Lloyd lab at the University of Western Australia

LL: Lloyd Lab with nucleic acid symbol: Genome Read & Genome Re-write

The Lloyd Lab is focused on understanding life at the molecular level, with a focus on reading and re-writing the genome, often of plants. Here we work on synthetic gene circuits, synthetic genomics, natural and synthetic epigenomics, and natural transcriptomics (focus on splicing and RNA decay).

Current lab members:

Lab alumni

Publications:

See Google Scholar

* Join first-author        † Corresponding author

Nieuwenhuyzen M, Lloyd, J. P. B.† (2026) Silencing the noise with gene body methylation. Trends in Genetics doi:10.1016/j.tig.2026.04.002

Fountain, L.L., Gilliham, M., Amitrano, C., Arouna, N., Barker, R.J., Böhmer, M., Braun, M., Brereton, N.J.B., Brocato, R.L., Bunchek, J.M., Canaday, E.L.J., Caplin, N., Castaño, P., Chamberlain, C., Decourteix, M., Del Bianco, M., De Micco, V., Doherty, C.J., Franke, M.F., Fuentes, S., Gilroy, S., Harrison, L., Hasenstein, K.H., Hauslage, J., Herranz, R., Iyer-Pascuzzi, A., Izuma, D.S., Junya, K., Kiss, J.Z., Legué, V., Lloyd, J.P.B., Maffei, M.E., Massa, G.D., Meyers, A.D., Perera, I.Y., Poulet, L., Roychoudry, S., Sena, G., Shippen, D.E., Stoochnoff, J., Takahashi, H., Wyatt, S.E. and Blancaflor, E.B. (2026) Expanding frontiers: harnessing plant biology for space exploration and planetary sustainability. New Phytologist doi:10.1111/nph.70662

Gong, P., Khan, A., Ly, F., Zhu, J.Y., Herring, G., Jadhav, H., Pflueger, C., Lloyd, J.P.B. †, Lister, R. (2025) CREation of an expanded plant memory gene circuit toolkit. bioRxiv 2025.10.28.684748

Bagherian, M., Harris, G., Sathishkumar, P., Lloyd, J.P.B. † (2025) Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification. Genes 16, 1297. doi:10.3390/genes16111297

Lloyd, J. P. B.* †, Khan, M and Lister, R (2025) The Switch-Liker’s Guide to Plant Synthetic Gene Circuits. The Plant Journal 121, e70090. doi:10.1111/tpj.70090

Khan, M.A., Herring, G., Zhu, J.Y., Oliva, M., Fourie, E., Johnston, B., Zhang, Z., Potter, J., Pineda, L., Pflueger, J., Swain, T., Pflueger, C., Lloyd, J.P.B., Secco, D., Small, I., Kidd, B.N., Lister, R. (2025) CRISPRi-based circuits to control gene expression in plants. Nature Biotechnology 43, 416–430. doi: 10.1038/s41587-024-02236-w

Cahn, J.*, Lloyd, J.P.B.*, Karemaker, I.D., Jansen, P.W.T.C., Pflueger, J., Duncan, O., Petereit, J., Bogdanovic, O., Millar, A.H., Vermeulen, M., & Lister, R. (2024) Characterization of DNA methylation reader proteins of Arabidopsis thaliana. Genome Research 34, 2229-2243. doi:10.1101/gr.279379.124

Roychoudhry S., Sageman-Furnas K., Wolverton C., Grones P., Tan S., Molnár G., De Angelis M., Goodman H. L., Capstaff N., Lloyd J. P. B., Mullen J., Hangarter R., Friml J., Kepinski S. (2023) Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants 9, 1500–1513. doi:10.1038/s41477-023-01478-x

Causier B., McKay M., Hopes T., Lloyd, J., Wang D., Harrison, J. C., Davies, B. (2023) The TOPLESS corepressor regulates developmental switches in the bryophyte Physcomitrium patens that were critical for plant terrestrialisation. The Plant Journal 115, 1331-1344. doi:10.1111/tpj.16322

Lloyd J.P.B., Ly F., Gong G., Pfleuger J., Swain T., Pfleuger C., Khan M.A., Fourie E., Kidd B., Lister R. (2022) Synthetic memory circuits for stable cell reprogramming in plants. Nature Biotechnology 40, 1862–1872. doi:10.1038/s41587-022-01383-2

Lloyd, J. P. B. and Lister, R (2022) Epigenome plasticity in plants. Nature Reviews Genetics 23, 55–68. doi:10.1038/s41576-021-00407-y

French, C.E., Gang, W., Lloyd, J.P.B., Hu Z., Brooks A.N., Brenner, S.E. (2020) Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential. bioRxiv 2020.07.01.183327

Desai A., Hu Z., French, C.E., Lloyd, J.P.B., Brenner, S.E. (2020) Networks of Splice Factor Regulation by Unproductive Splicing Coupled With Nonsense Mediated mRNA Decay. bioRxiv 2020.05.20.107375

Lloyd, J.P.B., French, C.E. and Brenner, S.E. (2020) Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay. bioRxiv 2020.03.08.981811

Harris, K.D., Lloyd, J.P.B., Domb K., Zilberman, D., Zemach, A. (2019) DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics & Chromatin 12, 62. doi:10.1186/s13072-019-0307-4

Lloyd, J.P.B.* †, Lang, D.*, Zimmer, A., Causier, B., Reski, R., Davies B. (2018) The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Research 46, 5822–5836. doi:10.1093/nar/gky225

Lloyd, J. P. B.† (2018) The evolution and diversity of the nonsense-mediated mRNA decay pathway [version 2; referees: 4 approved]. F1000Research 7, 1299. doi:10.12688/f1000research.15872.2

Paudyal, R., Roychoudhry, S., Lloyd, J.P.B. (2017) Functions and Remodelling of Plant Peroxisomes. eLS doi:10.1002/9780470015902.a0001677.pub3

Causier B., Li Z., De Smet R., Lloyd, J.P.B., Van de Peer, Y., Davies, B. (2017) Conservation of nonsense-mediated mRNA decay complex components throughout eukaryotic evolution. Scientific Reports 7, 16692. doi:10.1038/s41598-017-16942-w

Zhang, Z., Liu, G., Zhou, Y., Lloyd, J.P.B., McCauley, D.W., Li, W., Gu, X., Su, Z. (2015) Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates. bioRxiv 033233

Lloyd, J.P.B. and Davies, B. (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. The Plant Journal 76, 800–810. doi:10.1111/tpj.12329

Causier B., Lloyd J., Stevens L., Davies B. (2012) TOPLESS co-repressor interactions and their evolutionary conservation in plants. Plant Signalling and Behavior 7, 325–328. doi:10.4161/psb.19283