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3. Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

Author

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

Subjects
Neurosciences, Mental Health, Basic Behavioral and Social Science, Brain Disorders, Genetics, Behavioral and Social Science, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Adenosine, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Animals, Cells, Cultured, Conditioning, Classical, Cues, Embryo, Mammalian, Exploratory Behavior, Fear, Gene Expression Profiling, Male, Maze Learning, Memory, Mice, Mice, Inbred C57BL, Mice, Transgenic, Neurons, Prefrontal Cortex, Proteolysis, RNA, Small Interfering, epigenetics, memory, mRNA stability, RNA methylation, synaptic plasticity, transcription, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery
Abstract

UnlabelledThe RNA modification N(6)-methyladenosine (m(6)A) influences mRNA stability and cell-type-specific developmental programming, and is highly abundant in the adult brain. However, it has not been determined whether m(6)A is dynamically regulated by experience. Based on transcriptome-wide profiling of m(6)A, we report that the level of m(6)A increases in the medial prefrontal cortex (mPFC) of mice in response to behavioral experience. The modulation was enriched near the stop codon of mRNAs, including genes related to neuronal plasticity. In primary cortical neurons, in vitro, modulation of m(6)A by the RNA demethylase FTO influenced the degradation profiles of a subset of transcripts with modulated sites. In vivo, the expression of Fto and the m(6)A methyltransferase, Mettl3 correlated with the observed increase in m(6)A levels post-training. Furthermore, targeted knockdown of FTO in the mPFC led to enhanced consolidation of cued fear memory. Thus, together with its role in early development, the dynamic regulation of m(6)A in the adult brain serves as an important epitranscriptomic mechanism associated with behavioral adaptation.Significance statementN(6)-methyladenosine (m(6)A) is the most prevalent internal modification on RNA, however, its cellular dynamics in vivo remains elusive. Here we provide the first demonstration of m(6)A upregulation in the mouse medial prefrontal cortex (mPFC) following behavioral training. Knocking down the m(6)A demethylase FTO in the mPFC, which increases total m(6)A level, results in enhanced consolidation of fear memory. Our findings suggest that m(6)A is regulated in an activity-dependent manner in the adult brain, and may function to fine-tune mRNA turnover during memory-related processes.

Published
2016

5. A comparative study of techniques for differential expression analysis on RNA-Seq data.

Author

Bauer, Denis, Edson, Janette, Narayanan, Ramesh, Robinson, Gregory, Lundberg, Andreas, Bartlett, Perry, Wray, Naomi, Zhao, Qiong-Yi, Zhang, Zong, Jhaveri, Dhanisha, Marshall, Vikki, and Bauer, Douglas

Subjects
Animals, Benchmarking, Cell Line, DNA, Complementary, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Humans, Male, Mice, Inbred C57BL, RNA, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA, Software
Abstract

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.

Published
2014

7. Orphan C/D box snoRNAs modulate fear-related memory processes in mice

Author

Leighton, Laura J., primary, Zhao, Qiongyi, additional, Marshall, Paul R., additional, Madugalle, Sachithrani U., additional, Chan, Angelo H. C., additional, Musgrove, Mason R. B., additional, Ren, Haobin, additional, Periyakaruppiah, Ambika, additional, Edson, Janette, additional, Wei, Wei, additional, Li, Xiang, additional, Spitale, Robert C., additional, and Bredy, Timothy W., additional

Published
2022
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9. Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits

Author

Jiménez-Mena, Belén, Flávio, Hugo, Henriques, Romina, Manuzzi, Alice, Ramos, Miguel, Meldrup, Dorte, Edson, Janette, Pálsson, Snaebjörn, Ólafsdóttir, Guðbjörg Ásta, Ovenden, Jennifer R., Nielsen, Einar Eg, Jiménez-Mena, Belén, Flávio, Hugo, Henriques, Romina, Manuzzi, Alice, Ramos, Miguel, Meldrup, Dorte, Edson, Janette, Pálsson, Snaebjörn, Ólafsdóttir, Guðbjörg Ásta, Ovenden, Jennifer R., and Nielsen, Einar Eg

Abstract

Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.

