The Rockefeller University

2023

Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB. Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson’s disease. Nat Commun. 2023 Jul 5;14(1):3956. doi: 10.1038/s41467-023-39652-6. PMID: 37407548.
Ibrahim LA, Wamsley B, Alghamdi N, Yusuf N, Sevier E, Hairston A, Sherer M, Jaglin XH, Xu Q, Guo L, Khodadadi-Jamayran A, Favuzzi E, Yuan Y, Dimidschstein J, Darnell RB, Fishell G. Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing. Elife. 2023 Jun 22;12:e86842. doi: 10.7554/eLife.86842. PMID: 37347149.
Brewer RC, Lanz TV, Hale CR, Sepich-Poore GD, Martino C, Swafford AD, Carroll TS, Kongpachith S, Blum LK, Elliott SE, Blachere NE, Parveen S, Fak J, Yao V, Troyanskaya O, Frank MO, Bloom MS, Jahanbani S, Gomez AM, Iyer R, Ramadoss NS, Sharpe O, Chandrasekaran S, Kelmenson LB, Wang Q, Wong H, Torres HL, Wiesen M, Graves DT, Deane KD, Holers VM, Knight R, Darnell RB, Robinson WH, Orange DE. Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Sci Transl Med. 2023 Feb 22;15(684):eabq8476. doi: 10.1126/scitranslmed.abq8476. Epub 2023 Feb 22. PMID: 36812347
Tajima Y, Ito K, Yuan Y, Frank MO, Saito Y, Darnell RB. NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons. Cell Rep. 2023 Jan 29;42(2):112050. doi: 10.1016/j.celrep.2023.112050. PMID: 36716149.

2022

Saito Y, Hawley BR, Puno MR, Sarathy SN, Lima CD, Jaffrey SR, Darnell RB, Keeney S, Jain D. YTHDC2 control of gametogenesis requires helicase activity but not m(6)A binding. Genes Dev. 2022 Feb 1;36(3-4):180-194. doi: 10.1101/gad.349190.121. Epub 2022 Jan 20. PubMed PMID: 35058317.

2021

Hale CR, Sawicka K, Mora K, Fak JJ, Kang JJ, Cutrim P, Cialowicz K, Carroll TS, Darnell RB. FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons. Elife. 2021 Dec 23;10. doi: 10.7554/eLife.71892. PMID: 34939924
Frank MO, Blachere NE, Parveen S, Hacisuleyman E, Fak J, Luna JM, Michailidis E, Wright S, Stark P, Campbell A, Foo A, Sakmar TP, Huffman V, Bergh M, Goldfarb A, Mansisidor A, Patriotis AL, Palmquist KH, Poulton N, Leicher R, Vargas CDM, Duba I, Hurley A, Colagreco J, Pagane N, Orange DE, Mora K, Rakeman JL, Fowler RC, Fernandes H, Lamendola-Essel MF, Didkovsky N, Silvera L, Masci J, Allen M, Rice CM, Darnell RB. DRUL for school: Opening Pre-K with safe, simple, sensitive saliva testing for SARS-CoV-2. PLoS One. 2021 Jun 25 16(6):e0252949. doi: 10.1371/journal.pone.0252949. eCollection 2021. PMID: 34170927.
Knupp D, Cooper DA, Saito Y, Darnell RB, Miura P. NOVA2 regulates neural circRNA biogenesis. Nucleic Acids Res. 2021 Jul 9;49(12):6849-6862. doi: 10.1093/nar/gkab523. PMID: 34157123.
Hacisuleyman E, Hale C, Saito Y, Blachere NE, Bergh M, Conlon EG, Schaefer-Babajew DJ, DaSilva J, Muecksch F, Gaebler C, Lifton R, Nussenzweig MC, Hatziioannou T, Bieniasz PD, Darnell RB. Vaccine Breakthrough Infections with SARS-CoV-2 Variants. N Engl J Med. 2021 Jun 10;384(23):2212-2218. doi: 10.1056/NEJMoa2105000. Epub 2021 Apr 21. PMID: 33882219
O’Connor S, Murphy EA, Szwed SK, Kanke M, Marchildon F, Sethupathy P, Darnell RB, Cohen P. AGO HITS-CLIP reveals distinct miRNA regulation of white and brown adipose tissue identity. Genes Dev. 2021 May 1;35(9-10):771-781. doi: 10.1101/gad.345447.120. Epub 2021 Apr 8. PMID: 33832988.
Park CY, Zhou J, Wong AK, Chen KM, Theesfeld CL, Darnell RB, Troyanskaya OG. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet. 2021 Feb;53(2):166-173. doi: 10.1038/s41588-020-00761-3. Epub 2021 Jan 18. PMID: 33462483.

