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ECHO: an Application for Detection and Analysis of Oscillators Identifies Metabolic Regulation on Genome-Wide Circadian Output [article]

Hannah De los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett, Jennifer M. Hurley
2019 bioRxiv   pre-print
Motivation: Time courses utilizing genome scale data are a common approach to identifying the biological pathways that are controlled by the circadian clock, an important regulator of organismal fitness  ...  Results: We have created a program to efficaciously identify oscillations in large-scale datasets, called the Extended Circadian Harmonic Oscillator application, or ECHO.  ...  We would also like to thank Thomas Willemain for his statistical expertise, and Chendi Guan and Kristin Pratt for their assistance in developing and testing the ECHO application.  ... 
doi:10.1101/690941 fatcat:kq5xuhe52beedn3tzf2tb3fl4m

Post-Transcriptional Circadian Regulation in Macrophages Organizes Temporally Distinct Immunometabolic States [article]

Emily J Collins, Mariana P Cervantes-Silva, George A Timmons, James R O'Siorain, Annie M Curtis, Jennifer M Hurley
2020 bioRxiv   pre-print
As macrophages coordinate many immunological and inflammatory functions, an understanding of this regulation provides a framework to determine the impact of circadian regulation on a wide array of disease  ...  Ontological analysis of oscillating proteins revealed robust temporal enrichment for protein degradation and translation, providing potential insights into the source of this extensive post-transcriptional  ...  Kristen Bennett and Hannah De los Santos of the Rensselaer Institute for Data Exploration and Applications for their help with ECHO analyses.  ... 
doi:10.1101/2020.02.28.970715 fatcat:jxsmutvahba75kpxg3ckhfwdkq

ENCORE

Hannah De los Santos, Kristin P. Bennett, Jennifer M. Hurley
2019 Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '19  
Using ECHO, we found that circadian oscillations widely undergo a change in amplitude over time and that these amplitude changes have a biological function in the cell.  ...  Previously, we created the ECHO (Extended Circadian Harmonic Oscillator) tool to identify rhythms in these data sets.  ...  ACKNOWLEDGMENTS We would like to thank Emily Collins and Catherine Mann for their expertise in processing microarray data, Meaghan Jankowski for her expertise in Neurospora, and John Erickson for his campfire  ... 
doi:10.1145/3307339.3342137 pmid:31754663 pmcid:PMC6868525 dblp:conf/bcb/SantosBH19 fatcat:blxajb26fja65difimcdtfjkem

Global approaches for telling time: Omics and the Arabidopsis circadian clock

Brenda Y. Chow, Steve A. Kay
2013 Seminars in Cell and Developmental Biology  
Our understanding of the factors, regulation, and mechanistic connectivity between clock genes and with output processes has substantially broadened through genomic (cDNA libraries, yeast one-hybrid, protein  ...  The circadian clock is an endogenous timer that anticipates and synchronizes biological processes to the environment.  ...  Gendron, Elsebeth Kolmos, Naden Krogan, and Tsuyoshi Hirota for helpful discussion and critical reading of the manuscript; Naden Krogan for illustrating the figures; and funding by the NIH grants R01 GM50006  ... 
doi:10.1016/j.semcdb.2013.02.005 pmid:23435351 pmcid:PMC3759395 fatcat:qkkvzqd5tzf2rbfjcpqd7ei6bq

Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion

Audrey Jacq, Denis Becquet, Maria-Montserrat Bello-Goutierrez, Bénédicte Boyer, Séverine Guillen, Jean-Louis Franc, Anne-Marie François-Bellan
2021 Computational and Structural Biotechnology Journal  
The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to  ...  The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1  ...  Of course the use of ECHO to identify rhythmic genes, an application that has been shown to outperform existing approaches to identify oscillations in genomescale circadian datasets [45] , may explain  ... 
doi:10.1016/j.csbj.2021.04.022 pmid:33995907 pmcid:PMC8085668 fatcat:b7x72aegkveu3dkmbmwlwttgy4

Cytosolic and Transcriptional Cycles Underlying Circadian Oscillations [chapter]

