TIMELESS

Summary

TIMELESS (timeless circadian regulator, HGNC:11813) is a protein-coding gene on chromosome 12q13.3, encoding Protein timeless homolog (Q9UNS1). Plays an important role in the control of DNA replication, maintenance of replication fork stability, maintenance of genome stability throughout normal DNA replication, DNA repair and in the regulation of the circadian clock. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

The protein encoded by this gene is highly conserved and is involved in cell survival after damage or stress, increase in DNA polymerase epsilon activity, maintenance of telomere length, and epithelial cell morphogenesis. The encoded protein also plays a role in the circadian rhythm autoregulatory loop, interacting with the PERIOD genes (PER1, PER2, and PER3) and others to downregulate activation of PER1 by CLOCK/ARNTL. Changes in this gene or its expression may promote prostate cancer, lung cancer, breast cancer, and mental disorders.

Source: NCBI Gene 8914 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 218 total — 1 pathogenic
• GTEx eGene: eQTL in 12 tissues, sQTL in 4 (q < 0.05)
• Phenotypes (HPO): 2
• Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.86 (unconstrained)
• MANE Select transcript: NM_003920
• Interaction hub: 1,944 STRING partners (top 8% of genes corpus-wide)
• Notable: 218 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11813
Approved symbol	TIMELESS
Name	timeless circadian regulator
Location	12q13.3
Locus type	gene with protein product
Status	Approved
Aliases	hTIM, TIM, TIM1
Ensembl gene	ENSG00000111602
Ensembl biotype	protein_coding
OMIM	603887
Entrez	8914

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 17 protein_coding, 11 nonsense_mediated_decay, 3 retained_intron

MANE Select: ENST00000553532

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 2, TSL 5: 1

ENST00000553532, ENST00000229201, ENST00000553314, ENST00000555808, ENST00000557589, ENST00000865170, ENST00000865171, ENST00000865172, ENST00000865173, ENST00000927920, ENST00000927921, ENST00000927922, ENST00000927923, ENST00000927924, ENST00000927925, ENST00000927926, ENST00000971076, ENST00001024626, ENST00001062797, ENST00001062798, ENST00001062799, ENST00001062800, ENST00001062801, ENST00001062802, ENST00001062803, ENST00001062804, ENST00001062805, ENST00001062806, ENST00001062807, ENST00001109329, ENST00001143445

RefSeq mRNA: 2 — MANE Select: NM_003920 NM_001330295, NM_003920

CCDS: CCDS81699, CCDS8918

Canonical transcript exons

ENST00000553532 — 29 exons

Exon	Start	End
ENSE00000749520	56433773	56433926
ENSE00001116673	56431471	56431604
ENSE00001145588	56420963	56421134
ENSE00001145598	56421351	56421493
ENSE00001145604	56421727	56421809
ENSE00001145647	56423584	56423707
ENSE00001145662	56424762	56424913
ENSE00001181800	56428236	56428405
ENSE00001181811	56428883	56429100
ENSE00001181818	56430105	56430281
ENSE00001282517	56425015	56425152
ENSE00001282528	56428549	56428652
ENSE00001282545	56430881	56430968
ENSE00001282558	56432369	56432524
ENSE00001282564	56433026	56433127
ENSE00001282571	56433381	56433443
ENSE00001282578	56433538	56433652
ENSE00001391242	56434074	56434231
ENSE00002437580	56416363	56417786
ENSE00002438456	56449310	56449426
ENSE00003460637	56420569	56420687
ENSE00003462679	56423797	56423894
ENSE00003516106	56422847	56422992
ENSE00003524256	56418134	56418359
ENSE00003534010	56422106	56422191
ENSE00003564656	56417907	56418008
ENSE00003572682	56420813	56420881
ENSE00003599354	56423274	56423475
ENSE00003672242	56421899	56422016

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 93.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.4714 / max 108.6483, expressed in 1709 samples.

Highest expression (Bgee): ventricular zone, embryo, ganglionic eminence, primordial germ cell in gonad, mucosa of transverse colon.

Genetic regulation across tissues (GTEx eQTL / sQTL)

TIMELESS is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 12 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

16 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	eqtl	2.8e-17	+0.11	12:56434836:G:T
Cells EBV-transformed lymphocytes	sqtl	2.6e-15	+0.94	12:56436326:T:C
Testis	eqtl	8.5e-09	+0.19	12:56438263:A:T
Cells EBV-transformed lymphocytes	eqtl	6.5e-08	-0.15	12:56428594:T:A
Adipose Subcutaneous	eqtl	1.5e-03	-0.10	12:56428594:T:A
Esophagus Mucosa	sqtl	2.1e-03	-1.01	12:56235762:A:G
Muscle Skeletal	eqtl	2.3e-03	+0.09	12:56420869:G:A
Breast Mammary Tissue	eqtl	3.7e-03	-0.40	12:55569944:C:T
Esophagus Gastroesophageal Junction	eqtl	2.2e-02	-0.24	12:57073216:G:C
Artery Aorta	eqtl	2.2e-02	+0.33	12:56363401:A:G
Adrenal Gland	eqtl	2.4e-02	+0.85	12:56105651:G:A
Esophagus Mucosa	eqtl	2.6e-02	+0.14	12:56429533:A:G
Skin Sun Exposed Lower leg	eqtl	2.7e-02	-0.08	12:56422138:C:T
Spleen	sqtl	3.1e-02	-0.47	12:56429838:C:T
Colon Sigmoid	sqtl	3.8e-02	-1.19	12:56389740:G:C
Brain Hypothalamus	eqtl	4.7e-02	-0.45	12:56581131:G:A

