Jack Keene, PhD – Publications

James B. Duke Professor

researchbiography • publications

Google Scholar Profile 

Moon SL, Blackinton JG, Anderson JR, Dozier MK, Dodd BJ, Keene JD, Wilusz CJ,

Representative Publications:
Bisogno LS, Keene JD. RNA regulons in cancer and inflammation. Curr Opin Genet
Dev. 2017 Nov 22;48:97-103. doi: 10.1016/j.gde.2017.11.004. [Epub ahead of print]
Review. PubMed PMID: 29175729.

Bisogno LS, Keene JD. Analysis of post-transcriptional regulation during
cancer progression using a donor-derived isogenic model of tumorigenesis.
Methods. 2017 Aug 15;126:193-200. doi: 10.1016/j.ymeth.2017.05.012. Epub 2017 May
19. PubMed PMID: 28529064.

Nicholson CO, Friedersdorf MB, Bisogno LS, Keene JD. DO-RIP-seq to quantify
RNA binding sites transcriptome-wide. Methods. 2017 Apr 15;118-119:16-23. doi:
10.1016/j.ymeth.2016.11.004. Epub 2016 Nov 10. PubMed PMID: 27840290; PubMed
Central PMCID: PMC5411286.

Nicholson CO, Friedersdorf M, Keene JD. Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. RNA. 2017 Jan;23(1):32-46. Epub 2016 Oct 14. PubMed PMID: 27742911; PubMed Central PMCID: PMC5159647.

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM,
Calabrese JM, Weeks KM. SHAPE reveals transcript-wide interactions, complex
structural domains, and protein interactions across the Xist lncRNA in living
cells. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10322-7. doi:
10.1073/pnas.1600008113. Epub 2016 Aug 30. PubMed PMID: 27578869; PubMed Central PMCID: PMC5027438.

Blackinton JG, Keene JD. Functional coordination and HuR-mediated regulation
of mRNA stability during T cell activation. Nucleic Acids Res. 2016 Jan
8;44(1):426-36. doi: 10.1093/nar/gkv1066. Epub 2015 Oct 20. PubMed PMID:
26490963; PubMed Central PMCID: PMC4705648.

Bradrick SS, Wilusz J. XRN1 stalling in the 5′ UTR of Hepatitis C virus and
Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability.
PLoS Pathog. 2015 Mar 6;11(3):e1004708. doi: 10.1371/journal.ppat.1004708.
eCollection 2015 Mar. PubMed PMID: 25747802; PubMed Central PMCID: PMC4352041.

Keene JD (2014) The globalization of messenger RNA regulation. National Science Review (Chinese Academy of Science) 1:184-189.

*Payne TL, *Blackinton J, Frisbee A, Pickeral J, Sawant S, Vandergrift NA, Freel SA, Ferrari G, Keene JD and Tomaras GD (2014) *co-first author. Transcriptional and post-transcriptional regulation of cytokine gene expression in HIV-1 antigen-specific CD8+ T cells that mediate virus inhibition. Journal of Virology, Jun 4. pii: JVI.00802-14. PMID:24899193.

Blackinton JG and Keene JD. (2014) Post-transcriptional RNA regulons affecting cell cycle and proliferation. Seminars in Cellular & Developmental Biology, Jun 2. pii: S1084-9521(14)00160-8. PMID:24882724.

Friedersdorf MB and Keene JD. (2014) Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biology 15(1):R2.

Simone LE and Keene JD. (2013) Mechanisms Coordinating ELAV/Hu mRNA Regulons. Cancer Genetics: Current Opinions in Genetics & Development 23:35-43.

Mansfield KD and Keene JD. (2012) Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation. Nucleic Acids Research 40:2734-2746.

Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky R, Keene JD and Ohler U. (2011) PARalyzer: Definition of regulatory RNA binding sites from PAR-CLIP short-read sequence data. Genome Biology 12:R79.

Mukherjee N, Corcoran DL, Nusbaum J, Reid D, Georgiev S, Hafner M, Ascano Jr. M, Tuschl T, Ohler U and Keene JD. (2011) Integrative regulatory mapping indicates that RNA-binding protein HuR (ELAVL1) couples pre-mRNA splicing and mRNA stability. Molecular Cell 43:327-339.

Mazan-Mamczarz K, Hagner PR, Zhang Y, Dai B, Lehrmann E, Becker KG, Keene JD, Gorospe M, Liu Z, Gartenhaus RB. (2011) ATM regulates a DNA damage response post-transcriptional RNA operon in lymphocytes. Blood 117(8):2441-2450.

Morris AR, Mukherjee N, Keene JD. (2010) Systematic analysis of posttranscriptional gene expression. Wiley Interdiscip Rev Syst Biol Med. 2(2):162-180.

Neplioueva V, Dobrikova EY, Mukherjee N, Keene JD, Gromeier M. (2010) Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs. PLoS One 23;5(7):e11710.

Keene JD. (2010) The global dynamics of RNA stability orchestrates responses to cellular activation. BMC Biol. 8;8:95.

