James Patton
Last active: 11/14/2018


The Patton lab has 4 ongoing projects.  The first is investigation into the function of miRNAs during early vertebrate development using zebrafish as a model organism.  We use gain and loss of function experiments to determine miRNA function at specific developmental times.  As an example, we recently discovered a role for miR-27 in craniofacial bone development by regulating chondrogenesis.  The second project studies regeneration in fish and mice.  Zebrafish are remarkable in that they can regenerate severed spinal cords, hearts, fins, retina, and other organs and tissues.  After initially studying the role that miRNAs play in fin and retina regeneration, we are now focused on the mechanisms that regulate initiation of retina regeneration and control of progenitor cell proliferation.  We can blind zebrafish and they amazingly regain eyesight in about three weeks.  Why can fish do this and why can’t humans?  Especially when the cells and architecture of the retina are nearly identical between fish and humans.  The third project studies a novel cell-cell communication system via extracellular RNA.  We have discovered that RNAs can be packaged in extracellular vesicles and be transferred from donor to recipient cells in a way that challenges traditional beliefs about cell autonomous RNA.  Our focus is how RNAs get packaged into extracellular vesicles and how they move between cells to affect things like the tumor microenvironment and metastasis.  Our last project merges the extracellular vesicle work with our regeneration studies to test whether exosomes derived from stem cells can induce a regenerative response in the retina, screening first in zebrafish and then testing in mice, in collaboration with Ed Levine’s lab.


The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. miR-27 regulates chondrogenesis by suppressing focal adhesion kinase during pharyngeal arch development. Kara N, Wei C, Commanday AC, Patton JG (2017) Dev Biol 429(1): 321-334
    › Primary publication · 28625871 (PubMed) · PMC5582384 (PubMed Central)
  2. Blocking Zebrafish MicroRNAs with Morpholinos. Flynt AS, Rao M, Patton JG (2017) Methods Mol Biol : 59-78
    › Primary publication · 28364234 (PubMed)
  3. Neurotransmitter-Regulated Regeneration in the Zebrafish Retina. Rao MB, Didiano D, Patton JG (2017) Stem Cell Reports 8(4): 831-842
    › Primary publication · 28285877 (PubMed) · PMC5390103 (PubMed Central)
  4. Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes. Dou Y, Cha DJ, Franklin JL, Higginbotham JN, Jeppesen DK, Weaver AM, Prasad N, Levy S, Coffey RJ, Patton JG, Zhang B (2016) Sci Rep : 37982
    › Primary publication · 27892494 (PubMed) · PMC5125100 (PubMed Central)
  5. A transcription factor network controls cell migration and fate decisions in the developing zebrafish pineal complex. Khuansuwan S, Clanton JA, Dean BJ, Patton JG, Gamse JT (2016) Development 143(14): 2641-50
    › Primary publication · 27317804 (PubMed) · PMC4958332 (PubMed Central)
  6. Identification of a Paralog-Specific Notch1 Intracellular Domain Degron. Broadus MR, Chen TW, Neitzel LR, Ng VH, Jodoin JN, Lee LA, Salic A, Robbins DJ, Capobianco AJ, Patton JG, Huppert SS, Lee E (2016) Cell Rep 15(9): 1920-9
    › Primary publication · 27210761 (PubMed) · PMC4889555 (PubMed Central)
  7. KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes. McKenzie AJ, Hoshino D, Hong NH, Cha DJ, Franklin JL, Coffey RJ, Patton JG, Weaver AM (2016) Cell Rep 15(5): 978-987
    › Primary publication · 27117408 (PubMed) · PMC4857875 (PubMed Central)
  8. Biogenesis, delivery, and function of extracellular RNA. Patton JG, Franklin JL, Weaver AM, Vickers K, Zhang B, Coffey RJ, Ansel KM, Blelloch R, Goga A, Huang B, L'Etoille N, Raffai RL, Lai CP, Krichevsky AM, Mateescu B, Greiner VJ, Hunter C, Voinnet O, McManus MT (2015) J Extracell Vesicles : 27494
    › Primary publication · 26320939 (PubMed) · PMC4553266 (PubMed Central)
  9. KRAS-dependent sorting of miRNA to exosomes. Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG (2015) Elife : e07197
    › Primary publication · 26132860 (PubMed) · PMC4510696 (PubMed Central)
  10. Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Yin L, Maddison LA, Li M, Kara N, LaFave MC, Varshney GK, Burgess SM, Patton JG, Chen W (2015) Genetics 200(2): 431-41
    › Primary publication · 25855067 (PubMed) · PMC4492370 (PubMed Central)
  11. miR-216a regulates snx5, a novel notch signaling pathway component, during zebrafish retinal development. Olena AF, Rao MB, Thatcher EJ, Wu SY, Patton JG (2015) Dev Biol 400(1): 72-81
    › Primary publication · 25645681 (PubMed) · PMC4361363 (PubMed Central)
  12. Technical brief: Constant intense light exposure to lesion and initiate regeneration in normally pigmented zebrafish. Rajaram K, Summerbell ER, Patton JG (2014) Mol Vis : 1075-84
    › Primary publication · 25324680 (PubMed) · PMC4119235 (PubMed Central)
