Circadian clock mechanism driving mammalian photoperiodism

Wood, Shona H.; Hindle, Matthew; Mizoro, Yasutaka; Cheng, Yuanyuan; Saer, Ben; Miedzinska, Katarzyna; Christian, Helen C.; Begley, Nicola; McNeilly, J. R.; McNeilly, Alan S.; Meddle, Simone; Burt, Dave; Loudon, A. S. I.

doi:10.1038/s41467-020-18061-z

Cited by 53 publications

(28 citation statements)

References 84 publications

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“…Generation of experimental data to improve TSS annotation is one of the objectives defined by the Ovine FAANG Project and cap analysis gene expression (CAGE) data on 55 tissues and alveolar macrophages was recently published ( Salavati et al, 2020 ). CAGE is an excellent method to confirm function and location of promoters and enhancers ( Andersson et al, 2014 ) for validation of ChIP-seq ( Wood et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages

et al. 2021

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Alveolar macrophages function in innate and adaptive immunity, wound healing, and homeostasis in the lungs dependent on tissue-specific gene expression under epigenetic regulation. The functional diversity of tissue resident macrophages, despite their common myeloid lineage, highlights the need to study tissue-specific regulatory elements that control gene expression. Increasing evidence supports the hypothesis that subtle genetic changes alter sheep macrophage response to important production pathogens and zoonoses, for example, viruses like small ruminant lentiviruses and bacteria like Coxiella burnetii. Annotation of transcriptional regulatory elements will aid researchers in identifying genetic mutations of immunological consequence. Here we report the first genome-wide survey of regulatory elements in any sheep immune cell, utilizing alveolar macrophages. We assayed histone modifications and CTCF enrichment by chromatin immunoprecipitation with deep sequencing (ChIP-seq) in two sheep to determine cis-regulatory DNA elements and chromatin domain boundaries that control immunity-related gene expression. Histone modifications included H3K4me3 (denoting active promoters), H3K27ac (active enhancers), H3K4me1 (primed and distal enhancers), and H3K27me3 (broad silencers). In total, we identified 248,674 reproducible regulatory elements, which allowed assignment of putative biological function in macrophages to 12% of the sheep genome. Data exceeded the FAANG and ENCODE standards of 20 million and 45 million useable fragments for narrow and broad marks, respectively. Active elements showed consensus with RNA-seq data and were predictive of gene expression in alveolar macrophages from the publicly available Sheep Gene Expression Atlas. Silencer elements were not enriched for expressed genes, but rather for repressed developmental genes. CTCF enrichment enabled identification of 11,000 chromatin domains with mean size of 258 kb. To our knowledge, this is the first report to use immunoprecipitated CTCF to determine putative topological domains in sheep immune cells. Furthermore, these data will empower phenotype-associated mutation discovery since most causal variants are within regulatory elements.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages

et al. 2021

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“…Two types of homeorhetic regulation are relevant to temperament in cattle: (1) top down organization by the central nervous system of functions in somatic tissues that is coupled to external environmental cues; and (2) multiplex regulation integrating internal and external cues via dialogue between the central nervous system and somatic tissues providing both top down and bottom up inputs to the regulated physiological state. Top down regulation by a central controller in response to an external cue has recently been proposed for regulation of photoperiodism in sheep and other mammals by the circadian genes BMAL2, and DEC1, through their activating and suppressive effects on EYA3 in the pars tuberalis of the pituitary gland (Wood et al, 2020). The authors suggest that regulation of EYA3 constitutes a flip-flop switch for transitioning between two stable states recognized as summer and winter physiology.…”

Section: Homeorhetic Regulation Of Temperament Traitsmentioning

confidence: 99%

Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle

Colditz

2021

Front. Anim. Sci.

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The temperament of farm animals can influence their resilience to everyday variations within the managed production environment and has been under strong direct and indirect selection during the course of domestication. A prominent objective measure used for assessing temperament in beef cattle is the behavioral flight response to release from confinement in a crush or chute. This behavioral measure, termed flight speed (also known as escape velocity) is associated with physiological processes including body temperature, feeding behavior, growth rate, carcass composition, immune function, and health outcomes. This review examines the functional links between this suite of traits and adrenergic activity of the sympathetic nervous system and the adrenomedullary hormonal system. It is suggested that flight speed is the behavioral aspect of an underlying “flightiness” temperament syndrome, and that elevated adrenergic tone in animals with a high level of flightiness (i.e., flighty animals) tunes physiological activities toward a sustained “fight or flight” defense profile that reduces productivity and the capacity to flourish within the production environment. Nonetheless, despite a common influence of adrenergic tone on this suite of traits, variation in each trait is also influenced by other regulatory pathways and by the capacity of tissues to respond to a range of modulators in addition to adrenergic stimuli. It is suggested that tuning by adrenergic tone is an example of homeorhetic regulation that can help account for the persistent expression of behavioral and somatic traits associated with the flight speed temperament syndrome across the life of the animal. At a population level, temperament may modulate ecological fit within and across generations in the face of environmental variability and change. Associations of flight speed with the psychological affective state of the animal, and implications for welfare are also considered. The review will help advance understanding of the developmental biology and physiological regulation of temperament syndromes.

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“…TSH levels in the thyrotrophic cells of the PT display melatonin-dependent photoperiodic changes; high TSH under long photoperiod, and low levels under short photoperiod. EYA3 promotes transcription of the TSHβ subunit and thus acts as an ‘on-switch’ for TSH, making EYA3 a central player in photoperiodic time measurement [ 91 ]. EYA3 is induced 12.5 h after the onset of melatonin expression.…”

Section: Eya In Photoperiodismmentioning

confidence: 99%

The Eyes Absent proteins in development and in developmental disorders

Soni

Roychoudhury

Hegde

2021

Biochemical Society Transactions

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The Eyes Absent (EYA) transactivator-phosphatase proteins are important contributors to cell-fate determination processes and to the development of multiple organs. The transcriptional regulatory activity as well as the protein tyrosine phosphatase activities of the EYA proteins can independently contribute to proliferation, differentiation, morphogenesis and tissue homeostasis in different contexts. Aberrant EYA levels or activity are associated with numerous syndromic and non-syndromic developmental disorders, as well as cancers. Commensurate with the multiplicity of biochemical activities carried out by the EYA proteins, they impact upon a range of cellular signaling pathways. Here, we provide a broad overview of the roles played by EYA proteins in development, and highlight the molecular signaling pathways known to be linked with EYA-associated organ development and developmental disorders.

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Circadian clock mechanism driving mammalian photoperiodism

Cited by 53 publications

References 84 publications

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages

Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages

Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle

The Eyes Absent proteins in development and in developmental disorders

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