Circadian clock mechanism driving mammalian photoperiodism

[1]  David W. Burt,et al.  Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis , 2019, bioRxiv.

[2]  S. Wood,et al.  An integrative view of mammalian seasonal neuroendocrinology , 2019, Journal of neuroendocrinology.

[3]  E. Maywood,et al.  Translational switching of Cry1 protein expression confers reversible control of circadian behavior in arrhythmic Cry-deficient mice , 2018, Proceedings of the National Academy of Sciences.

[4]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[5]  Silvio C. E. Tosatto,et al.  The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..

[6]  S. Wood,et al.  Seasonal physiology: making the future a thing of the past , 2018, Current Opinion in Physiology.

[7]  S. Wood How can a binary switch within the pars tuberalis control seasonal timing of reproduction? , 2018, The Journal of endocrinology.

[8]  D. Hazlerigg,et al.  Neuroendocrine correlates of the critical day length response in the Soay sheep , 2018, Journal of neuroendocrinology.

[9]  N. Ershov,et al.  Consequences of early life stress on genomic landscape of H3K4me3 in prefrontal cortex of adult mice , 2018, BMC Genomics.

[10]  A. Loudon,et al.  The pars tuberalis: The site of the circannual clock in mammals? , 2017, General and comparative endocrinology.

[11]  A. Myburg,et al.  Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem , 2017, Scientific Reports.

[12]  A. Myburg,et al.  Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem , 2017, Scientific Reports.

[13]  Damian Szklarczyk,et al.  The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible , 2016, Nucleic Acids Res..

[14]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[15]  Gang Wu,et al.  MetaCycle: an integrated R package to evaluate periodicity in large scale data , 2016, bioRxiv.

[16]  Julian R. E. Davis,et al.  Binary Switching of Calendar Cells in the Pituitary Defines the Phase of the Circannual Cycle in Mammals , 2015, Current Biology.

[17]  A. C. Liu,et al.  Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C-terminus , 2015, Nature Structural &Molecular Biology.

[18]  K. Gardner,et al.  Coiled-coil Coactivators Play a Structural Role Mediating Interactions in Hypoxia-inducible Factor Heterodimerization* , 2015, The Journal of Biological Chemistry.

[19]  Mohammad M. Karimi,et al.  An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations , 2015, Nature Communications.

[20]  R. Klose,et al.  Understanding the relationship between DNA methylation and histone lysine methylation , 2014, Biochimica et biophysica acta.

[21]  C. Partch,et al.  Emerging Models for the Molecular Basis of Mammalian Circadian Timing , 2014, Biochemistry.

[22]  Ana Conesa,et al.  Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series , 2014, Bioinform..

[23]  A. Loudon,et al.  Clocks for all seasons: unwinding the roles and mechanisms of circadian and interval timers in the hypothalamus and pituitary , 2014, The Journal of endocrinology.

[24]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[25]  T. Yoshimura,et al.  Universality and diversity in the signal transduction pathway that regulates seasonal reproduction in vertebrates , 2014, Front. Neurosci..

[26]  D. Hazlerigg,et al.  Thyroid Hormone and Seasonal Rhythmicity , 2014, Front. Endocrinol..

[27]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[28]  J. Takahashi,et al.  Molecular architecture of the mammalian circadian clock. , 2014, Trends in cell biology.

[29]  Caroline Dean,et al.  Remembering the Prolonged Cold of Winter , 2013, Current Biology.

[30]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[31]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[32]  Julian R. E. Davis,et al.  Npas4 Is Activated by Melatonin, and Drives the Clock Gene Cry1 in the Ovine Pars Tuberalis , 2013, Molecular Endocrinology.

[33]  S. Salzberg,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[34]  Y. Fukada,et al.  FBXL21 Regulates Oscillation of the Circadian Clock through Ubiquitination and Stabilization of Cryptochromes , 2013, Cell.

[35]  Ralf Herwig,et al.  The ConsensusPathDB interaction database: 2013 update , 2012, Nucleic Acids Res..

[36]  Hong Zhang,et al.  Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex , 2012, Science.

[37]  Y. Iwasa,et al.  A stochastic model of chromatin modification: cell population coding of winter memory in plants. , 2012, Journal of theoretical biology.

[38]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[39]  T. Yoshimura,et al.  Circadian clocks and the measurement of daylength in seasonal reproduction , 2012, Molecular and Cellular Endocrinology.

[40]  C. Dean,et al.  A Polycomb-based switch underlying quantitative epigenetic memory , 2011, Nature.

[41]  H. Ueda,et al.  Acute Induction of Eya3 by Late-Night Light Stimulation Triggers TSHβ Expression in Photoperiodism , 2010, Current Biology.

[42]  A. Loudon,et al.  A Molecular Switch for Photoperiod Responsiveness in Mammals , 2010, Current Biology.

[43]  Karl Kornacker,et al.  JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets , 2010, Journal of biological rhythms.

[44]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[45]  Julian R. E. Davis,et al.  Identification of Eya3 and TAC1 as Long-Day Signals in the Sheep Pituitary , 2010, Current Biology.

[46]  Dustin E. Schones,et al.  A clustering approach for identification of enriched domains from histone modification ChIP-Seq data , 2009, Bioinform..

[47]  J. Fustin,et al.  Transcriptional feedback loops in the ovine circadian clock. , 2009, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.

[48]  J. Fustin,et al.  Implication of the F-Box Protein FBXL21 in Circadian Pacemaker Function in Mammals , 2008, PloS one.

