Publications

  • Potrykus K, Murphy M, Chen X, Epstein JA, and Cashel M. (2010) Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res 2010;38:1636-1651. doi: 10.1093/nar/gkp1150. Epub 2009 Dec 14. PMID: 20008510
  • Iben JR, Epstein JA, Bayfield MA, Bruinsma MW, Hasson S, Bacikova D, Ahmad D, Rockwell D, Kittler EL, Zapp ML, Maraia RJ. (2011) Comparative whole genomesequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants. Nucleic Acids Res. 2011 Jun;39(11):4728-42. doi: 10.1093/nar/gkr066. Epub 2011 Feb 11. PMID:21317186
  • Lamichhane TN, Blewett NH, Crawford AK, Cherkasova VA, Begley TJ, Farabaugh P, Iben JR, and Maraia RJ. (2013) Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast.  Mol Cell Biol. 2013 Aug;33(15):2918-29. doi: 10.1128/MCB.00278-13. Epub 2013 May 28. PMID: 23716598
  • Nagarajavel V, Iben JR, Howard BH, Maraia RJ, Clark DJ. (2013)  Global 'bootprinting' reveals the elastic architecture of the yeast TFIIIB-TFIIIC transcription complex in vivo.  Nucleic Acids Res. 2013 Sep; 41(17):8135-43. doi: 10.1093/nar/gkt611. Epub 2013 Jul 15. PMID: 23856458
  • *Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE (2013) Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood 2013 May 30;121(22):4575-85. doi: 10.1182/blood-2013-01-479451. Epub 2013 Apr 22.
  • Iben JR, Maraia RJ. (2014) tRNA gene copy number variation in humans. Gene. 2014 Feb 25; 536(2):376-84. doi: 10.1016/j.gene.2013.11.049. Epub 2013 Dec 14. PMID: 24342656
  • Cross JL, Iben J, Simpson C, Thurm A, Swedo S, Tierney E, Bailey-Wilson J, Biesecker LG, Porter FD, Wassif CA. (2014) Determination of the Allelic Frequency in Smith-Lemli-Opitz Syndrome by Analysis of Massively Parallel Sequencing Data Sets. Clin Genet. 2014 May 9; 87(6):570-5. doi: 10.1111/cge.12425.  PMID: 24813812
    Maraia RJ, Iben JR. (2014) Different types of secondary information in the genetic code [review].  RNA. 2014 Jul; 20(7):977-84. doi: 10.1261/rna.044115.113. PMID: 24935971
  • Ganguli D, Chereji RV, Iben JR, Cole HA, David J, Clark DJ.  RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast. (2014) Genome Res. 2014 Jul 11; 24(10):1637-49. pii: gr.177014.114. PMID: 25015381
  • You X, Bian C, Zan Q, Liu X, Chen J, Wang J, Qiu Y, Li W, Zhang X, Sun Y, Chen S, Hong W, Li Y, Cheng S, Fan G, Shi C, Liang J, Tang YT, Yang C, Ruan Z, Bai J, Peng C, Mu Q, Lu J, Fan M, Yang S, Huang Z, Jiang X, Fang X, Zhang G, Zhang Y, Yu H, Li J, Liu Z, Zhang G, Ravi V, Coon SL, Wang J, Yang H, Venkatesh B, Xu X, Wang J, and Shi Q (2014) Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nat Commun. 2014 Dec 2; 5:5594. doi: 10.1038/ncomms6594.
  • Cole HA, Ocampo J, Iben JR, Chereji RV, Clark DJ. Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases . Nucleic Acids Research 2014; 42(20):12512-22. doi: 10.1093/nar/gku1013
  • *Butler MG, Iben JR, Marsden KC, Epstein JA, Granato M, Weinstein BM. SNPfisher: Tools for Probing Genetic Variation in Laboratory Zebrafish. Development 2015 Apr 15;142(8):1542-52. doi: 10.1242/dev.118786.
  • Wassif CA, Cross JL, Iben J, Sanchez-Pulido L, Cougnoux A, Platt FM, Ory DS, Ponting CP, Bailey-Wilson JE, Biesecker LG, Porter FD. High incidence of unrecognized visceral/neurological late-onset Niemann-Pick disease, type C1, predicted by analysis of massively parallel sequencing data sets. Genet Med. 2015 Mar 12. doi: 10.1038/gim.2015.25.