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
131523	15.7973	1707
131524	0.3652	211
131525	0.3089	150

Top tissues by expression

showing 100 of 281 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	93.06	gold quality
embryo	UBERON:0000922	91.84	gold quality
ganglionic eminence	UBERON:0004023	91.51	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.95	gold quality
mucosa of transverse colon	UBERON:0004991	84.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.38	gold quality
right lobe of liver	UBERON:0001114	83.84	gold quality
vermiform appendix	UBERON:0001154	82.09	gold quality
stromal cell of endometrium	CL:0002255	82.07	gold quality
islet of Langerhans	UBERON:0000006	81.83	gold quality
endometrium epithelium	UBERON:0004811	81.66	gold quality
lymph node	UBERON:0000029	81.64	gold quality
rectum	UBERON:0001052	81.53	gold quality
granulocyte	CL:0000094	81.34	gold quality
bone marrow	UBERON:0002371	80.99	gold quality
esophagus mucosa	UBERON:0002469	80.84	gold quality
spleen	UBERON:0002106	80.45	gold quality
adenohypophysis	UBERON:0002196	79.79	gold quality
bone element	UBERON:0001474	79.17	gold quality
lower esophagus mucosa	UBERON:0035834	78.96	gold quality
bone marrow cell	CL:0002092	78.93	gold quality
caecum	UBERON:0001153	78.74	gold quality
pituitary gland	UBERON:0000007	78.71	gold quality
metanephros cortex	UBERON:0010533	78.71	gold quality
right adrenal gland cortex	UBERON:0035827	78.62	gold quality
right adrenal gland	UBERON:0001233	78.46	gold quality
body of pancreas	UBERON:0001150	78.44	gold quality
pancreas	UBERON:0001264	78.44	gold quality
amniotic fluid	UBERON:0000173	77.89	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.61	gold quality
trabecular bone tissue	UBERON:0002483	77.40	gold quality
secondary oocyte	CL:0000655	76.96	gold quality
body of stomach	UBERON:0001161	76.89	gold quality
ectocervix	UBERON:0012249	76.74	gold quality
left adrenal gland	UBERON:0001234	76.66	gold quality
esophagus	UBERON:0001043	76.51	gold quality
transverse colon	UBERON:0001157	76.37	gold quality
upper lobe of left lung	UBERON:0008952	76.34	gold quality
liver	UBERON:0002107	76.29	gold quality
small intestine	UBERON:0002108	76.13	gold quality
testis	UBERON:0000473	76.12	gold quality
right lobe of thyroid gland	UBERON:0001119	76.06	gold quality
upper lobe of lung	UBERON:0008948	75.97	gold quality
right testis	UBERON:0004534	75.90	gold quality
left adrenal gland cortex	UBERON:0035825	75.88	gold quality
pigmented layer of retina	UBERON:0001782	75.77	gold quality
retina	UBERON:0000966	75.76	gold quality
vagina	UBERON:0000996	75.75	gold quality
epithelium of esophagus	UBERON:0001976	75.55	gold quality
left testis	UBERON:0004533	75.53	gold quality
esophagus squamous epithelium	UBERON:0006920	75.47	gold quality
minor salivary gland	UBERON:0001830	75.37	gold quality
adrenal cortex	UBERON:0001235	75.31	gold quality
adrenal gland	UBERON:0002369	75.19	gold quality
tonsil	UBERON:0002372	75.19	gold quality
cervix squamous epithelium	UBERON:0006922	75.16	gold quality
gastrocnemius	UBERON:0001388	75.00	gold quality
stomach	UBERON:0000945	74.79	gold quality
oocyte	CL:0000023	74.59	gold quality
left lobe of thyroid gland	UBERON:0001120	74.54	gold quality
gall bladder	UBERON:0002110	74.47	gold quality
endometrium	UBERON:0001295	74.42	gold quality
smooth muscle tissue	UBERON:0001135	74.41	gold quality
mouth mucosa	UBERON:0003729	74.41	gold quality
body of uterus	UBERON:0009853	74.25	gold quality
skin of abdomen	UBERON:0001416	74.20	gold quality
intestine	UBERON:0000160	74.18	gold quality
squamous epithelium	UBERON:0006914	74.09	gold quality
omental fat pad	UBERON:0010414	74.01	gold quality
peritoneum	UBERON:0002358	73.98	gold quality
placenta	UBERON:0001987	73.97	gold quality
oral cavity	UBERON:0000167	73.93	silver quality
thyroid gland	UBERON:0002046	73.92	gold quality
leukocyte	CL:0000738	73.89	gold quality
left uterine tube	UBERON:0001303	73.89	gold quality
apex of heart	UBERON:0002098	73.89	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.83	gold quality
monocyte	CL:0000576	73.81	gold quality
muscle of leg	UBERON:0001383	73.80	gold quality
duodenum	UBERON:0002114	73.80	gold quality
thymus	UBERON:0002370	73.73	gold quality
colon	UBERON:0001155	73.67	gold quality
large intestine	UBERON:0000059	73.59	gold quality
mononuclear cell	CL:0000842	73.49	gold quality
endocervix	UBERON:0000458	73.47	gold quality
adipose tissue of abdominal region	UBERON:0007808	73.45	gold quality
cortical plate	UBERON:0005343	73.16	gold quality
saliva-secreting gland	UBERON:0001044	72.96	gold quality
adrenal tissue	UBERON:0018303	72.89	gold quality
skin of leg	UBERON:0001511	72.73	gold quality
muscle layer of sigmoid colon	UBERON:0035805	72.71	gold quality
uterus	UBERON:0000995	72.61	gold quality
right hemisphere of cerebellum	UBERON:0014890	72.45	gold quality
female reproductive system	UBERON:0000474	72.41	gold quality
epithelium of nasopharynx	UBERON:0001951	72.41	gold quality
right lung	UBERON:0002167	72.32	gold quality
spinal cord	UBERON:0002240	72.21	gold quality
sigmoid colon	UBERON:0001159	72.20	gold quality
subcutaneous adipose tissue	UBERON:0002190	72.18	gold quality
cerebellar hemisphere	UBERON:0002245	72.14	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.68