Published
2022

11. Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits

Author

Jiménez‐Mena, Belén, primary, Flávio, Hugo, additional, Henriques, Romina, additional, Manuzzi, Alice, additional, Ramos, Miguel, additional, Meldrup, Dorte, additional, Edson, Janette, additional, Pálsson, Snæbjörn, additional, Ásta Ólafsdóttir, Guðbjörg, additional, Ovenden, Jennifer R., additional, Nielsen, Einar Eg, additional, and Alexander, Alana, additional

Published
2022
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12. Fishing for DNA? Designing baits for population genetics in target enrichment experiments: guidelines, considerations and the new tool supeRbaits

Author

Mena, Belen Jimenez, primary, Flávio, Hugo, additional, Henriques, Romina, additional, Manuzzi, Alice, additional, Ramos, Miguel, additional, Meldrup, Dorte, additional, Edson, Janette, additional, Palsson, Snaebjorn, additional, Ólafsdóttir, Guðbjörg Ásta, additional, Ovenden, Jennifer, additional, and Nielsen, Einar, additional

Published
2021
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16. SARS-CoV-2 RNA monitoring in wastewater as a potential early warning system for COVID-19 transmission in the community: A temporal case study

Author

Ahmed, Warish, primary, Tscharke, Ben, additional, Bertsch, Paul M., additional, Bibby, Kyle, additional, Bivins, Aaron, additional, Choi, Phil, additional, Clarke, Leah, additional, Dwyer, Jason, additional, Edson, Janette, additional, Nguyen, Thi Minh Hong, additional, O'Brien, Jake W., additional, Simpson, Stuart L., additional, Sherman, Paul, additional, Thomas, Kevin V., additional, Verhagen, Rory, additional, Zaugg, Julian, additional, and Mueller, Jochen F., additional

Published
2021
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17. First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: A proof of concept for the wastewater surveillance of COVID-19 in the community

Author

Ahmed, Warish, primary, Angel, Nicola, additional, Edson, Janette, additional, Bibby, Kyle, additional, Bivins, Aaron, additional, O'Brien, Jake W., additional, Choi, Phil M., additional, Kitajima, Masaaki, additional, Simpson, Stuart L., additional, Li, Jiaying, additional, Tscharke, Ben, additional, Verhagen, Rory, additional, Smith, Wendy J.M., additional, Zaugg, Julian, additional, Dierens, Leanne, additional, Hugenholtz, Philip, additional, Thomas, Kevin V., additional, and Mueller, Jochen F., additional

Published
2020
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18. Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex

Author

Dick, Alec L.W., primary, Zhao, Qiongyi, additional, Crossin, Rose, additional, Baker‐Andresen, Danay, additional, Li, Xiang, additional, Edson, Janette, additional, Roeh, Simone, additional, Marshall, Victoria, additional, Bredy, Timothy W., additional, Lawrence, Andrew J., additional, and Duncan, Jhodie R., additional

Published
2020
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19. Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travellers

Author

Ahmed, Warish, primary, Bertsch, Paul M, additional, Angel, Nicola, additional, Bibby, Kyle, additional, Bivins, Aaron, additional, Dierens, Leanne, additional, Edson, Janette, additional, Ehret, John, additional, Gyawali, Pradip, additional, Hamilton, Kerry A, additional, Hosegood, Ian, additional, Hugenholtz, Philip, additional, Jiang, Guangming, additional, Kitajima, Masaaki, additional, Sichani, Homa T, additional, Shi, Jiahua, additional, Shimko, Katja M, additional, Simpson, Stuart L, additional, Smith, Wendy J M, additional, Symonds, Erin M, additional, Thomas, Kevin V, additional, Verhagen, Rory, additional, Zaugg, Julian, additional, and Mueller, Jochen F, additional

Published
2020
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20. Adolescent chronic intermittent toluene inhalation dynamically regulates the transcriptome and neuronal methylome within the rat medial prefrontal cortex.