  • *Wolf G, Yang P, Fuchtbauer A, Fuchtbauer EM, Silva AM, Park C, Nielsen AL, Pedersen FS, and Macfarlan TS (2015) The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev 2015 Mar1; 29(5):538-54.  doi: 10.1101/gad.252767.114.
  • Hartley SW, Coon SL, Savastano LE, Mullikin JC, NISC Comparative Sequencing Program, Fu C, Klein DC (2015) Neurotranscriptomics: The effects of neonatal stimulus deprivation on the rat pineal transcriptome. PLoS ONE 10(9): e0137548. doi: 10.1371/journal.pone.0137548.
  • Hickey A, Esnault C, Majumdar A, Chatterjee AG, Iben JR, McQueen PG, Yang AX, Mizuguchi T, Grewal SI, Levin HL. Single Nucleotide Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe. Genetics. 2015 Sep 9. pii: genetics.115.181602. PMID: 26358720
  • Lei H, Li T, Li B, Tsai S, Biggar RJ, Nkrumah F, Neequaye J, Gutierrez M, Epelman S, Mbulaiteye SM, Bhatia K, Lo SC. (2015) Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations. Sci Rep. 5:16706. PMID:26593963
  • Singh, P., Plumb, M., Ferris, A., Iben, J., Wu, X., Fadel, H., Poeschla, E., Hughes, S., Kvaratskhelia, M., and Levin, H. L.,  LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes, Genes & Development.  2015 Nov 1;29(21):2287-97.  PMID: 26545813
  • Arimbasseri AG, Blewett NH, Iben, JR, Lamichhane TN, Cherkasova V, Hafner M, Maraia RJ (accepted), RNA Polymerase III Output is Functionally Linked to tRNA Dimethyl-G26 Modification. PLOS Genetics. 2015 Dec 31;11(12):e1005671. doi: 10.1371/journal.pgen.1005671. PMID: 26720005
  • Li J, You X, Bian C, Yu H, Coon SL, Shi Q. Molecular evolution of aralkylamine N-acetyltransferase in fish: A genomic survey. Int J Mol Sci. 2015 Dec 31;17(1). pii: E51. doi: 10.3390/ijms17010051.
  • Peng C, Yao G, Gao B-M, Fan C-X, Bian C, Wang J, Cao Y, Wen B, Zhu Y, Ruan Z, Zhao X, You X, Bai J, Li J, Lin Z, Zou S, Zhang X, Qiu Y, Chen J, Coon SL, Yang J, Chen J-S, Shi Q. High-throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multitranscriptome sequencing. GigaScience (2016) 5:17 DOI 10.1186/s13742-016-0122-9.
  • Lamichhane TN, Arimbasseri AG, Rijal K, Iben JR, Wei FY, Tomizawa K, Maraia RJ. Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA. RNA. 2016 Apr;22(4):583-96. doi: 10.1261/rna.054064.115. PMID:26857223
  • *Gore AV, Athans B, Iben JR, Johnson K, Russanova V, Castranova D, Pham VN, Butler MG, Williams-Simons L, Nichols JT, Bresciani E, Feldman B, Kimmel CB, Liu PP, Weinstein BM. Epigenetic regulation of hematopoiesis by DNA methylation. Elife. 2016 Jan 27;5:e11813. doi: 10.7554/eLife.11813. PMID:26814702
  • *Gebert C, Rong Q, Jeong S, Iben J, Pfeifer K. H19ICR mediated transcriptional silencing does not require target promoter methylation.  Biochem Biophys Res Commun. 2016 Jul 29;476(3):121-6. PMID: 27178213
  • Arimbasseri AG, Iben J, Wei FY, Rijal K, Tomizawa K, Hafner M, Maraia RJ. Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37. RNA. 2016 Sep;22(9):1400-10. doi: 10.1261/rna.056259.116. Epub 2016 Jun 27. PMID: 27354703
  • Hartley, SW, Mullikin, JC, Klein, DC, Park, M, NISC Comparative Sequencing Program, Coon, SL (2016) Alternative isoform analysis of Ttc8 expression in the rat pineal gland using a multi-platform sequencing approach reveals neural regulation. PLoS ONE 2016 Sep 29;11(9):e0163590. PMID: 27684375
  • Blewett NH, Iben JR, Gaidamakov S, Maraia RJ.  La deletion from mouse brain alters pre-tRNA metabolism and accumulation of pre-5.8S rRNA, with neuron death and reactive astrocytosis.  Mol Cell Biol. 2017.  Epub 2017 Feb 21.
