# Research progress on the mutual regulatory mechanism of circadian clock genes and autophagy

**Authors:** Yueqi Ma, Ran Yu, Xueqing Zheng, Jiahui Rao, Gaiping Shi, Yumei Ding

PMC · DOI: 10.3389/fcell.2025.1696985 · Frontiers in Cell and Developmental Biology · 2025-10-29

## TL;DR

This paper explores how circadian clock genes and autophagy interact to maintain cellular balance and influence disease mechanisms.

## Contribution

It provides new insights into the mutual regulatory mechanisms between circadian clock genes and autophagy.

## Key findings

- Circadian clock genes influence autophagy-related gene expression and signaling pathways.
- Autophagy modulates the expression and activity of circadian clock genes.
- Understanding these interactions may lead to new therapeutic strategies for diseases.

## Abstract

Recent studies have highlighted the intricate relationship between the circadian rhythm, a natural biological process responsive to light and darkness, and autophagy, a mechanism crucial for maintaining cellular homeostasis. Circadian clock genes, which are pivotal in regulating our internal body clock, appear to be closely intertwined with autophagy. These genes can directly influence the expression of autophagy-related genes or modulate signalling pathways that govern autophagic processes. Conversely, autophagy also controls the expression and activity of circadian clock genes. Investigating these interactions will help elucidate how autophagy and circadian rhythms maintain cellular equilibrium and regulate physiological functions. Moreover, such studies help reveal disease mechanisms and develop potential therapeutic strategies.