Michael H. Hastings, John S. O'Neill
2015 Circadian Medicine  
Acknowledgements The work of the authors' laboratories is supported by the Medical Research Council (UK) (MC_ UP_1201/4) and the Wellcome Trust (Grant 093734/Z/10/Z, JSO'N).  ...  Margiotta, LMB Visual Aids Department, for expert assistance with the figures.  ...  Because the paradigm of biology for the last decades has been genes and genomes, it is perhaps unsurprising that analysis of the clock mechanism focused on gene expression, leading to the development of  ... 
doi:10.1002/9781118467831.ch1 fatcat:7mau6apdvzcythpbrimzb5m754

Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion [article]

Audrey Jacq, Denis Becquet, Maria-Montserrat Bello-Goutierrez, Benedicte Boyer, Severine Guillen, Jean-Louis Franc, Anne-Marie Francois-Bellan
2021 bioRxiv   pre-print
The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to  ...  The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1  ...  Of course the use of ECHO to identify rhythmic genes, an application that has been shown to out-perform existing approaches to identify oscillations in genome-scale circadian datasets (De Los Santos et  ... 
doi:10.1101/2021.01.06.425556 fatcat:pspsbpqyt5fnzf7xs5bcgvrk4a

Histone methyltransferase MLL3 contributes to genome-scale circadian transcription

Utham K. Valekunja, Rachel S. Edgar, Malgorzata Oklejewicz, Gijsbertus T. J. van der Horst, John S. O'Neill, Filippo Tamanini, Daniel J. Turner, Akhilesh B. Reddy
2013 Proceedings of the National Academy of Sciences of the United States of America  
Based on observations that a few specific clock-regulated genomic loci undergo changes in chromatin state over the circadian cycle (8-10), we hypothesized that this might be more generally applicable at  ...  circadian "output" genes in the liver.  ...  Based on observations that a few specific clock-regulated genomic loci undergo changes in chromatin state over the circadian cycle (8) (9) (10) , we hypothesized that this might be more generally applicable  ... 
doi:10.1073/pnas.1214168110 pmid:23297224 pmcid:PMC3557088 fatcat:e7xjx6jg5rc6thafeyjeza65nq

Comprehensive mapping of abiotic stress inputs into the soybean circadian clock

Meina Li, Lijun Cao, Musoki Mwimba, Yan Zhou, Ling Li, Mian Zhou, Patrick S. Schnable, Jamie A. O'Rourke, Xinnian Dong, Wei Wang
2019 Proceedings of the National Academy of Sciences of the United States of America  
Despite progress in Arabidopsis, our understanding of the crop circadian clock is still limited, impeding its rational improvement for enhanced fitness.  ...  Moreover, short-term iron deficiency targeted different clock components in soybean and Arabidopsis and thus had opposite effects on the clocks of these 2 species.  ...  Tylka and S. Whitham for sharing soybean seeds and P. Benfey for enlightening discussions about the project. We thank E. Pasoreck for editing and improving the manuscript.  ... 
doi:10.1073/pnas.1708508116 pmid:31676549 pmcid:PMC6876155 fatcat:avohvjtdurd6xipnygzo6br5wy

Systems dynamics of biology

David Lloyd
2005 Journal of Applied Biomedicine  
Systems biology takes account of the controls and balances on inputs and outputs between the environment and the open system of the functioning organism.  ...  Ancestral shorter-period (ultradian) oscillations, rhythms and clocks are all-pervasive in intracellular regulation and control.  ...  To most it suggests an initial microarray-based genome-wide transcriptome analysis, then proteomics (2D separation of thousands of proteins on gels followed by mass spectrometric sequencing of proteolytic-enzyme  ... 
doi:10.32725/jab.2005.001 fatcat:m2y62v6c3rfkdecttltdsbpwrm

Interaction of MAGED1 with nuclear receptors affects circadian clock function

Xiaohan Wang, Jing Tang, Lijuan Xing, Guangsen Shi, Haibin Ruan, Xiwen Gu, Zhiwei Liu, Xi Wu, Xiang Gao, Ying Xu
2010 EMBO Journal  
We have thus identified and defined a novel circadian regulator, Maged1, which is indispensable for the robustness of the circadian clock to better serve the organism.  ...  In a genetic screen for novel regulators of circadian rhythms, we found that mice lacking MAGED1 (Melanoma Antigen Family D1) exhibit a shortened period and altered rest-activity bouts.  ...  , Fu & Ptáček labs for PER2 antibody and human PER2 transgenic mice, Shi Yamazaki for rat Per1-Luc fibroblasts and technical support on LumiCycle, M Ikeda for Bmal1 promoter, Laure Bernard and Vincent  ... 
doi:10.1038/emboj.2010.34 pmid:20300063 pmcid:PMC2868574 fatcat:utjajmsfwrdd7gpsoofeyqhmxy