  • *Venero Galanternik M, Castranova D, Gore AV, Blewett NH, Jung HM, Stratman AN, Kirby MR, Iben J, Miller MF, Kawakami K, Maraia RJ, Weinstein BM. A novel perivascular cell population in the zebrafish brain. Elife. 2017 Apr 11;6. pii: e24369. doi: 10.7554/eLife.24369.
  • Zhang, K., Ruan Z, Li J, Bian C, You X, Coon SL and Shi Q, 2017. A Comparative Genomic and Transcriptomic Survey Provides Novel Insights into N-Acetylserotonin Methyltransferase (ASMT) in Fish. Molecules 22(10). pii: E1653. doi: 10.3390/molecules22101653 PMID: 28974055.
  • *Suzuki, S., Iben JRCoon SL and Kino T, 2017. SIRT1 is a transcriptional enhancer of the glucocorticoid receptor acting independently to its deacetylase activity. Mol Cell Endocrinol.  In press, doi: 10.1016/j.mce.2017.09.012 PMID: 28923345.
  • *Park KS, Mitra A, Rahat B, Kim K, Pfeifer K (2017) Loss of imprinting mutations define both distinct and overlapping roles for misexpression of IGF2 and of H19 lncRNA. Nucleic Acids Res 2017 Dec 15;45(22):12766-12779. doi: 10.1093/nar/gkx896.
  • Mattijssen S, Arimbasseri AG, Iben JR, Gaidamakov S, Lee J, Hafner M, Maraia RJ. LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection. Elife. 2017 Sep 12;6. pii: e28889. doi: 10.7554/eLife.28889. PMID: 28895529.
  • *Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun M-A, Wolf G, Baker M, Chien H-C, Lai N, Cheng X, Shen C-K J, and Macfarlan TS (2017) A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science 2017 May 19;356(6339):757-759. doi: 10.1126/science.aah6895.
  • *Cougnoux A, Drummond RA, Collar AL, Iben JR, Salman A, Westgarth H, Wassif CA, Cawley NX, Farhat NY, Ozato K, Lionakis MS, Porter FD (2018) Microglia activation in Niemann-Pick Disease, type C1 is amendable to therapeutic intervention. Hum Mol Genet 2018 Jun 15;27(12):2076-2089. doi: 10.1093/hmg/ddy112.
  • *Cougnoux A, Movassaghi M, Picache JA, Iben JR, Navid F, Salman A, Martin K, Farhat NY, Cluzeau C, Tseng WC, Burkert K, Sojka C, Wassif CA, Cawley NX, Bonnet R, Porter FD (2018) Gastrointestinal Tract Pathology in a BALB/c Niemann-Pick Disease Type C1 Null Mouse Model. Dig Dis Sci. 2018 Apr;63(4):870-880. doi: 10.1007/s10620-018-4914-x. Epub 2018 Jan 22.
  • *Brown JL, Sun M, and Kassis JA (2018)  Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho. PNAS 2018 Feb 20;115(8):E1839-E1848.
  • *Jee YH, Wang J, Yue S, Jennings M, Clokie SJH, Nilsson O, Lui J, Baron J (2018) Mir-374-5p, mir-379-5p, and mir-503-5p regulate proliferation and hypertrophic differentiation of growth plate chondrocytes in male rats. Endocrinology 159:1469-1478, 2018. doi: 10.1210/en.2017-00780. 
  • *Lui JC, Jee YH, Garrison P, Iben JR, Yue S, Ad M, Nguyen Q, Kikani B, Wakabayashi Y, Baron J. (2018) Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions. PLoS Biol. 2018 Jul 23;16(7):e2005263. doi: 10.1371/journal.pbio.2005263. eCollection 2018 Jul. PMID:30036371
  • *Patterson-West J, James TD, Fernández-Coll L, Iben JR, Moon K, Knipling L, Cashel M, Hinton DM. The E. coli global regulator DksA reduces transcription during T4 infection. Viruses. 2018 Jun 6;10(6). pii: E308. doi: 10.3390/v10060308. PMID:29882792
  • *Mays, JC, Kelly MC, Coon SL, Holtzclaw L, Rath MF, Kelley MW, Klein DC. (2018)  Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression.  PLoS ONE 13(10):e0205883. doi: 10.1371/journal.pone.0205883.