Keene JD. (2010) Global regulation and dynamics of ribonucleic acid. Endocrinology 151(4):1391-1397. Review.

Mukherjee N, Lager PJ, Friedersdorf M, Thompson M, Keene JD. (2009) Coordinated posttranscriptional mRNA population dynamics during T-cell activation. Molecular Systems Biology [doi:10.1038/msb.44].

Morris AD, Mukherjee N, Keene JD. (2009) Systematic analysis of posttranscriptional gene expression. Wiley Interdisciplinary Reviews WIRES: Systems Biology and Medicine [doi:10.1002/wsbm.54].

Papadaki O, Milatos S, Grammenoudi S, Mukherjee N, Keene JD, Kontoyiannis DL. (2009) Control of thymic T cell maturation, deletion and egress by the RNA-binding protein HuR. J Immunol. 182(11):6779-6788.

Mansfield KD, Keene JD. (2009) The ribonome: a dominant force in co-ordinating gene expression. Biol Cell. 101(3):169-181. Review.

Graner MW, Alzate O, Dechkovskaia AM, Keene JD, Sampson JH, Mitchell DA, Bigner DD. (2009) Proteomic and immunologic analyses of brain tumor exosomes.
FASEB J. 23(5):1541-1557.

Tiruchinapalli DM, Caron MG, Keene JD. (2008) Activity-dependent expression of ELAV/Hu RBPs and neuronal mRNAs in seizure and cocaine brain. J Neurochem. 107(6):1529-1543.

Tiruchinapalli DM, Ehlers MD, Keene JD. (2008) Activity-dependent expression of RNA binding protein HuD and its association with mRNAs in neurons. RNA Biol. 5(3):157-168.

Mazan-Mamczarz K, Hagner PR, Corl S, Srikantan S, Wood WH, Becker KG, Gorospe M, Keene JD, Levenson AS, Gartenhaus RB. (2008) Post-transcriptional gene regulation by HuR promotes a more tumorigenic phenotype. Oncogene. 27(47):6151-6163.

Keene JD. (2007) Biological clocks and the coordination theory of RNA operons and regulons. Cold Spring Harb Symp Quant Biol. 72:157-165. Review.

Morris AR, Mukherjee N, Keene JD. (2008) Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol Cell Biol. 28(12):4093-4103.

Beach DL, Keene JD.(2008) Ribotrap:targeted purification of RNA-specific RNPs from cell lysates through immunoaffinity precipitation to identify regulatory proteins and RNAs. Methods Mol Biol. 419:69-91.

Konopka JL, Penalva LO, Thompson JM, White LJ, Beard
CW, Keene JD, Johnston RE. (2007) A two-phase innate host response to alphavirus infection identified by mRNP-tagging in vivo. PLoS Pathog. 3(12):e199.

Pyhtila B, Zheng T, Lager PJ, Keene JD, Reedy MC,
Nicchitta CV. (2008) Signal sequence- and translation-independent mRNA localization to the endoplasmic reticulum. RNA. 14(3):445-453.

Mazroui R, Di Marco S, Clair E, von Roretz C,
Tenenbaum SA, Keene JD, Saleh M, Gallouzi IE. (2008) Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis. J Cell Biol. 180(1):113-127.

Keene JD. (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet.8(7):533-543. Review.

Keene JD, Komisarow JM, Friedersdorf MB.(2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc. 1(1):302-307.

Keene, J.D. and Lager, P.J. (2005) Posttranscriptional Operons and Regulons Coordinating Gene Expression. Chromosome Research 13:327-337.

Penalva LO, Burdick MD, Lin SM, Sutterluety H, Keene JD.(2004) RNA-binding proteins to assess gene expression states of co-cultivated cells in response to tumor cells. Mol Cancer. 3:24.

Mazan-Mamczarz K, Galbán S, López de Silanes I, Martindale JL, Atasoy U, Keene JD, Gorospe M .(2003) RNA-binding protein HuR enhances p53 translation in response to ultraviolet light irradiation. Proc Natl Acad Sci U S A. 100(14):8354-8359.

Keene JD, Tenenbaum SA. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell.9(6):1161-1167.

Eystathioy T, Chan EK, Tenenbaum SA, Keene JD, Griffith K, Fritzler MJ. (2002) A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol Biol Cell. 13(4):1338-1351.

Brown V, Jin P, Ceman S, Darnell JC, O’Donnell WT, Tenenbaum SA, Jin X, Feng Y, Wilkinson KD, Keene JD, Darnell RB, Warren ST. (2001) Microarray identification of
FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 107(4):477-487.

Keene JD. Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. (2001) Proc Natl Acad Sci U S A. 98(13):7018-7024.

Tenenbaum SA, Carson CC, Lager PJ, Keene JD. (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U
S A. 97(26):14085-14090.

Antic D., Lu N., Keene J.D. (1999) ELAV tumor antigen, Hel-N1, increases translation of neurofilament M mRNA and induces formation of neurites in human teratocarcinoma cells. Genes & Development 13:449-461.