## Full-text entities

- **Genes:** Map1lc3b (microtubule-associated protein 1 light chain 3 beta) [NCBI Gene 67443] {aka 1010001C15Rik, Atg8, LC3b, MAP1A/MAP1B, Map1lc3}, Ulk1 (unc-51 like kinase 1) [NCBI Gene 22241] {aka Unc51.1, mKIAA0722}, Keap1 (kelch-like ECH-associated protein 1) [NCBI Gene 50868] {aka INRF2, mKIAA0132}, Per2 (period circadian clock 2) [NCBI Gene 18627] {aka mKIAA0347, mPer2}, Becn1 (beclin 1, autophagy related) [NCBI Gene 56208] {aka Atg6}, Hmox1 (heme oxygenase 1) [NCBI Gene 15368] {aka D8Wsu38e, HO-1, HO1, Hemox, Hmox, Hsp32}, Atg7 (autophagy related 7) [NCBI Gene 74244] {aka 1810013K23Rik, Agp7, Apg7l, Atg7l, Gm21553}, Mtor (mechanistic target of rapamycin kinase) [NCBI Gene 56717] {aka 2610315D21Rik, FRAP, FRAP2, Frap1, RAFT1, RAPT1}, CLOCK (clock circadian regulator) [NCBI Gene 9575] {aka KAT13D, bHLHe8}, Crtc2 (CREB regulated transcription coactivator 2) [NCBI Gene 74343] {aka 4632407F12Rik, Torc2}, Nfe2l2 (nuclear factor, erythroid derived 2, like 2) [NCBI Gene 18024] {aka Nrf2}, Atg5 (autophagy related 5) [NCBI Gene 11793] {aka 2010107M05Rik, 3110067M24Rik, Apg5l, Atg5l, Paddy}, DBP (D-box binding PAR bZIP transcription factor) [NCBI Gene 1628] {aka DABP, taxREB302}, tim (timeless) [NCBI Gene 33571] {aka CG3234, Dmel\CG3234, Ritsu, Tim-1, dTIM, dTim}, Nqo1 (NAD(P)H dehydrogenase, quinone 1) [NCBI Gene 18104] {aka Dia4, Dtd, Nmo-1, Nmo1, Nmor1, Ox-1}, cma (cardiac myosin autoantibody) [NCBI Gene 12761], Csnk1a1 (casein kinase 1, alpha 1) [NCBI Gene 93687] {aka 2610208K14Rik, 4632404G05Rik, 5430427P18Rik, CK1a, Csnk1a}, Sirt1 (sirtuin 1) [NCBI Gene 93759] {aka SIR2L1, Sir2, Sir2a, Sir2alpha}, Pik3r1 (phosphoinositide-3-kinase regulatory subunit 1) [NCBI Gene 18708] {aka PI3K, p50alpha, p55alpha, p85alpha}, Map1lc3a (microtubule-associated protein 1 light chain 3 alpha) [NCBI Gene 66734] {aka 1010001H21Rik, 4922501H04Rik, LC3, LC3a}, Cry2 (cryptochrome circadian regulator 2) [NCBI Gene 12953] {aka D130054K12Rik}, Atg9a (autophagy related 9A) [NCBI Gene 245860] {aka Apg9l1, Atg9, Atg9l1}, Ppargc1a (peroxisome proliferative activated receptor, gamma, coactivator 1 alpha) [NCBI Gene 19017] {aka A830037N07Rik, Gm11133, PGC-1, PPARGC-1-alpha, Pgc-1alpha, Pgc1}, Gcg (glucagon) [NCBI Gene 14526] {aka GLP-1, Glu, PPG}, Sqstm1 (sequestosome 1) [NCBI Gene 18412] {aka A170, OSF-6, Osi, STAP, STONE14, p62}, Atg12 (autophagy related 12) [NCBI Gene 67526] {aka 4931423H11Rik, A330058M13Rik, Apg12l, Atg12l}, Atg14 (autophagy related 14) [NCBI Gene 100504663] {aka 4832427M01, Atg14L, D14Ertd114e, D14Ertd436e}, Nr1d2 (nuclear receptor subfamily 1, group D, member 2) [NCBI Gene 353187] {aka RVR, Rev-erb}, Atg1 (Autophagy-related 1) [NCBI Gene 39454] {aka CG10967, DK-4, DmATG1, Dmel\CG10967, ULK1, UNC 51-like}, PER2 (period circadian regulator 2) [NCBI Gene 8864] {aka FASPS, FASPS1}, Hif1a (hypoxia inducible factor 1, alpha subunit) [NCBI Gene 15251] {aka HIF-1-alpha, HIF1-alpha, HIF1alpha, MOP1, bHLHe78}, Hsf1 (heat shock factor 1) [NCBI Gene 15499] {aka HSTF, HSTF 1, Hsf1alpha, Hsf1beta}, Rptor (regulatory associated protein of MTOR, complex 1) [NCBI Gene 74370] {aka 4932417H02Rik, Rap, Raptor, mKIAA1303}, BMAL1 (basic helix-loop-helix ARNT like 1) [NCBI Gene 406] {aka ARNTL, ARNTL1, BMAL1c, JAP3, MOP3, PASD3}, Cebpb (CCAAT/enhancer binding protein beta) [NCBI Gene 12608] {aka C/EBPbeta, CRP2, IL-6DBP, LAP, LIP, NF-IL6}, Bnip3 (BCL2/adenovirus E1B interacting protein 3) [NCBI Gene 12176] {aka Nip3}, Per1 (period circadian clock 1) [NCBI Gene 18626] {aka Hftm, Per, m-rigui, mPer1}, Cry1 (cryptochrome circadian regulator 1) [NCBI Gene 