Sehgal, A. & Mignot, E. Genetics of sleep and sleep disorders. Cell 146, 194–207 (2011).
Google Scholar
Webb, J. M. & Fu, Y.-H. Recent advances in sleep genetics. Curr. Opin. Neurobiol. 69, 19–24 (2021).
Google Scholar
Zheng, L. & Zhang, L. The molecular mechanism of natural short sleep: a path towards understanding why we need to sleep. Brain Sci. Adv. 8, 165–172 (2022).
Google Scholar
Wang, G. et al. Somatic genetics analysis of sleep in adult mice. J. Neurosci. 42, 5617–5640 (2022).
Google Scholar
Lizcano, J. M. et al. LKB1 is a master kinase that activates 13 kinases of the AMPK subfamily, including MARK/PAR-1. EMBO J. 23, 833–843 (2004).
Google Scholar
Walkinshaw, D. R. et al. The tumor suppressor kinase LKB1 activates the downstream kinases SIK2 and SIK3 to stimulate nuclear export of class IIa histone deacetylases. J. Biol. Chem. 288, 9345–9362 (2013).
Google Scholar
Funato, H. et al. Forward-genetics analysis of sleep in randomly mutagenized mice. Nature 539, 378–383 (2016).
Google Scholar
Honda, T. et al. A single phosphorylation site of SIK3 regulates daily sleep amounts and sleep need in mice. Proc. Natl Acad. Sci. USA 115, 10458–10463 (2018).
Google Scholar
Li, X., Song, S., Liu, Y., Ko, S.-H. & Kao, H.-Y. Phosphorylation of the histone deacetylase 7 modulates its stability and association with 14-3-3 proteins. J. Biol. Chem. 279, 34201–34208 (2004).
Google Scholar
Wang, A. H. et al. Regulation of histone deacetylase 4 by binding of 14-3-3 proteins. Mol. Cell. Biol. 20, 6904–6912 (2000).
Google Scholar
Chen, Z. et al. The role of histone deacetylase 4 during chondrocyte hypertrophy and endochondral bone development. Bone Joint Res. 9, 82–89 (2020).
Google Scholar
Haberland, M., Montgomery, R. L. & Olson, E. N. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat. Rev. Genet. 10, 32–42 (2009).
Google Scholar
Grubbs, J. J., Lopes, L. E., van der Linden, A. M. & Raizen, D. M. A salt-induced kinase is required for the metabolic regulation of sleep. PLoS Biol. 18, e3000220 (2020).
Google Scholar
Banks, G. T. et al. Forward genetics identifies a novel sleep mutant with sleep state inertia and REM sleep deficits. Sci. Adv. 6, eabb3567 (2020).
Google Scholar
Sunagawa, G. A. et al. Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene. Cell Rep. 14, 662–677 (2016).
Google Scholar
Funato, H. & Yanagisawa, M. Hunt for mammalian sleep-regulating genes. Brain Sci. Adv. 7, 75–96 (2021).
Chan, K. Y. et al. Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. Nat. Neurosci. 20, 1172–1179 (2017).
Google Scholar
Xu, J. et al. Regulation of sleep quantity and intensity by long and short isoforms of SLEEPY kinase. Sleep https://doi.org/10.1093/sleep/zsac198 (2022).
Gruffat, H., Manet, E. & Sergeant, A. MEF2-mediated recruitment of class II HDAC at the EBV immediate early gene BZLF1 links latency and chromatin remodeling. EMBO Rep. 3, 141–146 (2002).
Google Scholar
Zhu, Y. et al. Class IIa HDACs regulate learning and memory through dynamic experience-dependent repression of transcription. Nat. Commun. 10, 3469 (2019).
Google Scholar
Mihaylova, M. M. et al. Class IIa histone deacetylases are hormone-activated regulators of FOXO and mammalian glucose homeostasis. Cell 145, 607–621 (2011).
Google Scholar
Chen, B. & Cepko, C. L. HDAC4 regulates neuronal survival in normal and diseased retinas. Science 323, 256–259 (2009).
Google Scholar
Guo, X. et al. A short N-terminal domain of HDAC4 preserves photoreceptors and restores visual function in retinitis pigmentosa. Nat. Commun. 6, 8005 (2015).
