The University of Queensland

DNA modifications in the brain: neuroepigenetic regulation of gene expression

Timothy W. Bredy ed. (2017). DNA modifications in the brain: neuroepigenetic regulation of gene expression. London, United Kingdom: Elsevier. doi: 10.1016/B978-0-12-801596-4.00001-0

What does the future hold for the study of nucleic acid modifications in the brain?

Marshall, P. R. and Bredy, T. W. (2017). What does the future hold for the study of nucleic acid modifications in the brain?. DNA modifications in the brain: Neuroepigenetic Regulation of Gene Expression. (pp. 149-159) edited by Timothy W. Bredy. London, United Kingdom: Academic Press. doi: 10.1016/B978-0-12-801596-4.00009-5

Developmental origins of neurobiological vulnerability for PTSD.

Bagot, Rose, Parent, Carine, Bredy, Timothy W., Zhang Tieyuan, Grattan, Alain and Meaney, Michael J. (2007). Developmental origins of neurobiological vulnerability for PTSD.. Understanding trauma : Integrating biological, clinical, and cultural perspectives. (pp. 98-117) edited by Laurence J. Kirmayer, Robert Lemelson and Mark Barad. Cambridge, England, U.K.: Cambridge University Press. doi: 10.1017/CBO9780511500008.009

DNA G-quadruplex is a transcriptional control device that regulates memory

Marshall, Paul R., Davies, Joshua, Zhao, Qiongyi, Liau, Wei-Siang, Lee, Yujin, Basic, Dean, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Musgrove, Mason, Kielar, Marcin, Brueckner, Arie Maeve, Gong, Hao, Ren, Haobin, Walsh, Alexander, Kaczmarczyk, Lech, Jackson, Walker S., Chen, Alon, Spitale, Robert C. and Bredy, Timothy W. (2024). DNA G-quadruplex is a transcriptional control device that regulates memory. The Journal of Neuroscience, e0093232024. doi: 10.1523/jneurosci.0093-23.2024

Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non‐coding <scp>RNAs</scp> spanning learning, memory and adaptive immunity

Musgrove, Mason R. B., Mikhaylova, Marina and Bredy, Timothy W. (2024). Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: Non‐coding RNAs spanning learning, memory and adaptive immunity. Journal of Neurochemistry. doi: 10.1111/jnc.16071

Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory

Chen, Claire C, Han, Joseph, Chinn, Carlene A, Rounds, Jacob S, Li, Xiang, Nikan, Mehran, Myszka, Marie, Tong, Liqi, Passalacqua, Luiz F M, Bredy, Timothy, Wood, Marcelo A and Luptak, Andrej (2024). Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory. eLife, 13. doi: 10.7554/elife.90116

Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours

Hoffmann, L. B., Li, B., Wei, W., Zhao, Q., Leighton, L. J., Bredy, T. W., Pang, T. Y. and Hannan, A. J. (2023). Chronically high stress hormone levels dysregulate sperm long noncoding RNAs and their embryonic microinjection alters development and affective behaviours. Molecular Psychiatry, 1-12. doi: 10.1038/s41380-023-02350-2

Huntingtin decreases susceptibility to a spontaneous seizure disorder in FVN/B mice

Van Raamsdonk, Jeremy M., Al-Shekaili, Hilal H., Wagner, Laura, Bredy, Tim W., Chan, Laura, Pearson, Jacqueline, Schwab, Claudia, Murphy, Zoe, Devon, Rebecca S., Lu, Ge, Kobor, Michael S., Hayden, Michael R. and Leavitt, Blair R. (2023). Huntingtin decreases susceptibility to a spontaneous seizure disorder in FVN/B mice. Aging and Disease, 14 (6), 2249-2266. doi: 10.14336/AD.2023.0423

Fear extinction is regulated by the activity of long noncoding RNAs at the synapse

Liau, Wei-Siang, Zhao, Qiongyi, Bademosi, Adekunle, Gormal, Rachel S., Gong, Hao, Marshall, Paul R., Periyakaruppiah, Ambika, Madugalle, Sachithrani U., Zajaczkowski, Esmi L., Leighton, Laura J., Ren, Haobin, Musgrove, Mason, Davies, Joshua, Rauch, Simone, He, Chuan, Dickinson, Bryan C., Li, Xiang, Wei, Wei, Meunier, Frédéric A., Fernández-Moya, Sandra M., Kiebler, Michael A., Srinivasan, Balakumar, Banerjee, Sourav, Clark, Michael, Spitale, Robert C. and Bredy, Timothy W. (2023). Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nature Communications, 14 (1) 7616, 1-16. doi: 10.1038/s41467-023-43535-1

Synapse-enriched m⁶A-modified Malat1 interacts with the novel m⁶A reader, DPYSL2, and is required for fear-extinction memory

