Review Circadian Rhythms of the Hypothalamus: From Function to Physiology Rachel Van Drunen 1,2 and Kristin Eckel-Mahan 1,2,* 1 MD Anderson UTHealth School Graduate School of Biomedical Sciences, Houston TX 77030, USA; [email protected] 2 Brown Foundation Institute of Molecular Medicine University of Texas McGovern Medical School, Houston, TX 77030, USA * Correspondence: [email protected] Abstract: The nearly ubiquitous expression of endogenous 24 h oscillations known as circadian rhythms regulate the timing of physiological functions in the body. These intrinsic rhythms are sensitive to external cues, known as zeitgebers, which entrain the internal biological processes to the daily environmental changes in light, temperature, and food availability. Light directly entrains the master clock, the suprachiasmatic nucleus (SCN) which lies in the hypothalamus of the brain and is responsible for synchronizing internal rhythms. However, recent evidence underscores the importance of other hypothalamic nuclei in regulating several essential rhythmic biological functions. These extra-SCN hypothalamic nuclei also express circadian rhythms, suggesting distinct regions that oscillate either semi-autonomously or independent of SCN innervation. Concurrently, the extra-SCN hypothalamic nuclei are also sensitized to fluctuations in nutrient and hormonal signals. Thus, food intake acts as another powerful entrainer for the hypothalamic oscillators’ mediation of energy homeostasis. Ablation studies and genetic mouse models with perturbed extra-SCN hypothalamic nuclei function reveal their critical downstream involvement in an array of functions including Citation: Van Drunen, R.; metabolism, thermogenesis, food consumption, thirst, mood and sleep. Large epidemiological Eckel-Mahan, K. Circadian Rhythms studies of individuals whose internal circadian cycle is chronically disrupted reveal that disruption of the Hypothalamus: From Function of our internal clock is associated with an increased risk of obesity and several neurological diseases to Physiology. Clocks&Sleep 2021, 3, and disorders. In this review, we discuss the profound role of the extra-SCN hypothalamic nuclei in 189–226. https://doi.org/10.3390/ rhythmically regulating and coordinating body wide functions. clockssleep3010012 Keywords: circadian rhythm; clock genes; hypothalamus; extra-SCN hypothalamic nuclei; metabolism; Academic Editor: Hiroshi Kadotani food-entrainable oscillator; obesity Received: 5 January 2021 Accepted: 18 February 2021 Published: 25 February 2021 1. Introduction Publisher’s Note: MDPI stays neutral Most organisms on earth exhibit highly conserved 24 h rhythms in physiology and with regard to jurisdictional claims in behavior. Constant 24 h rotations of the earth punctuated by the rising and setting of published maps and institutional affil- the sun contribute to an organism’s circadian (i.e., 24 h) biology at the molecular, cellular, iations. and behavioral levels. This internal clock not only sensitizes, but enables an organism to anticipate daily fluctuations in its environment. This time-keeping process operates in almost all cells of an organism and is self-perpetuating, even in the absence of external cues [1]. Although circadian clocks throughout the body are synchronized in large part through the suprachiasmatic nucleus (SCN) of the hypothalamus, rhythmicity in other Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. hypothalamic nuclei has proved to be a critical regulator of physiological rhythms such as This article is an open access article the sleep–wake cycle and daily food intake. distributed under the terms and The circadian clock in the hypothalamus and elsewhere ultimately depends on 24 h conditions of the Creative Commons rhythms at the cellular level, where a central transcription–translation feedback loop (TTFL) Attribution (CC BY) license (https:// regulates the expression of key clock transcription factors (TFs). The core loop is a het- creativecommons.org/licenses/by/ erodimer consisting of circadian locomotor output cycles kaput (CLOCK) and brain and 4.0/). muscle ARNT-like protein (BMAL1), which promote the rhythmic expression of numerous Clocks&Sleep 2021, 3, 189–226. https://doi.org/10.3390/clockssleep3010012 https://www.mdpi.com/journal/clockssleep Clocks & Sleep 2021, 3, FOR PEER REVIEW 2 Clocks&Sleep 2021, 3 190 and muscle ARNT-like protein (BMAL1), which promote the rhythmic expression of nu- merous E-Box-containing output genes, including the Period (Per 1–3) and Cryptochrome E-Box-containing(Cry 1–2) genes, outputwhich as genes, proteins including function the as Period direct (Per repressors 1–3) and of Cryptochrome the CLOCK:BMAL1 (Cry 1–2)heterodimer genes, which [1,2]. as Resumption proteins