Google Scholar
LeGates, T. A., Fernandez, D. C. & Hattar, S. Light as a central modulator of circadian rhythms, sleep and affect. Nat. Rev. Neurosci. 15, 443–454 (2014).
Google Scholar
Price, V., Wang, L. & D’Mello, S. R. Conditional deletion of histone deacetylase-4 in the central nervous system has no major effect on brain architecture or neuronal viability. J. Neurosci. Res. 91, 407–415 (2013).
Google Scholar
Fischle, W. et al. Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Mol. Cell 9, 45–57 (2002).
Google Scholar
Gvilia, I., Xu, F., McGinty, D. & Szymusiak, R. Homeostatic regulation of sleep: a role for preoptic area neurons. J. Neurosci. 26, 9426–9433 (2006).
Google Scholar
Kroeger, D. et al. Galanin neurons in the ventrolateral preoptic area promote sleep and heat loss in mice. Nat. Commun. 9, 4129 (2018).
Google Scholar
Yoo, S. H. et al. PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc. Natl Acad. Sci. USA 101, 5339–5346 (2004).
Google Scholar
Zhang, E. E. et al. A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139, 199–210 (2009).
Google Scholar
Okamoto, S. et al. Dominant-interfering forms of MEF2 generated by caspase cleavage contribute to NMDA-induced neuronal apoptosis. Proc. Natl Acad. Sci. USA 99, 3974–3979 (2002).
Google Scholar
Kozhemyakina, E., Cohen, T., Yao, T.-P. & Lassar, A. B. Parathyroid hormone-related peptide represses chondrocyte hypertrophy through a protein phosphatase 2A/histone deacetylase 4/MEF2 pathway. Mol. Cell. Biol. 29, 5751 (2009).
Google Scholar
Lundell, L. S., Massart, J., Altintas, A., Krook, A. & Zierath, J. R. Regulation of glucose uptake and inflammation markers by FOXO1 and FOXO3 in skeletal muscle. Mol. Metab. 20, 79–88 (2019).
Google Scholar
Ahn, S. et al. A dominant-negative inhibitor of CREB reveals that it is a general mediator of stimulus-dependent transcription of c-fos. Mol. Cell Biol. 18, 967–977 (1998).
Google Scholar
Graves, L. A. et al. Genetic evidence for a role of CREB in sustained cortical arousal. J. Neurophysiol. 90, 1152–1159 (2003).
Google Scholar
Hendricks, J. C. et al. A non-circadian role for cAMP signaling and CREB activity in Drosophila rest homeostasis. Nat. Neurosci. 4, 1108–1115 (2001).
Google Scholar
Wimmer, M. E., Cui, R., Blackwell, J. M. & Abel, T. Cyclic AMP response element-binding protein is required in excitatory neurons in the forebrain to sustain wakefulness. Sleep 44, zsaa267 (2020).
Google Scholar
Lamph, W. W., Dwarki, V. J., Ofir, R., Montminy, M. & Verma, I. M. Negative and positive regulation by transcription factor cAMP response element-binding protein is modulated by phosphorylation. Proc. Natl Acad. Sci. USA 87, 4320–4324 (1990).
Google Scholar
Li, J. et al. Nuclear accumulation of HDAC4 in ATM deficiency promotes neurodegeneration in ataxia telangiectasia. Nat. Med. 18, 783–790 (2012).
Google Scholar
Sen, T. & Sen, N. Isoflurane-induced inactivation of CREB through histone deacetylase 4 is responsible for cognitive impairment in developing brain. Neurobiol. Dis. 96, 12–21 (2016).
Google Scholar
Zada, D., Bronshtein, I., Lerer-Goldshtein, T., Garini, Y. & Appelbaum, L. Sleep increases chromosome dynamics to enable reduction of accumulating DNA damage in single neurons. Nat. Commun. 10, 895 (2019).
Google Scholar
Zada, D. et al. Parp1 promotes sleep, which enhances DNA repair in neurons. Mol. Cell 81, 4979–4993.e4977 (2021).
Google Scholar
Brüning, F. et al. Sleep-wake cycles drive daily dynamics of synaptic phosphorylation. Science 366, eaav3617 (2019).