Madugalle, Sachithrani U., Liau, Wei-Siang, Zhao, Qiongyi, Li, Xiang, Gong, Hao, Marshall, Paul R., Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Ren, Haobin, Musgrove, Mason R. B., Davies, Joshua W. A., Kim, Gwangmin, Rauch, Simone, He, Chuan, Dickinson, Bryan C., Fulopova, Barbora, Fletcher, Lee N., Williams, Stephen R., Spitale, Robert C. and Bredy, Timothy W. (2023). Synapse-enriched m6A-modified Malat1 interacts with the novel m6A reader, DPYSL2, and is required for fear-extinction memory. The Journal of Neuroscience, 43 (43), 7084-7100. doi: 10.1523/jneurosci.0943-23.2023

Localised Cdr1as activity is required for fear extinction memory

Lau Zajaczkowski, Esmi, Zhao, Qiongyi, Liau, Wei-Siang, Gong, Hao, Madugalle, Sachithrani Umanda, Periyakaruppiah, Ambika, Leighton, Laura Jane, Musgrove, Mason, Ren, Haobin, Davies, Joshua, Marshall, Paul Robert and Bredy, Timothy William (2023). Localised Cdr1as activity is required for fear extinction memory. Neurobiology of Learning and Memory, 203 107777, 107777. doi: 10.1016/j.nlm.2023.107777

ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

Wei, Wei, Zhao, Qiongyi, Wang, Ziqi, Liau, Wei-Siang, Basic, Dean, Ren, Haobin, Marshall, Paul R., Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Musgrove, Mason, Periyakaruppiah, Ambika, Shi, Jichun, Zhang, Jianjian, Mattick, John S., Mercer, Timothy R., Spitale, Robert C., Li, Xiang and Bredy, Timothy W. (2022). ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Reports, 38 (12) 110546, 110546. doi: 10.1016/j.celrep.2022.110546

From circuits to chromatin: the emerging role of epigenetics in mental health

Mews, Philipp, Calipari, Erin S., Day, Jeremy, Lobo, Mary Kay, Bredy, Timothy and Abel, Ted (2021). From circuits to chromatin: the emerging role of epigenetics in mental health. The Journal of Neuroscience, 41 (5), 873-882. doi: 10.1523/jneurosci.1649-20.2020

On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain

Liau, Wei-Siang, Samaddar, Sarbani, Banerjee, Sourav and Bredy, Timothy W. (2021). On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biology, 18 (7), 1-12. doi: 10.1080/15476286.2020.1868165

RNA N6-methyladenosine and the regulation of RNA localization and function in the brain

Madugalle, Sachithrani U., Meyer, Kate, Wang, Dan Ohtan and Bredy, Timothy W. (2020). RNA N6-methyladenosine and the regulation of RNA localization and function in the brain. Trends in Neurosciences, 43 (12), 1011-1023. doi: 10.1016/j.tins.2020.09.005

Circular RNAs in the brain: a possible role in memory?

Zajaczkowski, Esmi L. and Bredy, Timothy W. (2020). Circular RNAs in the brain: a possible role in memory?. The Neuroscientist, 27 (5), 1073858420963028-486. doi: 10.1177/1073858420963028

Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesis

Chen, Min, Zhao, Qiong-Yi, Edson, Janette, Zhang, Zong Hong, Li, Xiang, Wei, Wei, Bredy, Timothy and Reutens, David C. (2020). Genome-wide microRNA profiling in brain and blood samples in a mouse model of epileptogenesis. Epilepsy Research, 166 106400, 106400. doi: 10.1016/j.eplepsyres.2020.106400

Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex

Dick, Alec L. W., Zhao, Qiongyi, Crossin, Rose, Baker-Andresen, Danay, Li, Xiang, Edson, Janette, Roeh, Simone, Marshall, Victoria, Bredy, Timothy W., Lawrence, Andrew J. and Duncan, Jhodie R. (2020). Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex. Addiction Biology, 26 (3) e12937, e12937. doi: 10.1111/adb.12937

Publisher Correction: Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

Marshall, Paul R., Zhao, Qiongyi, Li, Xiang, Wei, Wei, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Basic, Dean, Wang, Ziqi, Yin, Jiayu, Liau, Wei-Siang, Gupte, Ankita, Walkley, Carl R. and Bredy, Timothy W. (2020). Publisher Correction: Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nature Neuroscience, 23 (8), 1034-1034. doi: 10.1038/s41593-020-0669-8

Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction

Marshall, Paul R., Zhao, Qiongyi, Li, Xiang, Wei, Wei, Periyakaruppiah, Ambika, Zajaczkowski, Esmi L., Leighton, Laura J., Madugalle, Sachithrani U., Basic, Dean, Wang, Ziqi, Yin, Jiayu, Liau, Wei-Siang, Gupte, Ankita, Walkley, Carl R. and Bredy, Timothy W. (2020). Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction. Nature Neuroscience, 23 (6), 718-729. doi: 10.1038/s41593-020-0627-5