Author

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., Duncan, Jhodie R., and Baker-Andresen, Danay

Subjects
PREFRONTAL cortex, TOLUENE, INHALANT abuse, INHALATION injuries, COGNITION disorders, TEENAGERS, NEURAL physiology, FRONTAL lobe, RESEARCH, ANIMAL experimentation, RESEARCH methodology, NEUROPLASTICITY, MEDICAL cooperation, EVALUATION research, DNA methylation, GENE expression, RATS, COMPARATIVE studies, GENE expression profiling, DNA-binding proteins, RESEARCH funding, INHALATION administration
Abstract

Inhalants containing the volatile solvent toluene are misused to induce euphoria or intoxication. Inhalant abuse is most common during adolescence and can result in cognitive impairments during an important maturational period. Despite evidence suggesting that epigenetic modifications may underpin the cognitive effects of inhalants, no studies to date have thoroughly investigated toluene-induced regulation of the transcriptome or discrete epigenetic modifications within the brain. To address this, we investigated effects of adolescent chronic intermittent toluene (CIT) inhalation on gene expression and DNA methylation profiles within the rat medial prefrontal cortex (mPFC), which undergoes maturation throughout adolescence and has been implicated in toluene-induced cognitive deficits. Employing both RNA-seq and genome-wide Methyl CpG Binding Domain (MBD) Ultra-seq analysis, we demonstrate that adolescent CIT inhalation (10 000 ppm for 1 h/day, 3 days/week for 4 weeks) induces both transient and persistent changes to the transcriptome and DNA methylome within the rat mPFC for at least 2 weeks following toluene exposure. We demonstrate for the first time that adolescent CIT exposure results in dynamic regulation of the mPFC transcriptome likely relating to acute inflammatory responses and persistent deficits in synaptic plasticity. These adaptations may contribute to the cognitive deficits associated with chronic toluene exposure and provide novel molecular targets for preventing long-term neurophysiological abnormalities following chronic toluene inhalation. [ABSTRACT FROM AUTHOR]

Published
2021
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21. An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

Author

Williams, Sarah M, An, Joon Yong, Edson, Janette, Watts, Michelle E, Murigneux, Valentine, Whitehouse, Andrew J.O, Jackson, Colin, Bellgrove, Mark, Cristino, Alexandre S, Claudianos, Charles, Williams, Sarah M, An, Joon Yong, Edson, Janette, Watts, Michelle E, Murigneux, Valentine, Whitehouse, Andrew J.O, Jackson, Colin, Bellgrove, Mark, Cristino, Alexandre S, and Claudianos, Charles

Abstract

A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify the rare single nucleotide variants (SNVs) that occur in non-coding regions and determined the regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, and microRNA genes and their target sites. Overall, we found that the regulatory variants in ASD cases were enriched in ASD-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of the regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were several rare inherited SNVs found in the mature sequence of microRNAs predicted to affect the regulation of ASD-risk genes. We show a paternally inherited miR-873-5p variant with altered binding affinity for several risk-genes including NRXN2 and CNTNAP2 putatively overlay maternally inherited lossof- function coding variations in NRXN1 and CNTNAP2 to likely increase the genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.

Published
2018

22. Additional file 2: Figure S1. of Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese

Author

Gratten, Jacob, Qiongyi Zhao, Beben Benyamin, Garton, Fleur, He, Ji, Leo, Paul, Mangelsdorf, Marie, Anderson, Lisa, Zong-Hong Zhang, Chen, Lu, Xiang-Ding Chen, Cremin, Katie, Hong-Weng Deng, Edson, Janette, Han, Ying-Ying, Harris, Jessica, Henders, Anjali, Zi-Bing Jin, Zhongshan Li, Lin, Yong, Xiaolu Liu, Marshall, Mhairi, Mowry, Bryan, Ran, Shu, Reutens, David, Song, Sharon, Tan, Li-Jun, Tang, Lu, Wallace, Robyn, Wheeler, Lawrie, Wu, Jinyu, Yang, Jian, Huji Xu, Visscher, Peter, Bartlett, Perry, Brown, Matthew, Wray, Naomi, and Dongsheng Fan