Google Scholar
Wang, Z. et al. Quantitative phosphoproteomic analysis of the molecular substrates of sleep need. Nature 558, 435–439 (2018).
Google Scholar
Benito, E., Valor, L. M., Jimenez-Minchan, M., Huber, W. & Barco, A. cAMP response element-binding protein is a primary hub of activity-driven neuronal gene expression. J. Neurosci. 31, 18237–18250 (2011).
Google Scholar
Sando, R. 3rd et al. HDAC4 governs a transcriptional program essential for synaptic plasticity and memory. Cell 151, 821–834 (2012).
Google Scholar
Noya, S. B. et al. The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Science 366, eaav2642 (2019).
Google Scholar
Kim, S. J. et al. Kinase signalling in excitatory neurons regulates sleep quantityand depth. Nature https://doi.org/10.1038/s41586-022-05450-1 (2022).
Lu, J., McKinsey, T. A., Zhang, C.-L. & Olson, E. N. Regulation of skeletal myogenesis by association of the MEF2 transcription factor with class II histone deacetylases. Mol. Cell 6, 233–244 (2000).
Google Scholar
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 11, 783–784 (2014).
Google Scholar
Yardeni, T., Eckhaus, M., Morris, H. D., Huizing, M. & Hoogstraten-Miller, S. Retro-orbital injections in mice. Lab. Anim. 40, 155–160 (2011).
Google Scholar
Zhao, H. et al. Absence of stress response in dorsal raphe nucleus in modulator of apoptosis 1-deficient mice. Mol. Neurobiol. 56, 2185–2201 (2019).
Google Scholar
Christakis, D. A., Ramirez, J. S. & Ramirez, J. M. Overstimulation of newborn mice leads to behavioral differences and deficits in cognitive performance. Sci. Rep. 2, 546 (2012).
Google Scholar
Horsch, M. et al. Requirement of the RNA-editing enzyme ADAR2 for normal physiology in mice. J. Biol. Chem. 286, 18614–18622 (2011).
Google Scholar
Liu, Q., Xu, Y., Wan, W. & Ma, Z. An unexpected improvement in spatial learning and memory ability in alpha-synuclein A53T transgenic mice. J. Neural Transm. 125, 203–210 (2018).
Google Scholar
Peters, J., Dieppa-Perea, L. M., Melendez, L. M. & Quirk, G. J. Induction of fear extinction with hippocampal-infralimbic BDNF. Science 328, 1288–1290 (2010).
Google Scholar
Soria-Gomez, E. et al. Habenular CB1 receptors control the expression of aversive memories. Neuron 88, 306–313 (2015).
Google Scholar
Zhang, J. et al. Presynaptic Excitation via GABAB receptors in habenula cholinergic neurons regulates fear memory expression. Cell 166, 716–728 (2016).
Google Scholar
Patti, C. L. et al. Effects of sleep deprivation on memory in mice: role of state-dependent learning. Sleep 33, 1669–1679 (2010).
Google Scholar
Savelyev, S. A., Larsson, K. C., Johansson, A. S. & Lundkvist, G. B. Slice preparation, organotypic tissue culturing and luciferase recording of clock gene activity in the suprachiasmatic nucleus. J. Vis. Exp. 48, 2439 (2011).
Mei, L. et al. Long-term in vivo recording of circadian rhythms in brains of freely moving mice. Proc. Natl Acad. Sci. USA 115, 4276–4281 (2018).
Google Scholar
Yang, J. et al. A quick protocol for the preparation of mouse retinal cryosections for immunohistochemistry. Open Biol. 11, 210076 (2021).
Google Scholar
Castel, M., Belenky, M., Cohen, S., Wagner, S. & Schwartz, W. J. Light-induced c-Fos expression in the mouse suprachiasmatic nucleus: immunoelectron microscopy reveals co-localization in multiple cell types. Eur. J. Neurosci. 9, 1950–1960 (1997).
Google Scholar
Xu, P. et al. NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior. Neuron 109, 3268–3282 (2021).
Google Scholar
Ju, D. et al. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci. Transl. Med. 12, eaba0769 (2020).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
Google Scholar
Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).
Google Scholar
Ramírez, F., Dündar, F., Diehl, S., Grüning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).
Google Scholar
Yu, G., Wang, L. G. & He, Q. Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).
Google Scholar