Disrupting the hippocampal Piwi pathway enhances contextual fear memory in mice

Leighton, Laura J., Wei, Wei, Marshall, Paul R., Ratnu, Vikram Singh, Li, Xiang, Zajaczkowski, Esmi L., Spadaro, Paola A., Khandelwal, Nitin, Kumar, Arvind and Bredy, Timothy W. (2019). Disrupting the hippocampal Piwi pathway enhances contextual fear memory in mice. Neurobiology of Learning and Memory, 161, 202-209. doi: 10.1016/j.nlm.2019.04.002

The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction

Li, Xiang, Zhao, Qiongyi, Wei, Wei, Lin, Quan, Magnan, Christophe, Emami, Michael R., Wearick-Silva, Luis E., Viola, Thiago W., Marshall, Paul R., Yin, Jiayu, Madugalle, Sachithrani U., Wang, Ziqi, Nainar, Sarah, Vågbø, Cathrine Broberg, Leighton, Laura J., Zajaczkowski, Esmi L., Ke, Ke, Grassi-Oliveira, Rodrigo, Bjørås, Magnar, Baldi, Pierre F., Spitale, Robert C. and Bredy, Timothy W. (2019). The DNA modification N6-methyl-2’-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction. Nature Neuroscience, 22 (4), 534-544. doi: 10.1038/s41593-019-0339-x

The DNA repair-associated protein gadd45γ regulates the temporal coding of immediate early gene expression within the prelimbic prefrontal cortex and is required for the consolidation of associative fear memory

Li, Xiang, Marshall, Paul R., Leighton, Laura J., Zajaczkowski, Esmi L., Wang, Ziqi, Madugalle, Sachithrani U., Yin, Jiayu, Bredy, Timothy W. and Wei, Wei (2019). The DNA repair-associated protein gadd45γ regulates the temporal coding of immediate early gene expression within the prelimbic prefrontal cortex and is required for the consolidation of associative fear memory. The Journal of Neuroscience, 39 (6), 970-983. doi: 10.1523/JNEUROSCI.2024-18.2018

Neuroepigenetic mechanisms underlying fear extinction: emerging concepts

Marshall, Paul R. and Bredy, Timothy W. (2019). Neuroepigenetic mechanisms underlying fear extinction: emerging concepts. Psychopharmacology, 236 (1), 133-142. doi: 10.1007/s00213-018-5084-4

Postnatal impoverished housing impairs adolescent risk-assessment and increases risk-taking: a sex-specific effect associated with histone epigenetic regulation of Crfr1 in the medial prefrontal cortex

Viola, Thiago Wendt, Wearick-Silva, Luis Eduardo, Creutzberg, Kerstin C., Kestering-Ferreira, Érika, Orso, Rodrigo, Centeno-Silva, Anderson, Albrechet-Souza, Lucas, Marshall, Paul R., Li, Xiang, Bredy, Timothy W., Riva, Marco A. and Grassi-Oliveira, Rodrigo (2019). Postnatal impoverished housing impairs adolescent risk-assessment and increases risk-taking: a sex-specific effect associated with histone epigenetic regulation of Crfr1 in the medial prefrontal cortex. Psychoneuroendocrinology, 99, 8-19. doi: 10.1016/j.psyneuen.2018.08.032

Prolonged-access to cocaine induces distinct Homer2 DNA methylation, hydroxymethylation, and transcriptional profiles in the dorsomedial prefrontal cortex of Male Sprague-Dawley rats

Ploense, Kyle L., Li, Xiang, Baker-Andresen, Danay, Carr, Amanda E., Woodward, Nick, Bagley, Jared, Szumlinski, Karen K., Bredy, Timothy W. and Kippin, Tod E. (2018). Prolonged-access to cocaine induces distinct Homer2 DNA methylation, hydroxymethylation, and transcriptional profiles in the dorsomedial prefrontal cortex of Male Sprague-Dawley rats. Neuropharmacology, 143, 299-305. doi: 10.1016/j.neuropharm.2018.09.029

Bioorthogonal metabolic labeling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling

Zajaczkowski, Esmi L., Zhao, Qiong-Yi, Zhang, Zong Hong, Li, Xiang, Wei, Wei, Marshall, Paul R., Leighton, Laura J., Nainar, Sarah, Feng, Chao, Spitale, Robert C. and Bredy, Timothy W. (2018). Bioorthogonal metabolic labeling of nascent RNA in neurons improves the sensitivity of transcriptome-wide profiling. ACS Chemical Neuroscience, 9 (7), 1858-1865. doi: 10.1021/acschemneuro.8b00197

Functional interplay between small non-coding RNAs and RNA modification in the brain

Leighton, Laura J. and Bredy, Timothy W. (2018). Functional interplay between small non-coding RNAs and RNA modification in the brain. Non-Coding RNA, 4 (2) 15, 15. doi: 10.3390/ncrna4020015

