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      CircadiOmics: circadian omic web portal

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          Abstract

          Circadian rhythms play a fundamental role at all levels of biological organization. Understanding the mechanisms and implications of circadian oscillations continues to be the focus of intense research. However, there has been no comprehensive and integrated way for accessing and mining all circadian omic datasets. The latest release of CircadiOmics ( http://circadiomics.ics.uci.edu) fills this gap for providing the most comprehensive web server for studying circadian data. The newly updated version contains high-throughput 227 omic datasets corresponding to over 74 million measurements sampled over 24 h cycles. Users can visualize and compare oscillatory trajectories across species, tissues and conditions. Periodicity statistics (e.g. period, amplitude, phase, P-value, q-value etc.) obtained from BIO_CYCLE and other methods are provided for all samples in the repository and can easily be downloaded in the form of publication-ready figures and tables. New features and substantial improvements in performance and data volume make CircadiOmics a powerful web portal for integrated analysis of circadian omic data.

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          Transcriptional architecture and chromatin landscape of the core circadian clock in mammals.

          Nobuya Koike, Seung-Hee Yoo, Hung-Chung Huang … (2012)
          The mammalian circadian clock involves a transcriptional feed back loop in which CLOCK and BMAL1 activate the Period and Cryptochrome genes, which then feedback and repress their own transcription. We have interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and find a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (RNAPII) recruitment, RNA expression, and chromatin states. We find that the circadian transcriptional cycle of the clock consists of three distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of messenger RNA (mRNA) cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. We also find that circadian modulation of RNAPII recruitment and chromatin remodeling occurs on a genome-wide scale far greater than that seen previously by gene expression profiling.
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            Molecular architecture of the mammalian circadian clock.

            Carrie L. Partch, Carla B Green, Joseph S Takahashi (2014)
            Circadian clocks coordinate physiology and behavior with the 24h solar day to provide temporal homeostasis with the external environment. The molecular clocks that drive these intrinsic rhythmic changes are based on interlocked transcription/translation feedback loops that integrate with diverse environmental and metabolic stimuli to generate internal 24h timing. In this review we highlight recent advances in our understanding of the core molecular clock and how it utilizes diverse transcriptional and post-transcriptional mechanisms to impart temporal control onto mammalian physiology. Understanding the way in which biological rhythms are generated throughout the body may provide avenues for temporally directed therapeutics to improve health and prevent disease. Copyright © 2013 Elsevier Ltd. All rights reserved.
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              Molecular components of the mammalian circadian clock.

              Caroline Ko, Joseph S Takahashi (2006)
              Circadian rhythms are approximately 24-h oscillations in behavior and physiology, which are internally generated and function to anticipate the environmental changes associated with the solar day. A conserved transcriptional-translational autoregulatory loop generates molecular oscillations of 'clock genes' at the cellular level. In mammals, the circadian system is organized in a hierarchical manner, in which a master pacemaker in the suprachiasmatic nucleus (SCN) regulates downstream oscillators in peripheral tissues. Recent findings have revealed that the clock is cell-autonomous and self-sustained not only in a central pacemaker, the SCN, but also in peripheral tissues and in dissociated cultured cells. It is becoming evident that specific contribution of each clock component and interactions among the components vary in a tissue-specific manner. Here, we review the general mechanisms of the circadian clockwork, describe recent findings that elucidate tissue-specific expression patterns of the clock genes and address the importance of circadian regulation in peripheral tissues for an organism's overall well-being.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 02 July 2018
                Publication date (Electronic): 15 June 2018
                Publication date PMC-release: 15 June 2018
                Volume: 46
                Issue: Web Server issue
                Pages: W157-W162
                Affiliations
                [1 ]Department of Computer Science, University of California, Irvine, CA 92617, USA
                [2 ]Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92617, USA
                [3 ]Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
                [4 ]Center for Epigenetics and Metabolism, School of Medicine, University of California, Irvine, CA 92617, USA
                [5 ]Department of Biochemistry, University of California, Irvine, CA 92617, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 949 824 5809; Fax: +1 949 824 9813; Email: pfbaldi@ 123456uci.edu

                The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

                Article
                Publisher ID: gky441
                DOI: 10.1093/nar/gky441
                PMC ID: 6030824
                PubMed ID: 29912458
                SO-VID: e0bcd166-1371-4877-a340-4b2ecf57ae73
                Copyright © © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 13 June 2018
                Date revision received : 17 April 2018
                Date received : 09 February 2018
                Page count
                Pages: 6
                Funding
                Funded by: National Institute of General Medical Sciences 10.13039/100000057
                Award ID: GM123558
                Funded by: Defense Advanced Research Projects Agency 10.13039/100000185
                Award ID: D17AP00002
                Categories
                Subject: Web Server Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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