2020

Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell. 2020 Oct 1;183(1):197-210.e32. doi: 10.1016/j.cell.2020.08.006. PMID: 33007263.
Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. N Engl J Med. 2020 Jul 16;383(3):218-228. doi: 10.1056/NEJMoa2004114. PMID: 32668112.
Darnell RB. The Genetic Control of Stoichiometry Underlying Autism. Annu Rev Neurosci. 2020 Jul 8;43:509-533. doi: 10.1146/annurev-neuro-100119-024851. PMID: 32640929.
Abel HJ, Larson DE, Regier AA, Chiang C, Das I, Kanchi KL, Layer RM, Neale BM, Salerno WJ, Reeves C, Buyske S; NHGRI Centers for Common Disease Genomics; Matise TC, Muzny DM, Zody MC, Lander ES, Dutcher SK, Stitziel NO, Hall IM. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020 Jul;583(7814):83-89. doi: 10.1038/s41586-020-2371-0. Epub 2020 May 27. PMID: 32460305.

2019

Sawicka K, Hale CR, Park CY, Fak JJ, Gresack JE, Van Driesche SJ, Kang JJ, Darnell JC, Darnell RB. FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory. Elife. 2019 Dec 20;8. doi: 10.7554/eLife.46919. PMID: 31860442.
Nachmani D, Bothmer AH, Grisendi S, Mele A, Bothmer D, Lee JD, Monteleone E, Cheng K, Zhang Y, Bester AC, Guzzetti A, Mitchell CA, Mendez LM, Pozdnyakova O, Sportoletti P, Martelli MP, Vulliamy TJ, Safra M, Schwartz S, Luzzatto L, Bluteau O, Soulier J, Darnell RB, Falini B, Dokal I, Ito K, Clohessy JG, Pandolfi PP. Germline NPM1 mutations lead to altered rRNA 2′-O-methylation and cause dyskeratosis congenita. Nat Genet. 2019 Oct;51(10):1518-1529. doi: 10.1038/s41588-019-0502-z. Epub 2019 Sep 30. PMID: 31570891.
Wrzeszczynski KO, Rahman S, Frank MO, Arora K, Shah M, Geiger H, Felice V, Manaa D, Dikoglu E, Khaira D, Chimpiri AR, Michelini VV, Jobanputra V, Darnell RB, Powers S, Choi M. Identification of targetable BRAF ΔN486_P490 variant by whole-genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma. Cold Spring Harb Mol Case Stud. 2019 Dec;5(6). doi: 10.1101/mcs.a004424. Print 2019 Dec. PMID: 31519698.
Kwart D, Gregg A, Scheckel C, Murphy EA, Paquet D, Duffield M, Fak J, Olsen O, Darnell RB, Tessier-Lavigne M. A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ. Neuron. 2019 Oct 23;104(2):256-270.e5. doi: 10.1016/j.neuron.2019.07.010. Epub 2019 Aug 12. PMID: 31416668.
Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB.AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. Cell Rep. 2019 Jul 23;28(4):979-991.e6. doi: 10.1016/j.celrep.2019.06.075. PMID: 31340158.
Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019 Jun;51(6):973-980. doi: 10.1038/s41588-019-0420-0. Epub 2019 May 27. PMID: 31133750.
Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB. Sequencing and curation strategies for identifying candidate glioblastoma treatments. BMC Med Genomics. 2019 Apr 25;12(1):56. doi: 10.1186/s12920-019-0500-0. PMID: 31023376.
Saito Y, Yuan Y, Zucker-Scharff I, Fak JJ, Jereb S, Tajima Y, Licatalosi DD, Darnell RB. Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. Neuron. 2019 Feb 20;101(4):707-720.e5. doi: 10.1016/j.neuron.2018.12.019. Epub 2019 Jan 9. PMID: 30638744.