A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons

Leighton, Laura J., Zhao, Qiongyi, Li, Xiang, Dai, Chuanyang, Marshall, Paul R., Liu, Sha, Wang, Yi, Zajaczkowski, Esmi L., Khandelwal, Nitin, Kumar, Arvind, Bredy, Timothy W. and Wei, Wei (2017). A Functional Role for the Epigenetic Regulator ING1 in Activity-induced Gene Expression in Primary Cortical Neurons. Neuroscience, 369, 248-260. doi: 10.1016/j.neuroscience.2017.11.018

Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics

Leighton, L. J., Ke, K., Zajaczkowski, E. L., Edmunds, J., Spitale, R. C. and Bredy, T. W. (2017). Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics. Genes, Brain, and Behavior, 17 (3) e12426, e12426. doi: 10.1111/gbb.12426

MicroRNA-mediated disruption of dendritogenesis during a critical period of development influences cognitive capacity later in life

Lin, Quan, Ponnusamy, Ravikumar, Widagdo, Jocelyn, Choi, Jung A., Ge, Weihong, Probst, Christine, Buckley, Tyler, Lou, Mimi, Bredy, Timothy W., Fanselow, Michael S., Ye, Keqiang and Sun, Yi E. (2017). MicroRNA-mediated disruption of dendritogenesis during a critical period of development influences cognitive capacity later in life. Proceedings from the National Academy of Sciences of the United States of America, 114 (34), 9188-9193. doi: 10.1073/pnas.1706069114

Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats

Castino, M. R., Baker-Andresen, D., Ratnu, V. S., Shevchenko, G., Morris, K. V., Bredy, T. W., Youngson, N. A. and Clemens, K. J. (2017). Persistent histone modifications at the BDNF and Cdk-5 promoters following extinction of nicotine-seeking in rats. Genes, Brain and Behavior, 17 (2), 98-106. doi: 10.1111/gbb.12421

MotifMap-RNA: a genome-wide map of RBP binding sites

Liu, Yu, Sun, Sha, Bredy, Timothy, Wood, Marcelo, Spitale, Robert C. and Baldi, Pierre (2017). MotifMap-RNA: a genome-wide map of RBP binding sites. Bioinformatics, 33 (13), 2029-2031. doi: 10.1093/bioinformatics/btx087

MicroRNA-mediated rescue of fear extinction memory by miR-144-3p in extinction-impaired mice

Murphy, Conor P., Li, Xiang, Maurer, Verena, Oberhauser, Michael, Gstir, Ronald, Wearick-Silva, Luis Eduardo, Viola, Thiago Wendt, Schafferer, Simon, Grassi-Oliverira, Rodrigo, Whittle, Nigel, Huttenhofer, Alexander, Bredy, Timothy W. and Singewald, Nicolas (2017). MicroRNA-mediated rescue of fear extinction memory by miR-144-3p in extinction-impaired mice. Biological Psychiatry, 81 (12), 979-989. doi: 10.1016/j.biopsych.2016.12.021

Maternal separation induces hippocampal changes in cadherin-1 (CDH-1) mRNA and recognition memory impairment in adolescent mice

de Azeredo, Lucas Araujo, Wearick-Silva, Luis Eduardo, Viola, Thiago Wendt, Tractenberg, Saulo Gantes, Centeno-Silva, Anderson, Orso, Rodrigo, Schroder, Nadja, Bredy, Timothy William and Grassi-Oliveira, Rodrigo (2017). Maternal separation induces hippocampal changes in cadherin-1 (CDH-1) mRNA and recognition memory impairment in adolescent mice. Neurobiology of Learning and Memory, 141, 157-167. doi: 10.1016/j.nlm.2017.04.006

Transgenerational paternal transmission of acquired traits: stress-induced modification of the sperm regulatory transcriptome and offspring phenotypes

Pang, Terence Y. C., Short, Annabel K., Bredy, Timothy W. and Hannan, Anthony J. (2017). Transgenerational paternal transmission of acquired traits: stress-induced modification of the sperm regulatory transcriptome and offspring phenotypes. Current Opinion in Behavioral Sciences, 14, 140-147. doi: 10.1016/j.cobeha.2017.02.007

Paternal environmental enrichment transgenerationally alters affective behavioral and neuroendocrine phenotypes

Yeshurun, Shlomo, Short, Annabel K., Bredy, Timothy W., Pang, Terence Y. and Hannan, Anthony J. (2017). Paternal environmental enrichment transgenerationally alters affective behavioral and neuroendocrine phenotypes. Psychoneuroendocrinology, 77, 225-235. doi: 10.1016/j.psyneuen.2016.11.013

Running during adolescence rescues a maternal separation-induced memory impairment in female mice: Potential role of differential exon-specific BDNF expression