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Bone marrow	tissue	20.8	low
Thymus	tissue	18.4
Tonsil	tissue	16.8	medium
Lymph node	tissue	14.3	medium
Retina	tissue	12.7
Appendix	tissue	10.4	high
Liver	tissue	9.1	low
Placenta	tissue	8.1	medium
Rectum	tissue	8.0	medium
Colon	tissue	6.3	medium
Spleen	tissue	6.2	low
Small intestine	tissue	5.9	medium
Testis	tissue	5.8	high
Parathyroid gland	tissue	5.6	low
Duodenum	tissue	5.6	medium
Esophagus	tissue	5.3	medium
Choroid plexus	tissue	5.3
Skin 1	tissue	5.2	medium
Stomach 1	tissue	5.2	low
Smooth muscle	tissue	5.2	not detected
Pituitary gland	tissue	5.0
Urinary bladder	tissue	4.4	medium
Thyroid gland	tissue	4.4	low
Breast	tissue	4.2	medium
Endometrium 1	tissue	4.1	low
Cervix	tissue	3.8	not detected
Lung	tissue	3.8	not detected
Vagina	tissue	3.7	low
Locus coeruleus	tissue	3.6
Kidney	tissue	3.5	medium
Pancreas	tissue	3.4	not detected
Seminal vesicle	tissue	3.2	low
Adipose tissue	tissue	3.2	not detected
Gallbladder	tissue	3.1	medium
Prostate	tissue	3.0	not detected
Fallopian tube	tissue	2.9	high
Salivary gland	tissue	2.6	medium
Adrenal gland	tissue	2.6	medium
Ovary	tissue	2.4	not detected
Hippocampus	tissue	2.4	medium
Epididymis	tissue	2.3	not detected
Nucleus accumbens	tissue	2.2
Postcentral gyrus	tissue	2.1
Spinal cord	tissue	1.6
Skeletal muscle	tissue	1.5	not detected
Tongue	tissue	1.5
Superior colliculi	tissue	1.5
Medulla oblongata	tissue	1.4
Hypothalamus	tissue	1.4
Cerebellum	tissue	1.4	medium
Heart muscle	tissue	1.3	low
Pons	tissue	1.2
Midbrain	tissue	1.2
Thalamus	tissue	1.2
Substantia nigra	tissue	1.2
Periaqueductal gray	tissue	1.2
Olfactory bulb	tissue	1.0
Frontal cortex	tissue	0.9
Corpus callosum	tissue	0.9
Septum	tissue	0.9

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Anterior thalamic nucleus, ventral (5.2), Reticular pontine nucleus, oral (4.8), Nucleus ambiguus (4.7), Nucleus reuniens (4.7), Temporal white matter (4.7).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR3C1, TP53

miRNA regulators (miRDB)

Targeting TIMELESS by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 52 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-7151-5P	99.37	67.82	613
HSA-MIR-501-3P	99.33	66.12	651
HSA-MIR-502-3P	99.33	66.12	651
HSA-MIR-6828-5P	99.31	69.21	1433

Functional genomics

gnomAD constraint: pLI 1.09e-30, LOEUF 0.857, missense Z 1.26 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000553532 — one region, missense o/e 0.95. DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): SNU-475 (-2.624), HPAF-II (-2.613), JHH-6 (-2.583), S-117 (-2.562), KMRC-3 (-2.532), KARPAS-422 (-2.519), DB (-2.503), EWS502 (-2.491), COV318 (-2.481), YH-13 (-2.464), EC-GI-10 (-2.461), COLO-800 (-2.433), EFO-21 (-2.417), KP-N-YN (-2.412), LN-428 (-2.358).

