The Keene Laboratory has a long-term interest in the structures and functions of viral and mammalian genomes. In the early 1980’s, they determined the first genomic sequences for rabies, Ebola and VS viruses, and discerned the origins of defective interfering viruses. Their research focused on small noncoding RNAs called the leader RNAs that are generated by these viruses. They found that leader RNAs of VSV and rabies bind to a cellular host RNA-binding protein (RBP) called La that is now known to assist virus infectivity by blocking access of the RIG-I protein to the leader RNA. RIG-I activates the type I interferon response when it binds to small noncoding RNAs like the leader RNAs. In 1984, the Keene lab derived cDNA clones of the La RBP using sera from patients with autoimmune diseases such as Lupus and Sjogren’s syndrome. Novel procedures developed in the Keene lab to clone the La gene led to the cloning of several other human genes involved in autoimmunity and to the development of the first recombinant diagnostic test for autoantibodies. These autoimmune RBPs were found to contain a common RNA-binding motif that Keene named the RNA Recognition Motif (RRM) and demonstrated that the RRM forms the core of a functional unit RNA-binding domain. Since 1991, the lab has focused on the functions of human RRM-ELAV/Hu RBPs demonstrating that they bind to AU-rich sequences, and increase the stability and translation of their mRNA targets.More recently, the Keene lab devised methods to identify structurally and functionally related cellular mRNAs and microRNAs that cluster together based upon their association with ELAV/Hu RBPs and other RNA-binding proteins. This general approach has been termed ribonomics because it uses microarrays or Solexa sequencing to determine mRNAs and microRNAs associated with ribonucleoprotein complexes. This novel approach to functional genomics is has been used and adapted in many laboratories to analyze biological responses such as virus infectivity, tumorigenesis, genotoxic agents, radiation and developmental inducers. These studies have revealed that functionally related mRNA subsets are post-transcriptionally coordinated, thereby, representing the organizational state of genetic information between the genome and the proteome. Based on these findings, Keene proposed the concept of Post-Transcriptional RNA Operons and Regulons (PTRO) based upon the combinatorial regulation of mRNAs at all steps between transcription and translation, potentially revealing a RNP-regulatory code or “USER-code”. The PTRO is a simplifying model that explains the organization and dynamic properties of multiple mRNA and noncoding RNAs located in the nucleus and cytoplasm. Many dozens of PTROs have since been reported in archaea, yeasts, worms, flies, trypanosomes, plants, humans and other mammals, and unexpectedly, in bacteria. The PTRO model has a variety of therapeutic implications as it can be used to identify dynamic changes in time and space of all cellular mRNAs and noncoding RNAs involved in growth regulation, neuronal plasticity, immune regulation and cancer.

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.