Publications

Ordway, A.J.*, Helt, R.N.*, and Johnston, R.J., Jr. (2024) Towards fundamental mechanisms of stochastic cell fate specification in eukaryotes. Philos Trans R Soc Lond B Biol Sci * indicates co-1st authors

Hadyniak, S., Eldred, K., Brenerman, B., Hussey, K., McCoy, R., Hagen, J., Sauria, M., Kuchenbecker, Reh, T., Glass, I., Neitz, J., Taylor, J., & Johnston Jr, R.J. (2024) Retinoic acid signaling regulates spatiotemporal specification of human green and red cones. PLoS Biology, 22, e3002464.

Urban, E. A., Chernoff, C., Layng, K. V., Han, J., Anderson, C., Konzman, D., & Johnston Jr, R. J. (2023). Activating and repressing gene expression between chromosomes during stochastic fate specification. Cell Reports, 42(1), 111910.

Johnston Jr, R. J. (2022). Beautiful (Re) Views of Visual System Development. Developmental biology, S0012-1606.

Hagen, J. F., Roberts, N., & Johnston Jr, R. J. (2022). The evolutionary history and spectral tuning of vertebrate visual opsins. Developmental Biology.

Roberts, N. S., Hagen, J., & Johnston Jr, R. J. (2022). The diversity of invertebrate visual opsins spanning Protostomia, Deuterostomia, and Cnidaria. Developmental Biology.

Voortman, L., Anderson, C., Urban, E., Yuan, R., Tran, S., Neuhaus-Follini, A., ... & Johnston Jr, R. J. (2022). Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Developmental Cell.

Hussey, K. A., Hadyniak, S. E., & Johnston, R. J., Jr (2022). Patterning and Development of Photoreceptors in the Human Retina. Frontiers in cell and developmental biology, 10, 878350. https://doi.org/10.3389/fcell.2022.878350

Voortman, L., & Johnston Jr, R. J. (2022). Transcriptional repression in stochastic gene expression, patterning, and cell fate specification. Developmental biology, 481, 129-138.

Guy, B., Zhang, J. S., Duncan, L. H., & Johnston Jr, R. J. (2021). Human neural organoids: Models for developmental neurobiology and disease. Developmental Biology.

McNerney, C., & Johnston Jr, R. J. (2021). Thyroid hormone signaling specifies cone photoreceptor subtypes during eye development: Insights from model organisms and human stem cell-derived retinal organoids. Vitamins and Hormones, 116, 51-90.

Miller, A. C., Urban, E., Lyons, E. L., Herman, T. G., & Johnston Jr, R. J. (2020). Interdependent regulation of stereotyped and stochastic photoreceptor fates in the fly eye. Developmental Biology.

Eldred KC, Avelis C, Johnston RJ Jr, Roberts E (2020) Modeling binary and graded cone cell fate patterning in the mouse retina. PLOS Computational Biology 16(3): e1007691. https://doi.org/10.1371/journal.pcbi.1007691

Viets, K., Sauria, M. E., Chernoff, C., Viales, R. R., Echterling, M., Anderson, C., ... & Johnston Jr, R. J. (2019). Characterization of button loci that promote homologous chromosome pairing and cell-type-specific interchromosomal gene regulation. Developmental cell, 51(3), 341-356.

Urban, E.A., and Johnston, R.J., Jr. (2018) Buffering and amplifying transcriptional noise during cell fate specification. Front Genet, doi: 10.3389/fgene.2018.00591

Eldred, K.C., Hadyniak, S.E., Hussey, K.A., Brenerman, B., Zhang, P., Chamling, X., Sluch, V.M., Welsbie, D.S., Hattar, S., Taylor, J., Wahlin, K., Zack, D.J., and Johnston, R.J., Jr. (2018) Thyroid hormone signaling specifies cone subtypes in human retinal organoids. Science, 362, 6411.