Literature-anchored findings (GeneRIF, showing 40)

• Down-regulation of Timeless in human cells seriously compromises replication and intra-S checkpoints, indicating an intimate connection between the circadian cycle and the DNA damage checkpoints that is in part mediated by the Timeless protein. (PMID:15798197)
• Tipin is a checkpoint mediator that cooperates with Tim and may regulate the nuclear relocation of Claspin in response to replication checkpoint (PMID:17102137)
• observation explains the similar checkpoint phenotypes observed in both Tipin- and Timeless-depleted cells (PMID:17116885)
• TIM and Tipin are functional orthologs of their replisome-associated yeast counterparts capable of coordinating replication with genotoxic stress responses, and distinguishes mammalian TIM from the circadian-specific paralogs. (PMID:17141802)
• These findings indicate that the Tim-Tipin complex mediates the UV-induced intra-S checkpoint, Tim is needed to maintain DNA replication fork movement, Tipin interacts with RPA on DNA. (PMID:17296725)
• HRPAP20 and TIMELESS as promising markers of tamoxifen resistance in women with ER alpha-positive breast tumors. (PMID:17909269)
• TIMELESS is required for ATM-dependent CHK2 activation and G2/M checkpoint control (PMID:19996108)
• The results suggest that Timeless-Tipin functions as a replication fork stabilizer that couples DNA replication with sister chromatid cohesion established at replication forks. (PMID:20124417)
• Data show significant association between TIMELESS variants and depression with fatigue in females, and association to depression with early morning awakening in males. (PMID:20174623)
• the interaction between dPERIOD and dCLOCK is TIM-dependent and modulated by light, revealing a novel and unanticipated in vivo role for TIM in circadian transcription (PMID:20980603)
• These findings demonstrate that Tim is essential for sustaining the episomal forms of EBV DNA in latently infected cells. (PMID:21490103)
• Timeless has a function in SCC that is independent of the Tim-Tipin complex, even though the abundance of Timeless is reduced when Tipin is targeted for depletion. (PMID:21508667)
• Tim coordinates mitotic kinase activation with termination of DNA replication. (PMID:21573113)
• observed a significant association between stage II, III, and IV breast cancers and TIMELESS promoter hypomethylation in peripheral blood lymphocytes in 80 breast cancer cases and 80 age-matched controls (PMID:22006848)
• Timeless functions together with TRF1 to prevent fork collapse at telomere repeat DNA and ensure stable maintenance of telomere length and integrity. (PMID:22672906)
• All lung cancer specimens but no matched normal lung tissues were positive for TIM expression. (PMID:23173913)
• TIMELESS has a distinct contribution to suppression of chromosomal instability that is independent of its heterodimeric partner, TIPIN. (PMID:23255133)
• Kaposi’s Sarcoma-associated herpesvirus episome maintenance requires Tim-assisted replication fork protection at the viral terminal repeats. (PMID:23325691)
• Data indicate that RNAi-mediated knockdown of TIMELESS (TIM) in NIH3T3 and U2OS cells shortens the period by 1 hour and diminishes DNA damage-dependent phase advancing. (PMID:23418588)
• Tim-Tipin complex (or Tim alone) is able to associate with DNA polymerase epsilon bound to a 40-/80-mer DNA ligand. (PMID:23511638)
• TIMELESS is frequently overexpressed in various types of tumor tissues, and elevated TIMELESS expression is associated with advanced tumor stage and poorer breast cancer prognosis. (PMID:24161199)
• The results of this study suggest that the TIMELESS gene may be associated with the lithium prophylactic response in bipolar illness. (PMID:24636202)
• TIMELESS and RORA genes may confer susceptibility to bipolar disorders and impact on circadian phenotypes (PMID:24716566)
• overexpression of TIM exerts oncogenic function in human HCCs, which is mediated via CHEK2 and EEF1A2. (PMID:25405317)
• Data reports the crystal structure of Timeless-PARP-1 complex and provides evidence that Timeless is recruited to sites of DNA damage through PARP-1 to mediate homologous recombination repair of DNA double-strand breaks. (PMID:26344098)
• TIMELESS mutants unable to bind PARP1. TIMELESS silencing significantly impairs DNA double-strand break repair. (PMID:26456830)
• results provide the first evidence that TIM is required for the correct chromatin association of the CMG complex to allow efficient DNA replication. (PMID:27587400)
• Our results show that TIMELESS overexpression correlates with pelvic lymph node metastasis, lymphovascular space involvement, as well as unfavorable OS and DFS in human cervical cancer. Therefore, TIMELESS expression may be a potential prognostic biomarker for cervical cancer patients (PMID:27909716)
• the 1.85 A crystal structure of a large N-terminal segment of human Timeless, spanning amino acids 1-463, is presented and this region of human Timeless harbours a partial binding site for Tipin. (PMID:28334766)
• Inhibition of MYC significantly blocked the effects of TIM on CSC population, cell invasion and anchor-independent cell growth. TIM plays an important role in promoting breast cancer progression and may represent a novel therapeutic target for breast cancer. (PMID:28464854)
• Stable ectopic overexpression of TIMELESS in nasopharyngeal carcinoma cell lines conferred resistance to cisplatin-induced apoptosis in vitro and in vivo, promoted an epithelial-to-mesenchymal transition phenotype, and activated the Wnt/beta-catenin pathway and downstream gene transcription. (PMID:28583847)
• TIM rs2291738 was associated with chronotype dimensions (PMID:28708003)
• Results provide evidence that Timeless displays the characteristics of an ERalpha co-activator: it binds directly to ERalpha, increases its transcriptional activity, and is required for full ERalpha activity. This activity likely contributes to the ability of Timeless to promote breast cancer cell proliferation and may underlie the observed associations between Timeless and breast cancer patient outcome. (PMID:29555554)
• TIMELESS participates in the regulation of cellular senescence. (PMID:30100061)
• The C allele at the rs631090 locus of C1q, the G allele at 1525A/G site of TRAIL, and the G allele of Tim-1 at -1454G/A site are susceptibility variants associated with SLE. The frequency of the G allele at -1454G/A of Tim-1 was dramatically higher in the study group than in the control group. (PMID:30183357)
• we suggest that disturbances in timeless expression may result in the disruption of the control of normal circadian rhythm, thus benefiting the survival of glioma cells and promoting carcinogenesis. (PMID:30249891)
• Results indicate a role for the DDX11-Timeless interaction in coordinating DNA replication with sister chromatid cohesion, and suggest implications for understanding the molecular basis of Warsaw breakage syndrome (WABS). (PMID:30303954)
• ERK activation promotes TIMELESS expression in colon cancer cell lines. TIMELESS depletion increases gammaH2AX, a marker of DNA damage, and triggers G2/M arrest via increased CHK1 and CDK1 phosphorylation. (PMID:30629587)
• the data indicate that enhanced levels of Claspin and Timeless represent a gain of function that protects cancer cells from oncogene-induced replication stress in a checkpoint-independent manner. (PMID:30796221)
• The mutation prevents TIM accumulation in the nucleus and has altered affinity for CRY2. (PMID:31138685)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	timeless	ENSDARG00000078497
mus_musculus	Timeless	ENSMUSG00000039994
rattus_norvegicus	Timeless	ENSRNOG00000031916
drosophila_melanogaster	timeout	FBGN0038118
caenorhabditis_elegans		WBGENE00006571