2018

Diolaiti D, Dela Cruz FS, Gundem G, Bouvier N, Boulad M, Zhang Y, Chou AJ, Dunkel IJ, Sanghvi R, Shah M, Geiger H, Rahman S, Felice V, Wrzeszczynski KO, Darnell RB, Antonescu CR, French CA, Papaemmanuil E, Kung AL, Shukla N. A recurrent novel MGA-NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma. Cold Spring Harb Mol Case Stud. 2018 Dec;4(6). doi: 10.1101/mcs.a003194. Print 2018 Dec. PMID: 30552129.
Darnell JC, Mele A, Hung KYS, Darnell RB. Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP). Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.top097931. PMID: 30510132.
Yuan Y, Xie S, Darnell JC, Darnell AJ, Saito Y, Phatnani H, Murphy EA, Zhang C, Maniatis T, Darnell RB. Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons. Genome Biol. 2018 Aug 15;19(1):117. doi: 10.1186/s13059-018-1493-2. PMID: 30111345.
Ule J, Hwang HW, Darnell RB. The Future of Cross-Linking and Immunoprecipitation (CLIP). Cold Spring Harb Perspect Biol. 2018 Aug 1;10(8). doi: 10.1101/cshperspect.a032243. Review. PMID: 30068528.
Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG. Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma. Am J Respir Crit Care Med. 2018 Jun 15;197(12):1552-1564. doi: 10.1164/rccm.201712-2529OC. PMID: 29509491.
Moore MJ, Blachere NE, Fak JJ, Park CY, Sawicka K, Parveen S, Zucker-Scharff I, Moltedo B, Rudensky AY, Darnell RB. ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity. Elife. 2018 May 31;7. doi: 10.7554/eLife.33057. PMID: 29848443.
Orange DE, Agius P, DiCarlo EF, Robine N, Geiger H, Szymonifka J, McNamara M, Cummings R, Andersen KM, Mirza S, Figgie M, Ivashkiv LB, Pernis AB, Jiang CS, Frank MO, Darnell RB, Lingampali N, Robinson WH, Gravallese E, Bykerk VP, Goodman SM, Donlin LT. Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data. Arthritis Rheumatol. 2018 May;70(5):690-701. doi: 10.1002/art.40428. Epub 2018 Apr 2. PMID: 29468833.
Jereb S, Hwang HW, Van Otterloo E, Govek EE, Fak JJ, Yuan Y, Hatten ME, Darnell RB. Differential 3′ Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. Elife. 2018 Mar 26;7. doi: 10.7554/eLife.34042. PMID: 29578408.

2017

Darnell RB, Ke S, Darnell JE Jr. Pre-mRNA processing includes N(6) methylation of adenosine residues that are retained in mRNA exons and the fallacy of “RNA epigenetics”. RNA. 2018 Mar;24(3):262-267. doi: 10.1261/rna.065219.117. Epub 2017 Dec 8. PMID: 29222117.
Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat Commun. 2018 Feb 23;9(1):791. doi: 10.1038/s41467-017-02659-x. PMID: 29476078.
Ogawa Y, Kakumoto K, Yoshida T, Kuwako KI, Miyazaki T, Yamaguchi J, Konno A, Hata J, Uchiyama Y, Hirai H, Watanabe M, Darnell RB, Okano H, Okano HJ. Elavl3 is essential for the maintenance of Purkinje neuron axons. Sci Rep. 2018 Feb 9;8(1):2722. doi: 10.1038/s41598-018-21130-5. PMID: 29426875.
Wrzeszczynski KO, Felice V, Shah M, Rahman S, Emde AK, Jobanputra V, O Frank M, Darnell RB. Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma. Methods Mol Biol. 2018;1741:1-29. doi: 10.1007/978-1-4939-7659-1_1. PubMed PMID: 29392687.
Blachère NE, Orange DE, Gantman EC, Santomasso BD, Couture GC, Ramirez-Montagut T, Fak J, O’Donovan KJ, Ru Z, Parveen S, Frank MO, Moore MJ, Darnell RB. T cells presenting viral antigens or autoantigens induce cytotoxic T cell anergy. JCI Insight. 2017 Nov 2;2(21). doi: 10.1172/jci.insight.96173. PMID: 29093272.
Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. Genomic Patterns of De Novo Mutation in Simplex Autism. Cell. 2017 Oct 19;171(3):710-722.e12. doi: 10.1016/j.cell.2017.08.047. Epub 2017 Sep 28. PMID: 28965761.
Hwang HW, Saito Y, Park CY, Blachère NE, Tajima Y, Fak JJ, Zucker-Scharff I, Darnell RB. cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. Neuron. 2017 Sep 13;95(6):1334-1349.e5. doi: 10.1016/j.neuron.2017.08.024. PMID: 28910620.
Korb E, Herre M, Zucker-Scharff I, Gresack J, Allis CD, Darnell RB. Excess Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by Brd4 Inhibition. Cell. 2017 Sep 7;170(6):1209-1223.e20. doi: 10.1016/j.cell.2017.07.033. Epub 2017 Aug 17. PMID: 28823556.
Shukla N, Roberts SS, Baki MO, Mushtaq Q, Goss PE, Park BH, Gundem G, Tian K, Geiger H, Redfield K, Behr G, Benayed R, Zehir A, Hechtman JF, Darnell RB, Papaemmanuil E, Ladanyi M, Ku N, Kung AL, Baselga J, Drilon A, Hyman DM. Successful Targeted Therapy of Refractory Pediatric ETV6-NTRK3 Fusion-Positive Secretory Breast Carcinoma. JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.17.00034. Epub 2017 Aug 18. PMID: 29623306.
Scheel TKH, Moore MJ, Luna JM, Nishiuchi E, Fak J, Darnell RB, Rice CM. Global mapping of miRNA-target interactions in cattle (Bos taurus). Sci Rep. 2017 Aug 15;7(1):8190. doi: 10.1038/s41598-017-07880-8. PMID: 28811507.
Luna JM, Barajas JM, Teng KY, Sun HL, Moore MJ, Rice CM, Darnell RB, Ghoshal K. Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. Mol Cell. 2017 Aug 3;67(3):400-410.e7. doi: 10.1016/j.molcel.2017.06.025. Epub 2017 Jul 20. PMID: 28735896.
Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB. Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma. Neurol Genet. 2017 Aug;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug. PMID: 28740869.
Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB. m(6)A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 2017 May 15;31(10):990-1006. doi: 10.1101/gad.301036.117. PMID: 28637692.
Linderman JA, Kobayashi M, Rayannavar V, Fak JJ, Darnell RB, Chao MV, Wilson AC, Mohr I. Immune Escape via a Transient Gene Expression Program Enables Productive Replication of a Latent Pathogen. Cell Rep. 2017 Jan 31;18(5):1312-1323. doi: 10.1016/j.celrep.2017.01.017. PMID: 28147283.
Hwang HW, Darnell RB. Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP. Methods Mol Biol. 2017;1648:79-93. doi: 10.1007/978-1-4939-7204-3_7. PubMed PMID: 28766291.