Datta, R.R., Ling. J, Ren, X., Xu, Z., Yucel, G., Yu, D., Moore, J., Baker, I., Kurland, J., Bulyk, M.L., Bishop, T., Struffi, P., Levina, R., Johnston, R., and Small, SJ. (2018) A Feed-forward Relay between Bicoid and Orthodenticle Regulates the Timing of Embryonic Patterning in Drosophila.Genes Dev, 32, 723-736.

Duan, H., de Navas, L.F., Hu, F., Kailiang, S., Mavromatakis, Y.E., Viets., K., Zhou C., Kavaler, J., Johnston, R.J., Tomlinson, A., and Lai, E.C. (2018) The mir-279/996 cluster represses receptor tyrosine kinase signaling to determine cell fates in the Drosophila eye. Development, 145, 7.

Anderson, C., Reiss, I., Zhou, C., Cho, A., Siddiqi, H., Morman, B., Aviles, C.M., Deford, P., Bergland, A., Roberts, E., Taylor, J., Vasiliauskas, D., and Johnston, R.J., Jr. (2017) Natural variation in binding site affinity controls stochastic gene expression and color perception. eLife, 6, e29593.

Yan, J., Anderson, C., Viets, K., Tran, S., Goldberg, G., Small, S., and Johnston, R.J., Jr. (2017) Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies. Development, 144, 844-855.

Viets, K.*, Eldred, K.C.*, and Johnston, R.J., (2016) Mechanisms of photoreceptor patterning in vertebrates and invertebrates.Trends Genet, 32, 638-659. * indicates equal contribution

Jukam, D., Viets, K., Anderson, C., Zhou, C., DeFord, P., Yan, J., Cao, J., and Johnston, R.J., Jr. (2016) The insulator protein BEAF-32 is required for Hippo pathway activity in the terminal differentiation of neuronal subtypes. Development, 143, 2389-2397.

Johnston, R.J., Jr., and Desplan, C. (2014) Interchromosomal communication coordinates intrinsically stochastic expression between alleles.Science, 343, 661-665.

Cochella, L., Tursun, B., Hsieh, Y.W., Galindo, S., Johnston, R.J., Chuang, C.F., and Hobert, O. (2014) Two distinct types of neuronal asymmetries are controlled by the Caenorhabditis elegans zinc finger transcription factor die-1. Genes Dev, 28, 34-43

Hsiao, H.Y., Jukam, D., Johnston, R., and Desplan, C. (2013) The neuronal transcription factor erect wing regulates specification and maintenance of Drosophila R8 photoreceptor subtypes. Dev Biol, 381, 482s-490.

Johnston, R.J., Jr. (2013) Lessons about terminal differentiation from the specification of color-detecting photoreceptors in the Drosophila retina. Ann N Y Acad Sci, 1293, 33-44.

Thanawala, S.U., Rister, J., Goldberg, G.W., Zuskov, A., Olesnicky, E.C., Flowers, J.M., Jukam, D., Purugganan, M.D., Gavis, E.R., Desplan, C., and Johnston, R.J., Jr. (2013) Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina. Dev Cell, 25, 93-105.

Hsiao H.Y., Johnston, R.J., Jukam, D., Vasiliauskas, D., Desplan, C., and Rister, J. (2012) Dissection and Immunohistochemistry of Larval, Pupal and Adult Drosophila Retinas. J Vis Exp, 69, e4347.

Sood, P., Johnston, R.J., Jr., and Kussell, E. (2012) Stochastic de-repression of Rhodopsins in single photoreceptors of the fly retina. PLoS Comput Biol, 8, e1002357.

Vasiliauskas, D., Mazzoni, E.O, Sprecher, S.G., Brodetskiy, K., Johnston R.J., Jr., Lidder, P., Vogt, N., Celik, A., and Desplan, C. (2011) Feedback from rhodopsin controls rhodopsin exclusion in Drosophila photoreceptors. Nature, 479, 108-112.