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1321393) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)	Records
embryonic lethality between implantation and somite formation, complete penetrance	1
preweaning lethality, complete penetrance	1

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
APOF	protein-coding	319
MIP	protein-coding	4284
STAT2	protein-coding	6773
GLS2	protein-coding	27165
SPRYD4	protein-coding	283377
SNORA105C	snoRNA	106635541
RBMS2	protein-coding	5939

Protein

Protein identifiers

Protein timeless homolog — Q9UNS1 (reviewed: Q9UNS1)

All UniProt accessions (1): Q9UNS1

UniProt curated annotations — full annotation on UniProt →

Function. Plays an important role in the control of DNA replication, maintenance of replication fork stability, maintenance of genome stability throughout normal DNA replication, DNA repair and in the regulation of the circadian clock. Required to stabilize replication forks during DNA replication by forming a complex with TIPIN: this complex regulates DNA replication processes under both normal and stress conditions, stabilizes replication forks and influences both CHEK1 phosphorylation and the intra-S phase checkpoint in response to genotoxic stress. During DNA replication, inhibits the CMG complex ATPase activity and activates DNA polymerases catalytic activities, coupling DNA unwinding and DNA synthesis. TIMELESS promotes TIPIN nuclear localization. Plays a role in maintaining processive DNA replication past genomic guanine-rich DNA sequences that form G-quadruplex (G4) structures, possibly together with DDX11. Involved in cell survival after DNA damage or replication stress by promoting DNA repair. In response to double-strand breaks (DSBs), accumulates at DNA damage sites and promotes homologous recombination repair via its interaction with PARP1. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light. Involved in the determination of period length and in the DNA damage-dependent phase advancing of the circadian clock. Negatively regulates CLOCK|NPAS2-ARTNL/BMAL1|ARTNL2/BMAL2-induced transactivation of PER1 possibly via translocation of PER1 into the nucleus. May play a role as destabilizer of the PER2-CRY2 complex. May also play an important role in epithelial cell morphogenesis and formation of branching tubules.