12952] {aka Phll1}, Per2 (period circadian regulator 2) [NCBI Gene 63840] {aka rPER2}, MAP1LC3B (microtubule associated protein 1 light chain 3 beta) [NCBI Gene 81631] {aka ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a}, Ulk3 (unc-51-like kinase 3) [NCBI Gene 71742] {aka 1200015E14Rik}, Tsc1 (TSC complex subunit 1) [NCBI Gene 64930], Clock (clock circadian regulator) [NCBI Gene 12753] {aka 5330400M04Rik, KAT13D}, Tsc2 (TSC complex subunit 2) [NCBI Gene 22084] {aka Nafld, Tcs2}, Bmal1 (basic helix-loop-helix ARNT like 1) [NCBI Gene 11865] {aka Arnt3, Arntl, BMAL1b, MOP3, bHLHe5, bmal1b'}, tor (tortured) [NCBI Gene 21977], Nr1d1 (nuclear receptor subfamily 1, group D, member 1) [NCBI Gene 217166] {aka A530070C09Rik}, Atg8a (Autophagy-related 8a) [NCBI Gene 32001] {aka ATG8, ATG8/LC3, Atg-8a, Atg8, Atg8/LC3, Atg8alpha}, Gabarapl1 (GABA type A receptor associated protein like 1) [NCBI Gene 57436] {aka 3110025G09Rik, 9130422N19Rik, Apg8l, Atg8l, GECI, MNCb-0091}, Akt1 (Akt serine/threonine kinase 1) [NCBI Gene 11651] {aka Akt, LTR-akt, PKB, PKB/Akt, PKBalpha, Rac}, Egln2 (egl-9 family hypoxia-inducible factor 2) [NCBI Gene 112406] {aka 0610011A13Rik, Hif-p4h-1, Ier4, Phd1, SM-20}, Creb1 (cAMP responsive element binding protein 1) [NCBI Gene 12912] {aka 2310001E10Rik, 3526402H21Rik, Creb, Creb-1}, ATG5 (autophagy related 5) [NCBI Gene 9474] {aka APG5, APG5-LIKE, APG5L, ASP, SCAR25, hAPG5}, Rora (RAR-related orphan receptor alpha) [NCBI Gene 19883] {aka 9530021D13Rik, Nr1f1, ROR1, ROR2, ROR3, nmf267}, Tfeb (transcription factor EB) [NCBI Gene 21425] {aka Tcfeb, bHLHe35}, Per3 (period circadian clock 3) [NCBI Gene 18628] {aka 2810049O06Rik, mPer3}
- **Diseases:** cancer (MESH:D009369), diabetes (MESH:D003920), Alzheimer's disease (MESH:D000544), hyperglycemia (MESH:D006943), neurodegeneration (MESH:D019636), metabolic diseases (MESH:D008659), ischaemia (MESH:D007511), hypoxia (MESH:D000860), NSCLC (MESH:D002289), oral squamous cell carcinoma (MESH:D000077195), AFL (MESH:D005235), hypoxic (MESH:D002534), autoimmune diseases (MESH:D001327), hepatic steatosis (MESH:D005234), prostaglandin carcinoma (MESH:C567786), COPD (MESH:D029424), myocardial hypertrophy (MESH:D006984), infection (MESH:D007239), age (MESH:D019588), toxicity (MESH:D064420), folate deficiency (MESH:C562799), colorectal cancer (MESH:D015179), brain injury (MESH:D001930), hepatic lipid degeneration (MESH:D011017), cognitive impairment (MESH:D003072), glioblastoma (MESH:D005909), heart disease (MESH:D006331), ovarian cancer (MESH:D010051), myocardial reperfusion injury (MESH:D015428)
- **Chemicals:** Nobiletin (MESH:C008661), rapamycin (MESH:D020123), blood glucose (MESH:D001786), AICAR (MESH:C031143), methamphetamine (MESH:D008694), Melatonin (MESH:D008550), ROS (-), chloroquine (MESH:D002738), folic acid (MESH:D005492), glucose (MESH:D005947), lipid (MESH:D008055)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], Homo sapiens (human, species) [taxon 9606], Danio rerio (leopard danio, species) [taxon 7955], Drosophila melanogaster (fruit fly, species) [taxon 7227]
- **Cell lines:** L-02 — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_6926), U2OS — Homo sapiens (Human), Osteosarcoma, Cancer cell line (CVCL_0042)

## Full text

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## Figures

3 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12605363/full.md

## References

119 references — full list in the complete paper: https://tomesphere.com/paper/PMC12605363/full.md

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Source: https://tomesphere.com/paper/PMC12605363