2016

Freudenberg-Hua Y, Li W, Abhyankar A, Vacic V, Cortes V, Ben-Avraham D, Koppel J, Greenwald B, Germer S, Darnell RB, Barzilai N, Freudenberg J, Atzmon G, Davies P. Differential burden of rare protein truncating variants in Alzheimer’s disease patients compared to centenarians. Hum Mol Genet. 2016 Jul 15;25(14):3096-3105. doi: 10.1093/hmg/ddw150. Epub 2016 Jun 3. PMID: 27260402.
Hwang JY, Lee J, Oh CK, Kang HW, Hwang IY, Um JW, Park HC, Kim S, Shin JH, Park WY, Darnell RB, Um HD, Chung KC, Kim K, Oh YJ. Proteolytic degradation and potential role of onconeural protein cdr2 in neurodegeneration. Cell Death Dis. 2016 Jun 2;7(6):e2240. doi: 10.1038/cddis.2016.151. PMID: 27253404.
Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB. NOVA2-mediated RNA regulation is required for axonal pathfinding during development. Elife. 2016 May 25;5. doi: 10.7554/eLife.14371. PMID: 27223325.
Leggere JC, Saito Y, Darnell RB, Tessier-Lavigne M, Junge HJ, Chen Z. NOVA regulates Dcc alternative splicing during neuronal migration and axon guidance in the spinal cord. Elife. 2016 May 25;5. doi: 10.7554/eLife.14264. PMID: 27223328.
Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB. PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. Cell Rep. 2016 Apr 12;15(2):423-35. doi: 10.1016/j.celrep.2016.03.023. Epub 2016 Mar 31. PMID: 27050522.
Scheel TK, Luna JM, Liniger M, Nishiuchi E, Rozen-Gagnon K, Shlomai A, Auray G, Gerber M, Fak J, Keller I, Bruggmann R, Darnell RB, Ruggli N, Rice CM. A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. Cell Host Microbe. 2016 Mar 9;19(3):409-23. doi: 10.1016/j.chom.2016.02.007. PMID: 26962949.
Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma’ayan A, Buxbaum JD, Darnell RB. Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. Elife. 2016 Feb 19;5. doi: 10.7554/eLife.10421. PMID: 26894958.