Abstract

Quantileâ quantile plots for exome-wide gene-based testing of rare coding variants in the primary analysis of 610 cases and 460 controls. (DOCX 235 kb)

Published
2017
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24. Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese

Author

Gratten, Jacob, primary, Zhao, Qiongyi, additional, Benyamin, Beben, additional, Garton, Fleur, additional, He, Ji, additional, Leo, Paul J., additional, Mangelsdorf, Marie, additional, Anderson, Lisa, additional, Zhang, Zong-Hong, additional, Chen, Lu, additional, Chen, Xiang-Ding, additional, Cremin, Katie, additional, Deng, Hong-Weng, additional, Edson, Janette, additional, Han, Ying-Ying, additional, Harris, Jessica, additional, Henders, Anjali K., additional, Jin, Zi-Bing, additional, Li, Zhongshan, additional, Lin, Yong, additional, Liu, Xiaolu, additional, Marshall, Mhairi, additional, Mowry, Bryan J., additional, Ran, Shu, additional, Reutens, David C., additional, Song, Sharon, additional, Tan, Li-Jun, additional, Tang, Lu, additional, Wallace, Robyn H., additional, Wheeler, Lawrie, additional, Wu, Jinyu, additional, Yang, Jian, additional, Xu, Huji, additional, Visscher, Peter M., additional, Bartlett, Perry F., additional, Brown, Matthew A., additional, Wray, Naomi R., additional, and Fan, Dongsheng, additional

Published
2017
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25. Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis

Author

Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J, Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A, Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L, Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, McCann, Emily P, Mowry, Bryan J, Ngo, Shyuan T, Pamphlett, Roger, Ran, Shu, Reutens, David C, Rowe, Dominic B, Sachdev, Perminder S., Shah, Sonia, Song, Sharon, Tan, Li-Jun, Tang, Lu, van den Berg, Leonard H, van Rheenen, Wouter, Veldink, Jan H, Wallace, Robyn H, Wheeler, Lawrie, Williams, Kelly L, Wu, Jinyu, Wu, Xin, Yang, Jian, Yue, Weihua, Zhang, Zong-Hong, Zhang, Dai, Noakes, Peter G, Blair, Ian P, Henderson, Robert D, McCombe, Pamela A, Visscher, Peter M., Xu, Huji, Bartlett, Perry F, Brown, Matthew A., Wray, Naomi R, Fan, Dongsheng, Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J, Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A, Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L, Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, McCann, Emily P, Mowry, Bryan J, Ngo, Shyuan T, Pamphlett, Roger, Ran, Shu, Reutens, David C, Rowe, Dominic B, Sachdev, Perminder S., Shah, Sonia, Song, Sharon, Tan, Li-Jun, Tang, Lu, van den Berg, Leonard H, van Rheenen, Wouter, Veldink, Jan H, Wallace, Robyn H, Wheeler, Lawrie, Williams, Kelly L, Wu, Jinyu, Wu, Xin, Yang, Jian, Yue, Weihua, Zhang, Zong-Hong, Zhang, Dai, Noakes, Peter G, Blair, Ian P, Henderson, Robert D, McCombe, Pamela A, Visscher, Peter M., Xu, Huji, Bartlett, Perry F, Brown, Matthew A., Wray, Naomi R, and Fan, Dongsheng