Wearick-Silva, Luis Eduardo, Marshall, Paul, Viola, Thiago Wendt, Centeno-Silva, Anderson, de Azeredo, Lucas Araujo, Orso, Rodrigo, Li, Xiang, Donadio, Marcio V., Bredy, Timothy W. and Grassi-Oliveira, Rodrigo (2017). Running during adolescence rescues a maternal separation-induced memory impairment in female mice: Potential role of differential exon-specific BDNF expression. Developmental Psychobiology, 59 (2), 268-274. doi: 10.1002/dev.21487

Cell-selective bioorthogonal metabolic labeling of RNA

Nguyen, Kim, Fazio, Michael, Kubota, Miles, Nainar, Sarah, Feng, Chao, Li, Xiang, Atwood, Scott X., Bredy, Timothy W. and Spitale, Robert C. (2017). Cell-selective bioorthogonal metabolic labeling of RNA. Journal of the American Chemical Society, 139 (6), 2148-2151. doi: 10.1021/jacs.6b11401

Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain

Ratnu, Vikram S., Emami, Michael R. and Bredy, Timothy W. (2017). Genetic and epigenetic factors underlying sex differences in the regulation of gene expression in the brain. Journal of Neuroscience Research, 95 (1-2), 301-310. doi: 10.1002/jnr.23886

Evolving insights into RNA modifications and their functional diversity in the brain

Nainar, Sarah, Marshall, Paul R., Tyler, Christina R., Spitale, Robert C. and Bredy, Timothy W. (2016). Evolving insights into RNA modifications and their functional diversity in the brain. Nature Neuroscience, 19 (10), 1292-1298. doi: 10.1038/nn.4378

Increased cocaine-induced conditioned place preference during periadolescence in maternally separated male BALB/c mice: the role of cortical BDNF, microRNA-212, and MeCP2

Viola, Thiago Wendt, Wearick-Silva, Luis Eduardo, De Azeredo, Lucas Araujo, Centeno-Silva, Anderson, Murphy, Conor, Marshall, Paul, Li, Xiang, Singewald, Nicolas, Garcia, Frederico, Bredy, Timothy W. and Grassi-Oliveira, Rodrigo (2016). Increased cocaine-induced conditioned place preference during periadolescence in maternally separated male BALB/c mice: the role of cortical BDNF, microRNA-212, and MeCP2. Psychopharmacology, 233 (17), 3279-3288. doi: 10.1007/s00213-016-4373-z

Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory?

Marshall, Paul and Bredy, Timothy W. (2016). Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory?. n p j Science of Learning, 1 (1) 16014, 16014. doi: 10.1038/npjscilearn.2016.14

Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice

Widagdo, Jocelyn, Zhao, Qiong-Yi, Kempen, Marie-Jeanne, Tan, Men Chee, Ratnu, Vikram S., Wei, Wei, Leighton, Laura, Spadaro, Paola A., Edson, Janette, Anggono, Victor and Bredy, Timothy W. (2016). Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice. Journal of Neuroscience, 36 (25), 6771-6777. doi: 10.1523/JNEUROSCI.4053-15.2016

Sex differences in learned fear expression and extinction involve altered gamma oscillations in medial prefrontal cortex

Fenton, Georgina E., Halliday, David M., Mason, Rob, Bredy, Timothy W. and Stevenson, Carl W. (2016). Sex differences in learned fear expression and extinction involve altered gamma oscillations in medial prefrontal cortex. Neurobiology of Learning and Memory, 135, 66-72. doi: 10.1016/j.nlm.2016.06.019

The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action

Alaghband, Yasaman, Bredy, Timothy W. and Wood, Marcelo A. (2016). The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action. Neuroscience Letters, 625, 40-46. doi: 10.1016/j.neulet.2016.01.023

Elevated paternal glucocorticoid exposure alters the small noncoding RNA profile in sperm and modifies anxiety and depressive phenotypes in the offspring

Short, A. K., Fennell, K. A., Perreau, V. M., Fox, A., O'Bryan, M. K., Kim, J. H., Bredy, T. W., Pang, T. Y. and Hannan, A. J. (2016). Elevated paternal glucocorticoid exposure alters the small noncoding RNA profile in sperm and modifies anxiety and depressive phenotypes in the offspring. Translational Psychiatry, 6 (6) e837, e837-e837. doi: 10.1038/tp.2016.109

Synergistic Actions of Ogg1 and Mutyh DNA Glycosylases Modulate Anxiety-like Behavior in Mice

Bjorge, Monica D., Hildrestrand, Gunn A., Scheffler, Katja, Suganthan, Rajikala, Rolseth, Veslemoy, Kusnierczyk, Anna, Rowe, Alexander D., Vagbo, Cathrine B., Vetlesen, Susanne, Eide, Lars, Slupphaug, Geir, Nakabeppu, Yusaku, Bredy, Timothy W., Klungland, Arne and Bjoras, Magnar (2015). Synergistic Actions of Ogg1 and Mutyh DNA Glycosylases Modulate Anxiety-like Behavior in Mice. Cell Reports, 13 (12), 2671-2678. doi: 10.1016/j.celrep.2015.12.001

Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice

Baker-Andresen, Danay, Zhao, Qiongyi, Li, Xiang, Jupp, Bianca, Chesworth, Rose, Lawrence, Andrew J. and Bredy, Timothy (2015). Persistent variations in neuronal DNA methylation following cocaine self-administration and protracted abstinence in mice. Neuroepigenetics, 4, 1-11. doi: 10.1016/j.nepig.2015.10.001

Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice

Spadaro, Paola A., Flavell, Charlotte R., Widagdo, Jocelyn, Ratnu, Vikram S., Troup, Michael, Ragan, Chikako, Mattick, John S. and Bredy, Timothy W. (2015). Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice. Biological Psychiatry, 78 (12), 848-859. doi: 10.1016/j.biopsych.2015.02.004

Activation-induced cytidine deaminase regulates activity-dependent BDNF expression in post-mitotic cortical neurons

Ratnu, Vikram S., Wei, Wei and Bredy, Timothy W. (2014). Activation-induced cytidine deaminase regulates activity-dependent BDNF expression in post-mitotic cortical neurons. European Journal of Neuroscience, 40 (7), 3032-3039. doi: 10.1111/ejn.12678

Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation

Li, X., Baker-Andresen, D., Zhao, Q., Marshall, V. and Bredy, T. W. (2014). Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation. Genes, Brain and Behavior, 13 (7), 721-731. doi: 10.1111/gbb.12150

Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

Li, Xiang, Wei, Wei, Zhao, Qiong-Yi, Widagdo, Jocelyn, Baker-Andresen, Danay, Flavell, Charlotte R., D'Alessio, Ana, Zhang, Yi and Bredy, Timothy W. (2014). Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation. Proceedings of the National Academy of Sciences, 111 (19), 7120-7125. doi: 10.1073/pnas.1318906111

Persistent prelimbic cortex activity contributes to enhanced learned fear expression in females

Fenton, Georgina E., Pollard, Amelia K, Halliday, David M., Mason, Rob, Bredy, Timothy W. and Stevenson, Carl W. (2014). Persistent prelimbic cortex activity contributes to enhanced learned fear expression in females. Learning and Memory, 21 (2), 55-60. doi: 10.1101/lm.033514.113

Mechanisms governing the reactivation-dependent destabilization of memories and their role in extinction

Flavell, Charlotte R., Lambert, Elliot A., Winters, Boyer D. and Bredy, Timothy W. (2013). Mechanisms governing the reactivation-dependent destabilization of memories and their role in extinction. Frontiers in Behavioral Neuroscience, 7 (DEC), 214.1-214.11. doi: 10.3389/fnbeh.2013.00214

Exposure to histone deacetylase inhibitors during Pavlovian conditioning enhances subsequent cue-induced reinstatement of operant behavior

Ploense, Kyle L., Kerstetter, Kerry A., Wade, Matthew A., Woodward, Nicholas C., Maliniak, Dan, Reyes, Michael, Uchizono, Russell S., Bredy, Timothy W. and Kippin, Tod E. (2013). Exposure to histone deacetylase inhibitors during Pavlovian conditioning enhances subsequent cue-induced reinstatement of operant behavior. Behavioural Pharmacology, 24 (3), 164-171. doi: 10.1097/FBP.0b013e32836104ea

Activation of BDNF signaling prevents the return of fear in female mice

Baker-Andresen, Danay, Flavell, Charlotte R., Li, Xiang and Bredy, Timothy W. (2013). Activation of BDNF signaling prevents the return of fear in female mice. Learning & Memory, 20 (5), 237-240. doi: 10.1101/lm.029520.112

The amygdala and medial prefrontal cortex: partners in the fear circuit

Marek, Roger, Strobel, Cornelia, Bredy, Timothy W. and Sah, Pankaj (2013). The amygdala and medial prefrontal cortex: partners in the fear circuit. Journal of Physiology, 591 (10), 2381-2391. doi: 10.1113/jphysiol.2012.248575

Dynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation

Baker-Andresen, Danay, Ratnu, Vikram and Bredy, Timothy (2013). Dynamic DNA methylation: a prime candidate for genomic metaplasticity and behavioral adaptation. Trends In Neurosciences, 36 (1), 3-13. doi: 10.1016/j.tins.2012.09.003

On the potential role of active DNA demethylation in establishing epigenetic states associated with neural plasticity and memory

Li, Xiang, Wei, Wei, Ratnu, Vikram and Bredy, Timothy (2013). On the potential role of active DNA demethylation in establishing epigenetic states associated with neural plasticity and memory. Neurobiology of Learning and Memory, 105, 125-132. doi: 10.1016/j.nlm.2013.06.009