function of CLOCK:BM as directAL1 repressors activity of occurs the CLOCK:BMAL1 only when these het- re- erodimerpressors [1are,2]. degraded Resumption by ofregulators CLOCK:BMAL1 such as activitythe serine/threonine occurs only when casein these kinases repressors (CK1δ areand degraded CK1ϵ), which by regulators phosphorylate such as thePER, serine/threonine initiating its ubiquitination. casein kinases CRY (CK1 turnoverδ and CK1 is also), whichcontrolled phosphorylate by phosphorylation; PER, initiating the itsmetabolic ubiquitination. sensor 5 CRY′ adenosine turnover monophosphate-acti- is also controlled byvated phosphorylation; protein kinase the (AMPK) metabolic tags sensor it for 5pr0 adenosineoteasome degradation monophosphate-activated by direct phosphoryla- protein kinasetion. Additional (AMPK) tags loops it for consisting proteasome of the degradation nuclear receptor by direct subfamily phosphorylation. 1 D member Additional 1 (NR1D1) loopsalso known consisting as REV-ER of the nuclearα/β and receptorthe retinoic subfamily acid receptor-related 1 D member 1orphan (NR1D1) receptors also known (RORs) assustain REV-ER thisα/ coreβ and transcriptional the retinoic acidloop receptor-relatedby transactivating orphan or repressing receptors Bmal1 (RORs) [3–5]. sustain An in- thistegral core non-circadian transcriptional loop loop intertwined by transactivating with the core or repressing clock includes Bmal1 the [3 circadian–5]. An integral metabo- non-circadianlite nicotinamide loop adenine intertwined dinucleotide with thecore (NAD clock+). The includes NAD the+-dependent circadian deacetylase metabolite nicoti- sirtuin namide1 (SIRT1) adenine directly dinucleotide binds to the (NAD CLOCK:BMAL+). The NAD+1-dependent heterodimer, deacetylase and thereby sirtuin regulates 1 (SIRT1) the directlyNAD+ bindssalvage to thepathway CLOCK:BMAL1 transcriptionally heterodimer, [6]. Together, and thereby these regulates feedback the NADloops+ salvagemediate pathwayrhythmic transcriptionally expression of hundreds [6]. Together, of clock- thesecontrolled feedback genes loops mediate(Figure 1). rhythmic Importantly, expression Bmal1 ofis hundreds the only gene of clock-controlled in which single-gene genes (Figure knockout1). Importantly,results in fullBmal1 loss ofis rhythmicity the only gene at inthe whichcellular single-gene and behavioral knockout levels results in a innormal full loss light–dark of rhythmicity cycle [7,8], at the though cellular double and behavioral knockouts levelsof Cry1 in aand normal Cry2 light–dark can result cyclein complete [7,8], though arrhythmicity double knockouts in constant of darknessCry1 and [9,10].Cry2 can This resultunderscores in complete the robust arrhythmicity and resilient, in constant though darkness highly intricate, [9,10]. This nature underscores of our internal the robust clocks andto maintaining resilient, though time. highly intricate, nature of our internal clocks to maintaining time. FigureFigure 1. 1.Interactions Interactions between betweenthe the core core clock clock and and intracellular intracellular metabolism. metabolism. The The heterodimerization heterodimerization of of BMAL1 and CLOCK proteins and subsequent binding to E-Box-containing regulatory elements BMAL1 and CLOCK proteins and subsequent binding to E-Box-containing regulatory elements leads to leads to expression of the repressor PER and CRY proteins, the REV-ERBs and RORs, which initiate expression of the repressor PER and CRY proteins, the REV-ERBs and RORs, which initiate the auxiliary the auxiliary loop, and the core clock genes (CCGs) that drive numerous other intracellular rhythms. loop,Cytoplasmic and the core PER clock and genesCRY (CCGs)proteins that are driveeventua numerouslly tagged other for intracellular degradation rhythms. by AMPK. Cytoplasmic Rhythmic PERcellular and CRYmetabolism, proteins aresuch eventually as rhythmic tagged NAD for+ abundance, degradation participates by AMPK. Rhythmic in the core cellular clock by metabolism, direct reg- + suchulation as rhythmic of clock-associated NAD abundance, factors, participates such as the in the anti-aging-associated core clock by direct regulation histone deacetylase of clock-associated protein, factors,SIRT1. such as the anti-aging-associated histone deacetylase protein, SIRT1. NumerousNumerous epidemiological epidemiological studies studies have have shed shed light light on on the the importance importance of of rhythmicity rhythmicity onon health. health. Over Over time, time, disruption disruption of of our our 24 24 h h cycle cycle can can lead lead to to deleterious deleterious physiological physiological outcomes,outcomes, such such as as premature premature aging, aging, and and an increasedan increased risk