Subunit / interactions. Monomer. Homodimer or homomultimer. Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, ARTNL/BMAL1 or ARTNL2/BMAL2, CSKN1D and/or CSNK1E, TIMELESS, and the PER proteins. Interacts with PER2. The interaction with PER2 is direct and via its second PAS domain. Interacts directly with PER1 and PER3. Interacts with CRY2, CHEK1, ATR and ATRIP. Interacts with CRY1. Interacts with CLSPN; the interaction is required for leading-strand replication. Interacts (via N-terminus) with TIPIN. The TIMELESS-TIPIN heterodimer binds preferably to guanine-rich quadruplex-forming (G4) DNA structures. Associates with the MCM2-7 complex. Interacts with DNA polymerases alpha, delta and epsilon. Interacts with DDX11; this interaction increases recruitment of both proteins onto chromatin in response to replication stress induction by hydroxyurea. Interacts with PARP1; interaction is direct and independent of poly-ADP-ribose.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Expressed in all tissues examined including brain, heart, lung, liver, skeletal muscle, kidney, placenta, pancreas, spleen, thymus and testis. Highest levels of expression in placenta, pancreas, thymus and testis.

Disease relevance. Advanced sleep phase syndrome, familial, 4 (FASPS4) [MIM:620015] An autosomal dominant disorder characterized by very early sleep onset and offset. Individuals are ‘morning larks’ with a 4 hours advance of the sleep, temperature and melatonin rhythms. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. Residues 1182-1199 comprise a putative nuclear localization signal; nuclear localization is required for the regulation of period length of the circadian clock. The DNA-binding domain (residues 816-954) binds to both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), and has high affinity for DNA sequences rich in guanine that form G-quadruplex (G4) structures. The C-terminal domain, comprising the DNA-binding domain and the PARP1-binding region, is required for the replication past genomic guanine-rich DNA sequences that form G-quadruplex (G4) structures.

Induction. Regulated by the cell cycle. High levels in S, G(2) and M phases, with highest level in S phase. Low expression in G(0) and G(1) phases.

Similarity. Belongs to the timeless family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UNS1-1	1	yes
Q9UNS1-2	2

RefSeq proteins (2): NP_001317224, NP_003911* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006906	Timeless_N	Domain
IPR007725	TIMELESS_PAB	Domain
IPR044998	Timeless	Family
IPR059212	HTH_TIMELESS	Domain
IPR060740	TOF-1-like_helical	Domain

Pfam: PF04821, PF05029, PF26019, PF27570

UniProt features (108 total): helix 60, sequence variant 12, strand 9, region of interest 8, turn 6, modified residue 6, compositionally biased region 4, chain 1, splice variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

9 structures by resolution:

PDB	Title	Method	Resolution (Å)
6T9Q	Crystal structure of the second, C-terminal repeat of the DNA-binding domain of human …	X-RAY DIFFRACTION	1.15
4XHT	Crystal structure of Timeless_PAB domain native form	X-RAY DIFFRACTION	1.65
5MQI	Crystal structure of the N-terminal domain of human Timeless	X-RAY DIFFRACTION	1.85
4XHU	The complex structure of Timeless_PAB and PARP-1_catalytic domain	X-RAY DIFFRACTION	2.09
7PLO	H. sapiens replisome-CUL2/LRR1 complex	ELECTRON MICROSCOPY	2.8
4XHW	Crystal structure of Timeless_PAB domain in SeMet-labelled form	X-RAY DIFFRACTION	2.85
7PFO	Core human replisome	ELECTRON MICROSCOPY	3.2
8B9D	Human replisome bound by Pol Alpha	ELECTRON MICROSCOPY	3.4
6TAZ	Timeless couples G quadruplex detection with processing by DDX11 during DNA replication	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UNS1-F1	74.56	0.26

Human Protein Atlas

Protein class: Predicted intracellular proteins, Disease related genes, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH enhanced · IF supported

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6)

Type	Positions
Phosphoserine	281, 1074, 1087, 1149, 1173
Phosphothreonine	1089

Mutagenesis-validated functional residues (1)

Position	Phenotype
1081	abolishes interaction with parp1.

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 5; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

5 pathways:

ID	Pathway	Evidence
R-HSA-5693607	Processing of DNA double-strand break ends	curated
R-HSA-5693532	DNA Double-Strand Break Repair	—
R-HSA-73894	DNA Repair	—
R-HSA-5693567	HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	—
R-HSA-5693538	Homology Directed Repair	—

MSigDB gene sets: 340 (showing top): GOBP_DNA_TEMPLATED_DNA_REPLICATION_MAINTENANCE_OF_FIDELITY, GOBP_CIRCADIAN_RHYTHM, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_DNA_RECOMBINATION, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_DNA_TEMPLATED_DNA_REPLICATION, MODULE_255, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_317, FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR_VIA_HOMOLOGOUS_RECOMBINATION

