networks. Current opinion in genetics & development. 2013 Feb ; 23 (1). 20-8

2012

Lim AS , Chang AM , Shulman JM , Raj T , Chibnik LB , Cain SW , Rothamel K , Benoist C , Myers AJ , Czeisler CA , Buchman AS , Bennett DA , Duffy JF , Saper CB , De Jager PL , A common polymorphism near PER1 and the timing of human behavioral rhythms. Annals of neurology. 2012 Sep ; 72 (3). 324-34
Benoist C , Lanier L , Merad M , Mathis D , Immunological Genome Project , Consortium biology in immunology: the perspective from the Immunological Genome Project. Nature reviews. Immunology. 2012 Oct ; 12 (10). 734-40
Ascano M , Mukherjee N , Bandaru P , Miller JB , Nusbaum JD , Corcoran DL , Langlois C , Munschauer M , Dewell S , Hafner M , Williams Z , Ohler U , Tuschl T , FMRP targets distinct mRNA sequence elements to regulate protein expression. Nature. 2012 Dec 20; 492 (7429). 382-6
Ascano M , Hafner M , Cekan P , Gerstberger S , Tuschl T , Identification of RNA-protein interaction networks using PAR-CLIP. Wiley interdisciplinary reviews. RNA. 2012 ; 3 (2). 159-77

2011

Hafner M , Ascano M , Tuschl T , New insights in the mechanism of microRNA-mediated target repression. Nature structural & molecular biology. 2011 Nov ; 18 (11). 1181-2
Mukherjee N , Corcoran DL , Nusbaum JD , Reid DW , Georgiev S , Hafner M , Ascano M , Tuschl T , Ohler U , Keene JD , Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Molecular cell. 2011 Aug 5; 43 (3). 327-39
Tian Y , Simanshu DK , Ascano M , Diaz-Avalos R , Park AY , Juranek SA , Rice WJ , Yin Q , Robinson CV , Tuschl T , Patel DJ , Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex. Nature structural & molecular biology. 2011 Jun ; 18 (6). 658-64

2010

Hafner M , Landthaler M , Burger L , Khorshid M , Hausser J , Berninger P , Rothballer A , Ascano M , Jungkamp AC , Munschauer M , Ulrich A , Wardle GS , Dewell S , Zavolan M , Tuschl T , PAR-CliP–a method to identify transcriptome-wide the binding sites of RNA binding proteins. Journal of visualized experiments : JoVE. 2010 ; (41).
Hafner M , Landthaler M , Burger L , Khorshid M , Hausser J , Berninger P , Rothballer A , Ascano M , Jungkamp AC , Munschauer M , Ulrich A , Wardle GS , Dewell S , Zavolan M , Tuschl T , Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 2010 Apr 2; 141 (1). 129-41
Tokhunts R , Singh S , Chu T , D'Angelo G , Baubet V , Goetz JA , Huang Z , Yuan Z , Ascano M , Zavros Y , Thérond PP , Kunes S , Dahmane N , Robbins DJ , The full-length unprocessed hedgehog protein is an active signaling molecule. The Journal of biological chemistry. 2010 Jan 22; 285 (4). 2562-8

2009

Jin LH , Choi JK , Kim B , Cho HS , Kim J , Kim-Ha J , Kim YJ , Requirement of Split ends for epigenetic regulation of Notch signal-dependent genes during infection-induced hemocyte differentiation. Molecular and cellular biology. 2009 Mar ; 29 (6). 1515-25
Farzan SF , Stegman MA , Ogden SK , Ascano M , Black KE , Tacchelly O , Robbins DJ , A quantification of pathway components supports a novel model of Hedgehog signal transduction. The Journal of biological chemistry. 2009 Oct 16; 284 (42). 28874-84

2008

Jin LH , Shim J , Yoon JS , Kim B , Kim J , Kim-Ha J , Kim YJ , Identification and functional analysis of antifungal immune response genes in Drosophila. PLoS pathogens. 2008 ; 4 (10). e1000168
Farzan SF , Ascano M , Ogden SK , Sanial M , Brigui A , Plessis A , Robbins DJ , Costal2 functions as a kinesin-like protein in the hedgehog signal transduction pathway. Current biology : CB. 2008 Aug 26; 18 (16). 1215-20

2006

Ascano Manuel , Robbins David J , Fused UCSD-Nature Molecule Pages. 2006 Mar 17;
Ogden SK , Casso DJ , Ascano M , Yore MM , Kornberg TB , Robbins DJ , Smoothened regulates activator and repressor functions of Hedgehog signaling via two distinct mechanisms. The Journal of biological chemistry. 2006 Mar 17; 281 (11). 7237-43

2004

Ascano M , Robbins DJ , An intramolecular association between two domains of the protein kinase Fused is necessary for Hedgehog signaling. Molecular and cellular biology. 2004 Dec ; 24 (23). 10397-405
Ogden SK , Ascano M , Stegman MA , Robbins DJ , Regulation of Hedgehog signaling: a complex story. Biochemical pharmacology. 2004 Mar 1; 67 (5). 805-14
Stegman MA , Goetz JA , Ascano M , Ogden SK , Nybakken KE , Robbins DJ , The Kinesin-related protein Costal2 associates with membranes in a Hedgehog-sensitive, Smoothened-independent manner. The Journal of biological chemistry. 2004 Feb 20; 279 (8). 7064-71

2003

Ogden SK , Ascano M , Stegman MA , Suber LM , Hooper JE , Robbins DJ , Identification of a functional interaction between the transmembrane protein Smoothened and the kinesin-related protein Costal2. Current biology : CB. 2003 Nov 11; 13 (22). 1998-2003

2002

Ascano M , Nybakken KE , Sosinski J , Stegman MA , Robbins DJ , The carboxyl-terminal domain of the protein kinase fused can function as a dominant inhibitor of hedgehog signaling. Molecular and cellular biology. 2002 Mar ; 22 (5). 1555-66

1999

Mukhopadhyay B , Johnson EF , Ascano M , Conditions for vigorous growth on sulfide and reactor-scale cultivation protocols for the thermophilic green sulfur bacterium chlorobium tepidum Applied and environmental microbiology. 1999 Jan ; 65 (1). 301-6

Wiser C , Kim B , Ascano M , G3BP1 enhances cytoplasmic DNA pattern recognition Nature immunology. ; 20 (1). 5-7