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

Barry, Guy, Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Vikram Ratnu, Nayler, S. P., Nones, K., Hu, J., Timothy Bredy, Nakagawa, S., Rigo, F., Taft, R. J., Cairns, M. J., Blackshaw, S., Wolvetang, E. J. and Mattick, J. S. (2013). The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular Psychiatry, 19 (4), 486-494. doi: 10.1038/mp.2013.45

p300/CBP-associated factor selectively regulates the extinction of conditioned fear

Wei, Wei, Coelho, Carlos M., Li, Xiang, Marek, Roger, Yan, Shanzhi, Anderson, Shawn, Meyers, David, Mukherjee, Chandrani, Sbardella, Gianluca, Castellano, Sabrina, Milite, Ciro, Rotili, Dante, Mai, Antonello, Cole, Philip A., Sah, Pankaj, Kobor, Michael S. and Bredy, Timothy W. (2012). p300/CBP-associated factor selectively regulates the extinction of conditioned fear. Journal of Neuroscience, 32 (35), 11930-11941. doi: 10.1523/JNEUROSCI.0178-12.2012

Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders

Spadaro, Paola A. and Bredy, Timothy W. (2012). Emerging role of non-coding RNA in neural plasticity, cognitive function, and neuropsychiatric disorders. Frontiers in Genetics, 3 (JUL) Article 132, 132.1-132.16. doi: 10.3389/fgene.2012.00132

The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory

Lin, Quan, Wei, Wei, Coelho, Carlos M., Li, Xiang, Baker-Andresen, Dannay, Dudley, Kevin, Ratnu, Vikram S., Boskovic, Zoran, Kobor, Michael S., Sun, Yi E. and Bredy, Timothy W. (2011). The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory. Nature Neuroscience, 14 (9), 1115-1117. doi: 10.1038/nn.2891

MicroRNA regulation of neural plasticity and memory

Bredy, Timothy W., Lin, Quan, Wei, Wei, Baker-Andresen, Danay and Mattick, John S. (2011). MicroRNA regulation of neural plasticity and memory. Neurobiology of Learning and Memory, 96 (1), 89-94. doi: 10.1016/j.nlm.2011.04.004

Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders

Dudley, Kevin J., Li, Xiang, Kobor, Michael S., Kippin, Tod E. and Bredy, Timothy W. (2011). Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders. Neuroscience and Biobehavioral Reviews, 35 (7), 1544-1551. doi: 10.1016/j.neubiorev.2010.12.016

Paradoxical enhancement of fear extinction memory and synaptic plasticity by inhibition of the histone acetyltransferase p300

Marek, Roger, Coelho, Carlos M., Sullivan, Robert K. P., Baker-Andresen, Danay, Li, Xiang, Ratnu, Vikram, Dudley, Kevin J., Meyers, David, Mukherjee, Chandrani, Cole, Philip A., Sah, Pankaj and Bredy, Timothy W. (2011). Paradoxical enhancement of fear extinction memory and synaptic plasticity by inhibition of the histone acetyltransferase p300. Journal of Neuroscience, 31 (20), 7486-7491. doi: 10.1523/JNEUROSCI.0133-11.2011

How the epigenome contributes to the development of psychiatric disorders

Bredy, Timothy W., Sun, Yi E. and Kobor, Michael S. (2010). How the epigenome contributes to the development of psychiatric disorders. Developmental Psychobiology, 52 (4), 331-342. doi: 10.1002/dev.20424

Paternal deprivation during infancy results in dendrite- and time-specific changes of dendritic development and spine formation in the orbitofrontal cortex of the biparental rodent Octodon degus

Helmekea, C., Seidel, K., Poeggel, G., Bredy, Timothy, Abraham, A. and Braun, K. (2009). Paternal deprivation during infancy results in dendrite- and time-specific changes of dendritic development and spine formation in the orbitofrontal cortex of the biparental rodent Octodon degus. Neuroscience, 163 (3), 790-798. doi: 10.1016/j.neuroscience.2009.07.008

Social modulation of associative fear learning by pheromone communication

Bredy, Timothy W. and Barad, Mark (2009). Social modulation of associative fear learning by pheromone communication. Learning and Memory, 16 (1), 12-18. doi: 10.1101/lm.1226009

The histone deacetylase inhibitor valproic acid enhances acquisition, extinction, and reconsolidation of conditioned fear

Timothy, Bredy and Barad, Mark (2008). The histone deacetylase inhibitor valproic acid enhances acquisition, extinction, and reconsolidation of conditioned fear. Learning & Memory, 15 (1), 39-45. doi: 10.1101/lm.801108

Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear

Bredy, Timothy, Wu, Hao, Crego, Cortney, Zellhoefer, Jessica, Sun, Yi E. and Barad, Mark (2007). Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear. Learning & Memory, 14 (4), 268-276. doi: 10.1101/lm.500907

Effect of resource availability on biparental care, and offspring neural and behavioral development in the California mouse (Peromyscus californicus)

Bredy, Timothy W., Brown, Richard E. and Meaney, Michael J. (2007). Effect of resource availability on biparental care, and offspring neural and behavioral development in the California mouse (Peromyscus californicus). European Journal of Neuroscience, 25 (2), 567-575. doi: 10.1111/j.1460-9568.2006.05266.x

Behavioural epigenetics and psychiatric disorders

Bredy, Timothy (2006). Behavioural epigenetics and psychiatric disorders. Medical Hypotheses, 68 (2), 453-453. doi: 10.1016/j.mehy.2006.07.009

Maternal programming of defensive responses through sustained effects on gene expression

Zhang, Tie-Yuan, Bagot, Rose, Parenta, Carine, Nesbitt, Cathy, Bredy, Timothy W., Caldji, Christian, Fish, Eric, Anisman, Hymie, Szyf, Moshe and Meaney, Michael J. (2006). Maternal programming of defensive responses through sustained effects on gene expression. Biological Psychology, 73 (1), 72-89. doi: 10.1016/j.biopsycho.2006.01.009

RNA modifications and memory

Bredy, T. (2019). RNA modifications and memory. ISN-ASN Meeting, Montreal, Canada, 4-8 August 2019. Chichester, West Sussex, United Kingdom: Wiley-Blackwell.

Transcriptional and epigenetic factors underlying the extinction of nicotine-seeking behaviour in the rat

Castino, M., Youngson, N., Baker-Andresen, D., Ratnu, V., Bredy, T. and Clemens, K. (2015). Transcriptional and epigenetic factors underlying the extinction of nicotine-seeking behaviour in the rat. 25th Biennial Meeting of the International-Society-for-Neurochemistry Jointly with the 13th Meeting of the Asian-Pacific-Society-for-Neurochemistry in Conjunction with the 35th Meeting of the Australasian-Neuroscience-Society, Cairns, Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell.

Activity-dependent RNA methylation in learning and memory

Widagdo, J., Zhao, Q. -Y., Anggono, V. and Bredy, T. (2015). Activity-dependent RNA methylation in learning and memory. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13188

Dissociable roles of GADD45A/B in the rat perirhinal cortex and hippocampus for object memory: different forms of dna methylation?

Mitchnick, K., Wei, W., Creighton, S., Kalisch, B., Bredy, T. and Winters, B. (2015). Dissociable roles of GADD45A/B in the rat perirhinal cortex and hippocampus for object memory: different forms of dna methylation?. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13188

Enhancing TRK mediated trophic signalling to augment cognitive processes

Camara, M. Iou, Matusica, D., Qian, L., Bredy, T., Nykjaer, A. and Coulson, E. (2015). Enhancing TRK mediated trophic signalling to augment cognitive processes. 25th Biennial Meeting of the International Society for Neurochemistry jointly with the 13th Meeting of the Asian‐Pacific Society for Neurochemistry in conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD, Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13189

Epitranscriptomic mechanisms of memory stability

Bredy, T., Widagdo, J. and Zhao, Q.-Y. (2015). Epitranscriptomic mechanisms of memory stability. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13185

Exploring the role of histone demethylase, UTX, in mediating sex differences in fear-related learning and memory

Ratnu, V., Li, X., Emami, M., Zhao, Q. -Y. and Bredy, T. (2015). Exploring the role of histone demethylase, UTX, in mediating sex differences in fear-related learning and memory. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, 23-27 August 2015. Chichester, West Sussex, United Kingdom: Wiley-Blackwell Publishing. doi: 10.1111/jnc.13188

Prolonged Access to Cocaine Results in Distinct Epigenetic Changes in the Prefrontal Cortex

Ploense, Kyle, Carr, Amanda, Baker-Andresen, Danay, Li, Xiang, Woodward, Nick, Sun, Yi, Bredy, Timothy and Kippin, Tod (2014). Prolonged Access to Cocaine Results in Distinct Epigenetic Changes in the Prefrontal Cortex. Experimental Biology 2014 Meeting, San Diego CA, United States, 26-30 April 2014. Bethesda, MD United States: Federation of American Societies for Experimental Biology.

Epigenetic programming of stress responses through variations in maternal care

Fish, Eric W., Shahrokh, Dara, Bagot, Rose, Caldji, Christian, Bredy, Timothy W., Szyf, Moshe and Meaney, Michael J. (2004). Epigenetic programming of stress responses through variations in maternal care. Conference on Scientific Approaches to Youth Violence Prevention, New York, United States, 24-26 April 2004. Hoboken, NJ, United States: Wiley-Blackwell Publishing. doi: 10.1196/annals.1330.011