GO Biological Process (20): DNA replication checkpoint signaling (GO:0000076), morphogenesis of an epithelium (GO:0002009), DNA repair (GO:0006281), DNA-templated transcription (GO:0006351), DNA damage response (GO:0006974), circadian rhythm (GO:0007623), detection of abiotic stimulus (GO:0009582), replication fork processing (GO:0031297), mitotic intra-S DNA damage checkpoint signaling (GO:0031573), regulation of circadian rhythm (GO:0042752), replication fork arrest (GO:0043111), cell cycle phase transition (GO:0044770), negative regulation of DNA-templated transcription (GO:0045892), cell division (GO:0051301), cellular response to hydroxyurea (GO:0072711), cellular response to cisplatin (GO:0072719), cellular response to bleomycin (GO:1904976), positive regulation of double-strand break repair via homologous recombination (GO:1905168), positive regulation of double-strand break repair (GO:2000781), rhythmic process (GO:0048511)

GO Molecular Function (4): DNA binding (GO:0003677), enzyme activator activity (GO:0008047), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), replication fork protection complex (GO:0031298), site of double-strand break (GO:0035861), nuclear replication fork (GO:0043596), chromosome (GO:0005694)

Reactome top-level categories

4 top-level categories:

Category	Pathways
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	1
DNA Repair	1
DNA Double-Strand Break Repair	1
Homology Directed Repair	1

GO top-level categories

54 GO namespaces:

Category	Terms
DNA-templated DNA replication maintenance of fidelity	2
cellular response to nitrogen compound	2
cellular anatomical structure	2
DNA integrity checkpoint signaling	1
tissue morphogenesis	1
epithelium development	1
DNA metabolic process	1
DNA damage response	1
gene expression	1
RNA biosynthetic process	1
cellular response to stress	1
rhythmic process	1
response to abiotic stimulus	1
detection of stimulus	1
mitotic S phase	1
mitotic DNA damage checkpoint signaling	1
circadian rhythm	1
regulation of biological process	1
negative regulation of DNA-templated DNA replication	1
cell cycle process	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
cellular process	1
response to hydroxyurea	1
cellular response to chemical stimulus	1
response to cisplatin	1
cellular response to oxygen-containing compound	1
response to bleomycin	1
double-strand break repair via homologous recombination	1
regulation of double-strand break repair via homologous recombination	1
positive regulation of DNA recombination	1
positive regulation of double-strand break repair	1
double-strand break repair	1
positive regulation of DNA repair	1
regulation of double-strand break repair	1
biological_process	1
nucleic acid binding	1
catalytic activity	1
enzyme regulator activity	1
molecular function activator activity	1
protein binding	1
binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear replication fork	1
nuclear protein-containing complex	1
site of DNA damage	1
nuclear chromosome	1
nucleus	1
replication fork	1
CMG complex	1
intracellular membraneless organelle	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 16 of 31 annotations. The rest are phylogenetic / computational / electronic (IEA).

16 experimentally-supported GO terms:

GO term	NS	Evidence
DNA damage response	BP	mutant phenotype
cell cycle phase transition	BP	mutant phenotype
cellular response to bleomycin	BP	mutant phenotype
cellular response to cisplatin	BP	mutant phenotype
cellular response to hydroxyurea	BP	mutant phenotype
mitotic intra-S DNA damage checkpoint signaling	BP	direct assay
negative regulation of DNA-templated transcription	BP	direct assay
positive regulation of double-strand break repair	BP	mutant phenotype
positive regulation of double-strand break repair via homologous recombination	BP	direct assay
regulation of circadian rhythm	BP	mutant phenotype
replication fork processing	BP	mutant phenotype
chromatin	CC	direct assay
nucleoplasm	CC	direct assay
nucleus	CC	direct assay
site of double-strand break	CC	direct assay
enzyme activator activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 1,944 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TIMELESS	TIPIN	Q9BVW5	976
TIMELESS	CRY2	Q49AN0	914
TIMELESS	CRY1	Q16526	903
TIMELESS	CLOCK	O15516	902
TIMELESS	BMAL1	O00327	889
TIMELESS	CLSPN	Q9HAW4	887
TIMELESS	PER3	P56645	882
TIMELESS	NPAS2	Q99743	868
TIMELESS	PER2	O15055	859
TIMELESS	CSNK1E	P49674	815
TIMELESS	NR1D1	P20393	800
TIMELESS	WDHD1	O75717	771
TIMELESS	NFIL3	Q16649	760
TIMELESS	NR1D2	Q14995	744
TIMELESS	RORB	Q92753	736

IntAct

Human interaction partners of TIMELESS in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

10 partners by confidence:

Partner	Interaction type	MIscore	Records
TIPIN	direct interaction	0.730	2
PARP1	physical association	0.520	2
CHEK1	physical association	0.400	2
CRY2	physical association	0.400	1
DDX11	physical association	0.400	1
RPA2	physical association	0.400	1
PCBD1	physical association	0.370	1
TF	physical association	0.370	1
ZSCAN1	physical association	0.370	1
ATR	association	0.350	1