  13. Dynamic miRNA expression patterns during retinal regeneration in zebrafish: reduced dicer or miRNA expression suppresses proliferation of Müller glia-derived neuronal progenitor cells. Rajaram K, Harding RL, Bailey T, Patton JG, Hyde DR (2014) Dev Dyn 243(12): 1591-605
    › Primary publication · 25220904 (PubMed) · PMC4237695 (PubMed Central)
  14. RNAi-mediated gene silencing in zebrafish triggered by convergent transcription. Andrews OE, Cha DJ, Wei C, Patton JG (2014) Sci Rep : 5222
    › Primary publication · 24909225 (PubMed) · PMC4048883 (PubMed Central)
  15. miR-203 regulates progenitor cell proliferation during adult zebrafish retina regeneration. Rajaram K, Harding RL, Hyde DR, Patton JG (2014) Dev Biol 392(2): 393-403
    › Primary publication · 24858486 (PubMed) · PMC4104251 (PubMed Central)
  16. Strain-specific suppression of microRNA-320 by carcinogenic Helicobacter pylori promotes expression of the antiapoptotic protein Mcl-1. Noto JM, Piazuelo MB, Chaturvedi R, Bartel CA, Thatcher EJ, Delgado A, Romero-Gallo J, Wilson KT, Correa P, Patton JG, Peek RM (2013) Am J Physiol Gastrointest Liver Physiol 305(11): G786-96
    › Primary publication · 24136787 (PubMed) · PMC3882435 (PubMed Central)
  17. miR-153 regulates SNAP-25, synaptic transmission, and neuronal development. Wei C, Thatcher EJ, Olena AF, Cha DJ, Perdigoto AL, Marshall AF, Carter BD, Broadie K, Patton JG (2013) PLoS One 8(2): e57080
    › Primary publication · 23451149 (PubMed) · PMC3581580 (PubMed Central)
  18. Transcriptome-wide analysis of small RNA expression in early zebrafish development. Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG (2012) RNA 18(5): 915-29
    › Primary publication · 22408181 (PubMed) · PMC3334700 (PubMed Central)
  19. Regulation of endoderm formation and left-right asymmetry by miR-92 during early zebrafish development. Li N, Wei C, Olena AF, Patton JG (2011) Development 138(9): 1817-26
    › Primary publication · 21447552 (PubMed) · PMC3074454 (PubMed Central)
  20. Small RNAs have a big impact on regeneration. Thatcher EJ, Patton JG (2010) RNA Biol 7(3): 333-8
    › Primary publication · 20458186 (PubMed) · PMC4444050 (PubMed Central)
  21. Analysis of SRrp86-regulated alternative splicing: control of c-Jun and IκBβ activity. Solis AS, Patton JG (2010) RNA Biol 7(4): 486-94
    › Primary publication · 20400856 (PubMed) · PMC3070911 (PubMed Central)
  22. Crosstalk between planar cell polarity signaling and miR-8 control of NHERF1-mediated actin reorganization. Flynt AS, Patton JG (2010) Cell Cycle 9(2): 235-7
    › Primary publication · 20023383 (PubMed) · PMC4020509 (PubMed Central)
  23. Genomic organization of microRNAs. Olena AF, Patton JG (2010) J Cell Physiol 222(3): 540-5
    › Primary publication · 20020507 (PubMed) · PMC4028663 (PubMed Central)
  24. A molecular basis for variation in clinical severity of isolated growth hormone deficiency type II. Hamid R, Phillips JA, Holladay C, Cogan JD, Austin ED, Backeljauw PF, Travers SH, Patton JG (2009) J Clin Endocrinol Metab 94(12): 4728-34
    › Primary publication · 19837935 (PubMed) · PMC2795644 (PubMed Central)
  25. miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos. Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, Patton JG (2009) J Cell Biol 185(1): 115-27
    › Primary publication · 19332888 (PubMed) · PMC2700511 (PubMed Central)
  26. Regulation of zebrafish fin regeneration by microRNAs. Thatcher EJ, Paydar I, Anderson KK, Patton JG (2008) Proc Natl Acad Sci U S A 105(47): 18384-9
    › Primary publication · 19015519 (PubMed) · PMC2587605 (PubMed Central)
  27. Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically. Solis AS, Peng R, Crawford JB, Phillips JA, Patton JG (2008) J Biol Chem 283(35): 23619-26
    › Primary publication · 18586677 (PubMed) · PMC2527097 (PubMed Central)
  28. Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites. Li N, Flynt AS, Kim HR, Solnica-Krezel L, Patton JG (2008) Nucleic Acids Res 36(13): 4277-85
    › Primary publication · 18583362 (PubMed) · PMC2490740 (PubMed Central)
  29. Isolated growth hormone deficiency type II caused by a point mutation that alters both splice site strength and splicing enhancer function. Shariat N, Holladay CD, Cleary RK, Phillips JA, Patton JG (2008) Clin Genet 74(6): 539-45
    › Primary publication · 18554279 (PubMed) · PMC4445398 (PubMed Central)
  30. Genomic organization of zebrafish microRNAs. Thatcher EJ, Bond J, Paydar I, Patton JG (2008) BMC Genomics : 253
    › Primary publication · 18510755 (PubMed) · PMC2427041 (PubMed Central)
  31. Rescue of pituitary function in a mouse model of isolated growth hormone deficiency type II by RNA interference. Shariat N, Ryther RC, Phillips JA, Robinson IC, Patton JG (2008) Endocrinology 149(2): 580-6
    › Primary publication · 18006625 (PubMed) · PMC2219309 (PubMed Central)
  32. Splicing fidelity, enhancers, and disease. Solis AS, Shariat N, Patton JG (2008) Front Biosci : 1926-42
    › Primary publication · 17981680 (PubMed)
  33. MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways. Thatcher EJ, Flynt AS, Li N, Patton JR, Patton JG (2007) Dev Dyn 236(8): 2172-80
    › Primary publication · 17584857 (PubMed)