  • *Lee PC, Machner MP. (2018) The Legionella effector kinase LegK7 hijacks the host Hippo pathway to promote infection. Cell Host Microbe. 24(3):429-438. PMID:30212651
  • *Tabor KM, Marquart GD, Hurt C, Smith TS, Geoca AK, Bhandiwad AA, Subedi A, Sinclair JL, Rose HM, Polys NF and Burgess HA. (2019) Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping. Elife. 8. pii: e42687. doi: 10.7554/eLife.42687.
  • *Shainer I, Michel M, Marquart GD, Bhandiwad AA, Zmora N, Ben-Moshe Livne Z, Zohar Y, Hazak A, Mazon Y, Förster D, Hollander-Cohen L, Cone RD, Burgess HA, Gothilf Y. (2019) Agouti-related protein 2 is a new player in the teleost stress response system. Curr Biol. 29(12):2009-2019.e7. doi: 10.1016/j.cub.2019.05.021.
  • *Wester JC, Mahadevan V, Rhodes CT, Calvigioni D, Vankatesh S, Maric D, Hunt S, Yuan X, Zhang Y, Petros TJ, McBain CJ (2019) Neocortical projection neurons instruct inhibitory interneuron circuit development in a lineage dependent manner. Neuron. 2019 Jun 5;102(5):960-975.e6. doi: 10.1016/j.neuron.2019.03.036. PMID: 31027966.
  • *Coon SL, Fu C, Hartley SW, Holtzclaw L, Mays JC, Kelly MC, Kelley MW, Mullikin JC, Rath MF, Savastano LE and Klein DC. (2019) Single Cell Sequencing of the Pineal Gland: The Next Chapter. Front. Endocrinol. 2019 Sep 20;10:590. doi: 10.3389/fendo.2019.00590. PMID: 31616371; PMCID: PMC6764290.
  • *Fletcher PA, Smiljanic K, Previde RM, Iben JLi T, Rokic MB, Sherman A, Coon SL, and Stojilkovic SS. (2019) Cell type- and sex-dependent transcriptome profiles of rat anterior pituitary cells.  Front Endocrinol. 2019 Sep 18;10:623. doi: 10.3389/fendo.2019.00623. PMID: 31620083; PMCID: PMC6760010.
  • *Gore AV, Tomins KA, Iben J, Ma L, Castranova D, Davis AE, Parkhurst A, Jeffery WR, Weinstein BM. (2018) An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol. 2018 Jul;2(7):1155-1160. doi: 10.1038/s41559-018-0569-4. Epub 2018 May 28. PMID: 29807993; PMCID: PMC6023768.
  • *Jia R, Bonifacino JS. (2019) Negative regulation of autophagy by UBA6-BIRC6-mediated ubiquitination of LC3. Elife. 2019 Nov 6;8:e50034. doi: 10.7554/eLife.50034. PMID: 31692446; PMCID: PMC6863627.
  • *Jung HM, Hu CT, Fister AM, Davis AE, Castranova D, Pham VN, Price LM, Weinstein BM. (2019) MicroRNA-mediated control of developmental lymphangiogenesis. Elife. 2019 Sep 3;8:e46007. doi: 10.7554/eLife.46007. PMID: 31478836; PMCID: PMC6721793.
  • *Martin KB, Williams IM, Cluzeau CV, Cougnoux A, Dale RK, Iben JR, Cawley NX, Wassif CA, Porter FD. (2019) Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1. Int J Mol Sci. 2019 Dec 31;21(1):292. doi: 10.3390/ijms21010292. PMID: 31906248; PMCID: PMC6981888.
  • *Cougnoux A, Drummond RA, Fellmeth M, Navid F, Collar AL, Iben J, Kulkarni AB, Pickel J, Schiffmann R, Wassif CA, Cawley NX, Lionakis MS, Porter FD. (2019) Unique molecular signature in mucolipidosis type IV microglia. J Neuroinflammation. 2019 Dec 28;16(1):276. doi: 10.1186/s12974-019-1672-4. PMID: 31883529; PMCID: PMC6935239.