REVERBa couples the circadian clock to hepatic glucocorticoid action

Giorgio Caratti, Mudassar Iqbal, Louise Hunter, Donghwan Kim, Ping Wang, Ryan M. Vonslow, Nicola Begley, Abigail J. Tetley, Joanna L. Woodburn, Marie Pariollaud, Robert Maidstone, Ian J. Donaldson (+14 others)
2018 Journal of Clinical Investigation  
Our results reveal a mechanism by which the circadian clock acts through REVERBa in liver on elements bound by HNF4A/HNF6 to direct GR action on energy metabolism.  ...  Importantly, deletion of Reverba inverted circadian liver GC sensitivity and protected mice from hepatosteatosis induced by chronic GC administration.  ...  Acknowledgments We gratefully acknowledge Andy Hayes and Stacey Holden (University of Manchester Genomics facility), Peter Walker and Natalie Partington (University of Manchester Histology facility), Peter  ... 
doi:10.1172/jci96138 pmid:30179226 pmcid:PMC6160001 fatcat:6rqkgswvqjhizb3j2zim6ffvlu

Simultaneous Monitoring of Behavior & Peripheral Clocks in Drosophila Reveals Unstructured Sleep in an Alzheimer's Model [article]

Eleonora Khabirova, Ko-Fan Chen, John S O'Neill, Damian C Crowther
2015 bioRxiv   pre-print
Sleep and circadian rhythms are ancient, related biological phenomena controlled by distinct neuronal circuits, whose appropriate regulation is critical for health.  ...  We go on to show unambiguously that peripheral cellular rhythms can free-run independently of the central pacemakers that drive behavioural cycles.  ...  ., and Sehgal, A. (2008). Regulation of Feeding and Metabolism by Neuronal 30 and Peripheral Clocks in Drosophila.  ... 
doi:10.1101/013730 fatcat:jf6s3v535zfllo2hszin2pqe2a

Integrin signaling via actin cytoskeleton activates MRTF/SRF to entrain circadian clock [article]

Ke Ma, Xuekai Xiong, Weini Li, Jin Nam
2021 bioRxiv   pre-print
Mechanistically, we identify specific core clock transcription regulators, Per1 , Per2 and Nr1d1 , as direct target genes of MRTF-A/SRF.  ...  of core clock components, and that this signaling cascade modulates key properties of clock circadian activity.  ...  Regulation of circadian behaviour and metabolism by REV-ERB-alpha and REV-ERB-beta. Nature. Yoo SH, Park YS, Kim KH, Wei S, Buhr E, et al.  ... 
doi:10.1101/2021.08.12.456061 fatcat:cn4zgfio2vfkplyq6kkftu5hvy

Circadian phase-dependent effect of nitric oxide on L-type voltage-gated calcium channels in avian cone photoreceptors

Michael L. Ko, Liheng Shi, Cathy C.-Y. Huang, Kirill Grushin, So-Young Park, Gladys Y.-P. Ko
2013 Journal of Neurochemistry  
kinase) and Ras-phosphatidylinositol 3 kinase (PI3K)-protein kinase B (Akt) are part of the circadian output pathways regulating L-VGCCs.  ...  Nitric oxide (NO) plays an important role in phase-shifting of circadian neuronal activities in the suprachiasmatic nucleus and circadian behavior activity rhythms.  ...  Acknowledgments We thank Darya Vernikovskaya for her assistance with the cGMP and NO assays. This work was supported by NIHR01EY017452 (National Eye Institute) to G.K.  ... 
doi:10.1111/jnc.12384 pmid:23895452 pmcid:PMC4112736 fatcat:vvm3rptebrhcxasp2iodx53nii
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