Johnston, R.J., Jr.*, Otake, Y.*, Sood, P., Vogt, N., Behnia, R., Vasiliauskas, D., McDonald, E., Xie, B., Koenig, S., Wolf, R., Cook, T., Gebelein, B., Kussell, E., Nakagoshi, H., and Desplan, C. (2011) Interlocked feedforward loops control cell-type-specific Rhodopsin expression in the Drosophila eye. Cell, 145, 956-968. * indicates equal contribution

Johnston, R.J., Jr., and Desplan, C. (2010) Stochastic mechanisms of cell fate specification that yield random or robust outcomes. Annu Rev Cell Dev Biol, 26, 689-719.

Johnston, R.J., Jr., and Desplan, C. (2010) A penetrating look at stochasticity in development.Cell, 140, 610-612.

Vasiliauskas, D., Johnston, R., and Desplan, C. (2009) Maintaining a stochastic neuronal cell fate decision.Genes Dev, 23, 385-390.

Johnston, R.J., Jr., and Desplan, C. (2008) Stochastic neuronal cell fate choices.Curr Opin Neurobiol, 18, 20-27.

Mazzoni, E.O., Celik, A., Wernet, M.F., Vasiliauskas, D., Johnston, R.J., Cook, T.A., Pichaud, F., and Desplan, C. (2008) Iroquois complex genes induce co-expression of rhodopsins in Drosophila. PLoS Biol, 6, e97.

Sarin, S., O’Meara, M.M., Flowers, E.B., Antonio, C., Poole, R.J., Didiano, D., Johnston R.J., Jr., Chang, S, Narula, S., and Hobert, O. (2007) Genetic screens for Caenorhabditis elegans mutants defective in left/right asymmetric neuronal fate specification.Genetics, 176, 2109-2130.

Johnston, R.J., Jr., Copeland, J.W., Fasnacht, M., Etchberger, J.F., Liu, J., Honig, B., and Hobert, O. (2006) An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development, 133, 3317-3328.

Johnston, R.J., Jr., and Hobert, O. (2005) A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA. Development, 132, 5451-5460.

Johnston, R.J., Jr., Chang, S., Etchberger, J.F., Ortiz, C.O., and Hobert, O. (2005) MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl Acad Sci USA, 102, 12449-12454.

Chang, S., Johnston, R.J., Jr., Frokjaer-Jensen, C., Lockery, S., and Hobert, O. (2004) MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature, 430, 785-789.

Johnston, R.J., and Hobert, O. (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature, 426, 845-849.

Chang, S.*, Johnston, R.J., Jr.*, and Hobert, O (2003) A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans. Genes Dev, 17, 2123-2137. * indicates equal contribution

Hobert, O., Johnston, R.J., Jr., and Chang, S. (2002) Left-right asymmetry in the nervous system: the Caenorhabditis elegans model. Nat Rev Neurosci, 3, 629-640.

Melia, T.J., Weber, T., McNew, J.A., Fisher, L.E., Johnston, R.J., Parlati, F., Mahal, L.K., Sollner, T.H., and Rothman, J.E. (2002) Regulation of membrane fusion by the membrane-proximal coil of the t-SNARE during zippering of SNAREpins.J Cell Biol, 158, 929-940.

McNew, J.A., Parlati, F., Fukuda, R., Johnston, R.J., Paz, K., Paumet, F., Sollner, T.H., and Rothman, J.E. (2000) Compartmental specificity of cellular membrane fusion encoded in SNARE proteins.Nature, 407, 153-159.

McNew, J.A., Weber, T., Parlati, F., Johnston, R.J., Melia, T.J., Sollner, T.H., and Rothman, J.E. (2000)
Close is not enough: SNARE-dependent membrane fusion requires an active mechanism that transduces force to membrane anchors. J Cell Biol, 150, 105-117.

Weber, T., Parlati, F., McNew, J.A., Johnston, R.J., Westermann, B., Sollner, T.H., and Rothman, J.E. (2000)
SNAREpins are functionally resistant to disruption by NSF and alphaSNAP. J Cell Biol, 149, 1063-1072.