BioGRID (190 interactions; top human partners by supporting records): TIPIN (Affinity Capture-MS; 11 records), CLSPN (Affinity Capture-Western; 5 records), MCM3 (Affinity Capture-MS; 4 records), MCM7 (Affinity Capture-MS; 4 records), GINS3 (Affinity Capture-MS; 3 records), PLK1 (Affinity Capture-Western; 3 records), SSRP1 (Affinity Capture-MS; 3 records), ATRIP (Affinity Capture-Western; 2 records), AURKA (Affinity Capture-Western; 2 records), CD70 (Affinity Capture-MS; 2 records), CSGALNACT1 (Affinity Capture-MS; 2 records), FCGRT (Affinity Capture-MS; 2 records), H2AFX (Affinity Capture-MS; 2 records), MCM2 (Affinity Capture-MS; 2 records), RPA1 (Affinity Capture-MS; 2 records)

SIGNOR signaling

3 signaling interactions:

A	Effect	B	Mechanism
NR3C1	“up-regulates quantity by expression”	TIMELESS	“transcriptional regulation”
TIMELESS	“up-regulates activity”	CRY1	binding
TIMELESS	“up-regulates activity”	CHEK1	binding

Protein complexes (CORUM) (4)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

4 complexes by size:

Complex	Subunits	Members
ATR-ATRIP-TIM complex	3	ATR, ATRIP, TIMELESS
Tim-Tipin complex	2	TIMELESS, TIPIN
CRY2-TIM complex	2	CRY2, TIMELESS
★ PARP1-TIMELESS complex	2	PARP1, TIMELESS

Disease & clinical

Genetic variants

Variant evidence for TIMELESS: 218 ClinVar records (1 pathogenic / likely pathogenic); 3 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

218 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	164
Likely benign	20
Benign	4

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
1702937	NM_003920.5(TIMELESS):c.3241C>T (p.Arg1081Ter)	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore TIMELESS’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 25 predictions of 1,881):

Position(s)	Effect	Δscore	Sites
12:56418009–56418010	acceptor_loss	1.0000	6
12:56418013	acceptor_gain	1.0000
12:56418019–56418020	acceptor_gain	1.0000	3
12:56420567–56420568	donor_loss	1.0000	5
12:56420965	donor_gain	1.0000
12:56421013	donor_gain	1.0000
12:56421140	acceptor_gain	1.0000
12:56421144	acceptor_gain	1.0000
12:56421152	acceptor_gain	1.0000
12:56422104–56422105	donor_loss	1.0000	5

AlphaMissense

1,775 missense substitutions predicted likely pathogenic (of 7,919 scored), across 563 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M453	9	0.826	0.968
F278	8	0.935	0.994
F632	8	0.923	0.981
D64	8	0.899	0.947
N165	8	0.898	0.993
D374	8	0.895	0.957
F584	8	0.893	0.986
D37	8	0.884	0.941
F385	8	0.865	0.960
D187	8	0.847	0.917
F408	8	0.838	0.970
F793	8	0.834	0.974
F473	8	0.832	0.942
F748	8	0.793	0.925
W889	7	0.987	0.998
W626	7	0.960	0.992
E220	7	0.949	0.983
F97	7	0.920	0.979
W1080	7	0.901	0.981
W214	7	0.896	0.985

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

5 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Chromophobe (TCGA)	unfavorable	5.63e-05
Liver Hepatocellular Carcinoma (validation)	unfavorable	0.000271
Skin Cutaneous Melanoma (TCGA)	unfavorable	0.000455
Lung Adenocarcinoma (TCGA)	unfavorable	0.000619
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	0.0007

Disease associations

OMIM: gene MIM:603887 | disease phenotypes: MIM:620015

GenCC curated gene-disease

Mondo (1): advance sleep phase syndrome, familial, 4 (MONDO:0031044)

HPO phenotypes

2 phenotypes (HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0031873	Early chronotype

GWAS associations

3 associations:

Study	Trait	p-value
GCST010002_69	Refractive error	6e-174
GCST001538_4	Immune reponse to smallpox (secreted IFN-alpha)	6e-10
GCST002115_16	Axial length	4e-7

EFO canonical traits (from GWAS)

3 canonical traits:

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0004873	cytokine measurement
EFO:0005318	axial length measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

58 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	5
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Air Pollutants	increases expression, affects methylation, increases abundance, decreases expression	3
Resveratrol	affects cotreatment, increases expression	2
Arsenic	increases expression, affects cotreatment, decreases expression, increases abundance	2
Cisplatin	affects cotreatment, increases expression	2
Estradiol	increases expression	2
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
Cyclosporine	decreases expression, increases expression	2
Particulate Matter	affects methylation, increases abundance, decreases expression	2
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
geraniol	decreases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
cyanoginosin LR	affects binding, decreases reaction, increases reaction, decreases expression	1
phenethyl isothiocyanate	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.