  • *Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS. (2020) Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice.  Elife. 2020 Apr 30;9:e53360. doi: 10.7554/eLife.53360.PMID: 32352380
  • *Mahadevan V, Peltekian A, McBain CJ (2020) Translatome Analyses using Conditional Ribosomal Tagging in GABAergic Interneurons and Other Sparse Cell Types. Current Protocols in Neuroscience. Jun;92(1): e93. PMID: 32584517
  • *Wolf G, de Iaco A, Sun MA, Bruno M, Tinkham M, Hoang D, Mitra A, Ralls S, Trono D, Macfarlan TS. (2020) KRAB-zinc finger protein gene expansion in response to active retrotransposons in the murine lineage. Elife. 2020 Jun 1;9:e56337. doi: 10.7554/eLife.56337.PMID: 32479262
  • *Jee YH, Won S, Lui JC, Jennings M, Whalen P, Yue S, Temnycky A, Barnes KM, Cheetham T, Boden MG, Radovick S, Quinton, Leschek E, Aguilera G, Yanovski JA, Seminara SB, Crowley WF, Delaney A, Roche KW, Baron J. (2020) DLG2 mutations in patients with delayed or absent puberty. Genet Med, 2020 Aug;22(8):1329-1337.
  • *Nakajima, K, Tanizaki, Y, Luu, N, Zhang, H, Shi, Y-B (2020) Comprehensive RNA-seq analysis of notochord-specific genes induced during Xenopus tropicalis tail resorption. Gen Comp Endocrinol 287:113349, 1-9. doi: 10.1016/j.ygcen.2019.113349
  • *Tanizaki, Y, Shibata, Y,  Zhang, H, Shi, Y-B (2020) Analysis of thyroid hormone receptor α knockout tadpoles reveals that the activation of cell cycle program is involved in thyroid hormone-induced larval epithelial cell death and adult intestinal stem cell development during Xenopus tropicalis metamorphosis. Thyroid  2020 Jul 1. doi: 10.1089/thy.2020.0022. Online ahead of print.
  • *Aksenova V, Smith A, Lee H, Bhat P, Esnault C, Chen S, Iben J, Kaufhold R, Yau KC, Echeverria C, Fontoura B, Arnaoutov A, Dasso M. (2020) Nucleoporin TPR is an integral component of the TREX-2 mRNA export pathway. Nat Commun. 2020 Sep 11;11(1):4577. doi: 10.1038/s41467-020-18266-2. PMID: 32917881.
  • *Melamed S, Adams PP, Zhang A, Zhang H, Storz G. (2020) RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles. Mol Cell. 2020 Jan 16;77(2):411-425.e7. doi: 10.1016/j.molcel.2019.10.022. Epub 2019 Nov 21. PMID: 31761494; PMCID: PMC6980735.
  • *Horstick EJ, Bayleyen Y, Burgess HA. (2020) Molecular and cellular determinants of motor asymmetry in zebrafish. Nat Commun. 2020 Mar 3;11(1):1170. doi: 10.1038/s41467-020-14965-y. PMID: 32127541; PMCID: PMC7054361.
  • *Bhandiwad AA, Li T, Iben JRCoon SL, Burgess HA (2020) Integration site mapping by high-throughput sequencing of Tol2-oligo pulldown-enriched fragments. Bio-protocol. bio-protocol.org/prep311 external link. (invited, but not peer-reviewed)
  • *Clark SC, Chereji RV, Lee PR, Fields RD, Clark DJ. (2020) Differential nucleosome spacing in neurons and glia. Neurosci Lett. 2020 Jan 1;714:134559. doi: 10.1016/j.neulet.2019.134559. Epub 2019 Oct 19. PMID: 31639421; PMCID: PMC6943982.
  • *Li L, Mitra A, Cui K, Zhao B, Choi S, Lee JY, Stamos DB, El-Khoury D, Warzecha C, Pfeifer K, Hardwick J, Zhao K, Venters B, Davé UP, Love PE. (2020) Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood. 2020 Jun 18;135(25):2252-2265. doi: 10.1182/blood.2019000794. PMID: 32181817; PMCID: PMC7316212.
  • *Mattijssen S, Iben JRLi TCoon SL, Maraia RJ. (2020) Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. Elife. 2020 Aug 3;9:e59186. doi: 10.7554/eLife.59186. PMID: 32744499; PMCID: PMC7413741.
  • *Cougnoux A, Yerger JC, Fellmeth M, Serra-Vinardell J, Martin K, Navid F, Iben J, Wassif CA, Cawley NX, Porter FD. (2020) Single Cell Transcriptome Analysis of Niemann-Pick Disease, Type C1 Cerebella. Int J Mol Sci. 2020 Jul 28;21(15):5368. doi: 10.3390/ijms21155368. PMID: 32731618; PMCID: PMC7432835.

 

*: sequencing done at the Molecular Genomics Core

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