Published
2017

26. Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis

Author

Projectafdeling ALS, Brain, Regenerative Medicine and Stem Cells, ZL Neuromusculaire Ziekten Medisch, Opleiding Neurologie, Neurogenetica, Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J, Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A, Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L, Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, McCann, Emily P, Mowry, Bryan J, Ngo, Shyuan T, Pamphlett, Roger, Ran, Shu, Reutens, David C, Rowe, Dominic B, Sachdev, Perminder S., Shah, Sonia, Song, Sharon, Tan, Li-Jun, Tang, Lu, van den Berg, Leonard H, van Rheenen, Wouter, Veldink, Jan H, Wallace, Robyn H, Wheeler, Lawrie, Williams, Kelly L, Wu, Jinyu, Wu, Xin, Yang, Jian, Yue, Weihua, Zhang, Zong-Hong, Zhang, Dai, Noakes, Peter G, Blair, Ian P, Henderson, Robert D, McCombe, Pamela A, Visscher, Peter M., Xu, Huji, Bartlett, Perry F, Brown, Matthew A., Wray, Naomi R, Fan, Dongsheng, Projectafdeling ALS, Brain, Regenerative Medicine and Stem Cells, ZL Neuromusculaire Ziekten Medisch, Opleiding Neurologie, Neurogenetica, Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J, Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A, Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L, Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, McCann, Emily P, Mowry, Bryan J, Ngo, Shyuan T, Pamphlett, Roger, Ran, Shu, Reutens, David C, Rowe, Dominic B, Sachdev, Perminder S., Shah, Sonia, Song, Sharon, Tan, Li-Jun, Tang, Lu, van den Berg, Leonard H, van Rheenen, Wouter, Veldink, Jan H, Wallace, Robyn H, Wheeler, Lawrie, Williams, Kelly L, Wu, Jinyu, Wu, Xin, Yang, Jian, Yue, Weihua, Zhang, Zong-Hong, Zhang, Dai, Noakes, Peter G, Blair, Ian P, Henderson, Robert D, McCombe, Pamela A, Visscher, Peter M., Xu, Huji, Bartlett, Perry F, Brown, Matthew A., Wray, Naomi R, and Fan, Dongsheng

Published
2017

27. Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis

Author

Benyamin, Beben, primary, He, Ji, additional, Zhao, Qiongyi, additional, Gratten, Jacob, additional, Garton, Fleur, additional, Leo, Paul J., additional, Liu, Zhijun, additional, Mangelsdorf, Marie, additional, Al-Chalabi, Ammar, additional, Anderson, Lisa, additional, Butler, Timothy J., additional, Chen, Lu, additional, Chen, Xiang-Ding, additional, Cremin, Katie, additional, Deng, Hong-Weng, additional, Devine, Matthew, additional, Edson, Janette, additional, Fifita, Jennifer A., additional, Furlong, Sarah, additional, Han, Ying-Ying, additional, Harris, Jessica, additional, Henders, Anjali K., additional, Jeffree, Rosalind L., additional, Jin, Zi-Bing, additional, Li, Zhongshan, additional, Li, Ting, additional, Li, Mengmeng, additional, Lin, Yong, additional, Liu, Xiaolu, additional, Marshall, Mhairi, additional, McCann, Emily P., additional, Mowry, Bryan J., additional, Ngo, Shyuan T., additional, Pamphlett, Roger, additional, Ran, Shu, additional, Reutens, David C., additional, Rowe, Dominic B., additional, Sachdev, Perminder, additional, Shah, Sonia, additional, Song, Sharon, additional, Tan, Li-Jun, additional, Tang, Lu, additional, van den Berg, Leonard H., additional, van Rheenen, Wouter, additional, Veldink, Jan H., additional, Wallace, Robyn H., additional, Wheeler, Lawrie, additional, Williams, Kelly L., additional, Wu, Jinyu, additional, Wu, Xin, additional, Yang, Jian, additional, Yue, Weihua, additional, Zhang, Zong-Hong, additional, Zhang, Dai, additional, Noakes, Peter G., additional, Blair, Ian P., additional, Henderson, Robert D., additional, McCombe, Pamela A., additional, Visscher, Peter M., additional, Xu, Huji, additional, Bartlett, Perry F., additional, Brown, Matthew A., additional, Wray, Naomi R., additional, and Fan, Dongsheng, additional

Published
2017
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28. Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort

Author

Garton, Fleur C., primary, Benyamin, Beben, additional, Zhao, Qiongyi, additional, Liu, Zhijun, additional, Gratten, Jacob, additional, Henders, Anjali K., additional, Zhang, Zong-Hong, additional, Edson, Janette, additional, Furlong, Sarah, additional, Morgan, Sarah, additional, Heggie, Susan, additional, Thorpe, Kathryn, additional, Pfluger, Casey, additional, Mather, Karen A., additional, Sachdev, Perminder S., additional, McRae, Allan F., additional, Robinson, Matthew R., additional, Shah, Sonia, additional, Visscher, Peter M., additional, Mangelsdorf, Marie, additional, Henderson, Robert D., additional, Wray, Naomi R., additional, and McCombe, Pamela A., additional

Published
2017
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29. Experience-Dependent Accumulation of N 6 -Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

Author

Widagdo, Jocelyn, primary, Zhao, Qiong-Yi, additional, Kempen, Marie-Jeanne, additional, Tan, Men Chee, additional, Ratnu, Vikram S., additional, Wei, Wei, additional, Leighton, Laura, additional, Spadaro, Paola A., additional, Edson, Janette, additional, Anggono, Victor, additional, and Bredy, Timothy W., additional

Published
2016
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30. Molecular phylogeny, biogeography, and habitat preference evolution of Marsupials

Author

Mitchell, Kieren, Pratt, Renae, Watson, Laura, Gibb, Gillian, Llamas, Bastien, Kasper, Marta, Edson, Janette, Hopwood, Blair, Male, Dean, Armstrong, Kyle, Meyer, Matthias, Hofreiter, Michael, Austin, Jeremy, Donnellan, Steve, Lee, Michael, Phillips, Matthew, Cooper, Alan, Mitchell, Kieren, Pratt, Renae, Watson, Laura, Gibb, Gillian, Llamas, Bastien, Kasper, Marta, Edson, Janette, Hopwood, Blair, Male, Dean, Armstrong, Kyle, Meyer, Matthias, Hofreiter, Michael, Austin, Jeremy, Donnellan, Steve, Lee, Michael, Phillips, Matthew, and Cooper, Alan

Abstract

Marsupials exhibit great diversity in ecology and morphology. However, compared to their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene, and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Published
2014

32. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, Levchenko, Tanya, Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, and Levchenko, Tanya

Abstract

BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Published
2011

33. Experience-Dependent Accumulation of N6-Methyiadenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice.

Author

Widagdo, Jocelyn, Qiong-Yi Zhao, Kempen, Marie-Jeanne, Men Chee Tan, Ratnu, Vikram S., Wei Wei, Leighton, Laura, Spadaro, Paola A., Edson, Janette, Anggono, Victor, and Bredy, Timothy W.

Subjects
NEUROPLASTICITY, PREFRONTAL cortex, BRAIN physiology, MESSENGER RNA, RNA methylation, BRAIN imaging, MEMORY
Abstract

The RNA modification N6-methyladenosine (m6A) influences mRNA stability and cell-type-specific developmental programming, and is highly abundant in the adult brain. However, it has not been determined whether m6A is dynamically regulated by experience. Based on transcriptome-wide profiling of m6A, we report that the level of m6A increases in the medial prefrontal cortex (mPFC) of mice in response to behavioral experience. The modulation was enriched near the stop codon of mRNAs, including genes related to neuronal plasticity. In primary cortical neurons, in vitro, modulation of m6A by the RNA demethylase FTO influenced the degradation profiles of a subset of transcripts with modulated sites. In vivo, the expression of Fto and the m6A methyltransferase, Mettl3 correlated with the observed increase in m6A levels post-training. Furthermore, targeted knockdown of FTO in the mPFC led to enhanced consolidation of cued fear memory. Thus, together with its role in early development, the dynamic regulation of m6A in the adult brain serves as an important epitranscriptomic mechanism associated with behavioral adaptation. [ABSTRACT FROM AUTHOR]

Published
2016
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34. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional

Published
2011
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