2015

Moore MJ, Scheel TK, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM, Darnell RB. miRNA-target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity. Nat Commun. 2015 Nov 25;6:8864. doi: 10.1038/ncomms9864. PMID: 26602609.
Korb E, Herre M, Zucker-Scharff I, Darnell RB, Allis CD. BET protein Brd4 activates transcription in neurons and BET inhibitor Jq1 blocks memory in mice. Nat Neurosci. 2015 Oct;18(10):1464-73. doi: 10.1038/nn.4095. Epub 2015 Aug 24. PMID: 26301327.
Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kusśnierczyk A, Klungland A, Darnell JE Jr, Darnell RB. A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation. Genes Dev. 2015 Oct 1;29(19):2037-53. doi: 10.1101/gad.269415.115. Epub 2015 Sep 24. PMID: 26404942.
Roberts WK, Blachère NE, Frank MO, Dousmanis A, Ransohoff RM, Darnell RB. A destructive feedback loop mediated by CXCL10 in central nervous system inflammatory disease. Ann Neurol. 2015 Oct;78(4):619-29. doi: 10.1002/ana.24494. Epub 2015 Aug 21. PMID: 26224283.
Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A. Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5391-400. doi: 10.1073/pnas.1515737112. Epub 2015 Sep 15. PMID: 26374839.
Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB. Hepatitis C virus RNA functionally sequesters miR-122. Cell. 2015 Mar 12;160(6):1099-110. doi: 10.1016/j.cell.2015.02.025. PMID: 25768906.
Cheung J, Ginter C, Cassidy M, Franklin MC, Rudolph MJ, Robine N, Darnell RB, Hendrickson WA. Structural insights into mis-regulation of protein kinase A in human tumors. Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1374-9. doi: 10.1073/pnas.1424206112. Epub 2015 Jan 20. PMID: 25605907.
Scheckel C, Darnell RB. Microexons–tiny but mighty. EMBO J. 2015 Feb 3;34(3):273-4. doi: 10.15252/embj.201490651. Epub 2014 Dec 22. PMID: 25535247.
Frank MO, Kaufman J, Parveen S, Blachère NE, Orange DE, Darnell RB. Dendritic cell vaccines containing lymphocytes produce improved immunogenicity in patients with cancer. J Transl Med. 2014 Dec 5;12:338. doi: 10.1186/s12967-014-0338-3. PMID: 25475068.
Blachère NE, Orange DE, Santomasso BD, Doerner J, Foo PK, Herre M, Fak J, Monette S, Gantman EC, Frank MO, Darnell RB. T cells targeting a neuronal paraneoplastic antigen mediate tumor rejection and trigger CNS autoimmunity with humoral activation. Eur J Immunol. 2014 Nov;44(11):3240-51. doi: 10.1002/eji.201444624. PMID: 25103845.
Vanharanta S, Marney CB, Shu W, Valiente M, Zou Y, Mele A, Darnell RB, Massagué J. Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer. Elife. 2014 Jun 4;3. doi: 10.7554/eLife.02734. PMID: 24898756.
Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 2014 Mar 27;6(6):1139-1152. doi: 10.1016/j.celrep.2014.02.005. Epub 2014 Mar 6. PMID: 24613350.
Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9. PMID: 24407355.
Poulos MG, Batra R, Li M, Yuan Y, Zhang C, Darnell RB, Swanson MS. Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice. Hum Mol Genet. 2013 Sep 1;22(17):3547-58. doi: 10.1093/hmg/ddt209. Epub 2013 May 8. PMID: 23660517.
Zhang C, Lee KY, Swanson MS, Darnell RB. Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18. PMID: 23685613.
Darnell RB. RNA protein interaction in neurons. Annu Rev Neurosci. 2013 Jul 8;36:243-70. doi: 10.1146/annurev-neuro-062912-114322. Epub 2013 May 20. Review. PMID: 23701460.
Orange DE, Blachere NE, Fak J, Parveen S, Frank MO, Herre M, Tian S, Monette S, Darnell RB. Dendritic cells loaded with FK506 kill T cells in an antigen-specific manner and prevent autoimmunity in vivo. Elife. 2013 Feb 5;2:e00105. doi: 10.7554/eLife.00105. PMID: 23390586.
Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB. NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. Elife. 2013 Jan 22;2:e00178. doi: 10.7554/eLife.00178. PMID: 23359859.

**For publications older than 2013, please see this link.

News from the Darnell Lab

July 15, 2020

Novel cells might act as a warning sign for rheumatoid arthritis flares

A genomics study has identified a previously unknown cell type whose blood levels tend to rise and fall in patients with rheumatoid arthritis. The findings could make it easier to manage the disease and help scientists understand its root causes.

April 3, 2020

Rockefeller scientists launch a broad range of studies into novel coronavirus

Over 130 scientists in 18 labs are conducting research to advance the development of new, urgently needed approaches for the prevention and treatment of COVID-19.