[49]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[50]  J. Fustin,et al.  Ancestral TSH Mechanism Signals Summer in a Photoperiodic Mammal , 2008, Current Biology.

[51]  C. Pittendrigh,et al.  The Circadian Component in Photoperiodic Induction , 2008 .

[52]  H. Ueda,et al.  Thyrotrophin in the pars tuberalis triggers photoperiodic response , 2008, Nature.

[53]  D. Hazlerigg,et al.  Characterizing a Mammalian Circannual Pacemaker , 2006, Science.

[54]  D. Hazlerigg,et al.  Multiple effects of melatonin on rhythmic clock gene expression in the mammalian pars tuberalis. , 2006, Endocrinology.

[55]  G. Lincoln Melatonin Entrainment of Circannual Rhythms , 2006, Chronobiology international.

[56]  Bruce M. Spiegelman,et al.  Biological Control through Regulated Transcriptional Coactivators , 2004, Cell.

[57]  S. Kida,et al.  A BMAL1 mutant with arginine 91 substituted with alanine acts as a dominant negative inhibitor. , 2004, Gene.

[58]  A. Harris,et al.  The hypoxia‐regulated transcription factor DEC1 (Stra13, SHARP‐2) and its expression in human tissues and tumours , 2004, The Journal of pathology.

[59]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[60]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[61]  P. Pévet,et al.  MT1 Melatonin Receptor mRNA Expressing Cells in the Pars Tuberalis of the European Hamster: Effect of Photoperiod , 2003, Journal of neuroendocrinology.

[62]  P. Pévet,et al.  Melatonin induces Cry1 expression in the pars tuberalis of the rat. , 2003, Brain research. Molecular brain research.

[63]  P. Pévet,et al.  The mt1 Melatonin Receptor and RORβ Receptor Are Co-localized in Specific TSH-immunoreactive Cells in the Pars Tuberalis of the Rat Pituitary , 2002, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[64]  T. Kawamoto,et al.  Dec1 and Dec2 are regulators of the mammalian molecular clock , 2002, Nature.

[65]  D. Hazlerigg,et al.  Temporal expression of seven clock genes in the suprachiasmatic nucleus and the pars tuberalis of the sheep: Evidence for an internal coincidence timer , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[66]  B. Goldman Mammalian Photoperiodic System: Formal Properties and Neuroendocrine Mechanisms of Photoperiodic Time Measurement , 2001, Journal of biological rhythms.

[67]  John B. Hogenesch,et al.  Mop3 Is an Essential Component of the Master Circadian Pacemaker in Mammals , 2000, Cell.

[68]  Michael Q. Zhang,et al.  Large-scale human promoter mapping using CpG islands , 2000, Nature Genetics.

[69]  N. Wayne,et al.  Photoperiodic synchronization of a circannual reproductive rhythm in sheep: identification of season-specific time cues. , 1994, Biology of reproduction.

[70]  M. Hastings,et al.  The timed infusion paradigm for melatonin delivery: What has it taught us about the melatonin signal, its reception, and the photoperiodic control of seasonal responses? , 1993, Journal of pineal research.

[71]  D. Kennaway,et al.  The influence of exogenous melatonin on the seasonal patterns of ovulation and oestrus in sheep , 1992 .

[72]  E. Maywood,et al.  The Effect of Signal Frequency on the Gonadal Response of Male Syrian Hamsters to Programmed Melatonin Infusions , 1992, Journal of neuroendocrinology.

[73]  Jane E. Robinson,et al.  Circannual cycles of luteinizing hormone and prolactin secretion in ewes during prolonged exposure to a fixed photoperiod: evidence for an endogenous reproductive rhythm. , 1989, Biology of reproduction.

[74]  F. Ebling,et al.  Effects of Constant Darkness and Constant Light on Circadian Organization and Reproductive Responses in the Ram , 1988, Journal of biological rhythms.

[75]  R. Dempsey,et al.  Pineal melatonin secretion drives the reproductive response to daylength in the ewe. , 1983, Endocrinology.

[76]  D. Farner,et al.  Circadian function in the photoperiodic induction of gonadotropin secretion in the white-crowned sparrow, Zonotrichia leucophrys gambelii. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[77]  C. Pittendrigh,et al.  The Entrainment of Circadian Oscillations by Light and Their Role as Photoperiodic Clocks , 1964, The American Naturalist.

[78]  K. Nanda,et al.  Studies on the Nature of the Endogenous Rhythm Affecting Photoperiodic Response of Biloxi Soybean , 1958, Botanical Gazette.

[79]  Nian Huang Crystal Structure of the Heterodimeric CLOCK:BMAL1 , 2012 .

[80]  Piero Carninci,et al.  CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. , 2012, Methods in molecular biology.

[81]  Claude-Alain H. Roten,et al.  Theoretical and practical advances in genome halving , 2004 .

[82]  F. Ebling,et al.  Effect of constant-release implants of melatonin on seasonal cycles in reproduction, prolactin secretion and moulting in rams. , 1985, Journal of reproduction and fertility.

[83]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[84]  D. Mouzaki,et al.  Edinburgh Research Explorer Identification of Melatonin-Regulated Genes in the Ovine Pituitary Pars Tuberalis, a Target Site for Seasonal Hormone Control , 2022 .

[85]  Thomas Lengauer,et al.  Bioinformatics Original Paper Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating Go Graph Structure , 2022 .