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2019

Journal Article

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

2019

Journal Article

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

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

2019

Journal Article

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

Neuroepigenetic mechanisms underlying fear extinction: emerging concepts

2019

Journal Article

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

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

2018

Journal Article

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

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

2018

Journal Article

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

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

2018

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

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

2017

Journal Article

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

Paternal environmental enrichment transgenerationally alters affective behavioral and neuroendocrine phenotypes

2017

Journal Article

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

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

2017

Journal Article

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

Cell-selective bioorthogonal metabolic labeling of RNA

2017

Book Chapter

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

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

2017

Journal Article

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

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