CHRAC1

Summary

CHRAC1 (chromatin accessibility complex subunit 1, HGNC:13544) is a protein-coding gene on chromosome 8q24.3, encoding Chromatin accessibility complex protein 1 (Q9NRG0). Forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1.

CHRAC1 is a histone-fold protein that interacts with other histone-fold proteins to bind DNA in a sequence-independent manner. These histone-fold protein dimers combine within larger enzymatic complexes for DNA transcription, replication, and packaging.

Source: NCBI Gene 54108 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 26 total — 1 pathogenic
• MANE Select transcript: NM_017444

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13544
Approved symbol	CHRAC1
Name	chromatin accessibility complex subunit 1
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	CHRAC15, YCL1
Ensembl gene	ENSG00000104472
Ensembl biotype	protein_coding
OMIM	607268
Entrez	54108

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 retained_intron

ENST00000220913, ENST00000518971, ENST00000519533, ENST00000519618, ENST00000523569, ENST00000970390

RefSeq mRNA: 1 — MANE Select: NM_017444 NM_017444

CCDS: CCDS6379

Canonical transcript exons

ENST00000220913 — 3 exons

Exon	Start	End
ENSE00000704277	140514369	140514495
ENSE00001231189	140515126	140517154
ENSE00002092195	140511322	140511646

Expression profiles

Bgee: expression breadth ubiquitous, 216 present calls, max score 91.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.8854 / max 197.4026, expressed in 1820 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91263	14.4165	1798
91265	10.0771	1775
91266	4.1299	1499
91269	2.0780	842
91267	2.0533	1079
91268	1.0883	672
91264	0.8610	571
91270	0.1814	56

Top tissues by expression

245 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	91.30	gold quality
monocyte	CL:0000576	91.05	gold quality
tibial artery	UBERON:0007610	90.99	gold quality
popliteal artery	UBERON:0002250	90.98	gold quality
leukocyte	CL:0000738	90.90	gold quality
muscle of leg	UBERON:0001383	90.82	gold quality
gastrocnemius	UBERON:0001388	90.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.64	gold quality
tibialis anterior	UBERON:0001385	89.94	gold quality
smooth muscle tissue	UBERON:0001135	89.91	gold quality
ileal mucosa	UBERON:0000331	89.84	gold quality
aorta	UBERON:0000947	89.79	gold quality
lower esophagus muscularis layer	UBERON:0035833	89.41	gold quality
lower esophagus	UBERON:0013473	89.40	gold quality
right coronary artery	UBERON:0001625	89.29	gold quality
islet of Langerhans	UBERON:0000006	89.22	gold quality
descending thoracic aorta	UBERON:0002345	89.17	gold quality
rectum	UBERON:0001052	89.13	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	89.04	gold quality
left coronary artery	UBERON:0001626	88.83	gold quality
mucosa of stomach	UBERON:0001199	88.79	gold quality
thoracic aorta	UBERON:0001515	88.60	gold quality
vermiform appendix	UBERON:0001154	88.52	gold quality
ascending aorta	UBERON:0001496	88.37	gold quality
gall bladder	UBERON:0002110	88.25	gold quality
skeletal muscle organ	UBERON:0014892	88.08	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.77	gold quality
esophagus	UBERON:0001043	87.73	gold quality
coronary artery	UBERON:0001621	87.40	gold quality
calcaneal tendon	UBERON:0003701	87.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting CHRAC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-12121	99.99	66.64	255
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-7845-5P	99.88	64.88	771
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4728-5P	99.85	69.39	4718

Literature-anchored findings (GeneRIF, showing 3)

• -RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells (PMID:24148822)
• CHRAC1 promotes human lung cancer growth through regulating YAP transcriptional activity. (PMID:34718437)
• Chromatin accessibility complex subunit 1 enhances tumor growth by regulating the oncogenic transcription of YAP in breast and cervical cancer. (PMID:38223760)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Chrac1	ENSMUSG00000068391
rattus_norvegicus		ENSRNOG00000087692

Protein

Protein identifiers

Chromatin accessibility complex protein 1 — Q9NRG0 (reviewed: Q9NRG0)

Alternative names: Chromatin accessibility complex 15 kDa protein, DNA polymerase epsilon subunit p15

All UniProt accessions (4): Q9NRG0, E5RGS9, H0YBP8, H0YBX4

UniProt curated annotations — full annotation on UniProt →

Function. Forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1. Does not enhance nucleosome sliding activity of the ACF-5 ISWI chromatin remodeling complex.

Subunit / interactions. Heterodimer with POLE3; binds to DNA. Component of the CHRAC ISWI chromatin remodeling complex at least composed of SMARCA5/SNF2H, BAZ1A/ACF1, CHRAC1 and POLE3; the complex preferentially binds DNA through the CHRAC1-POLE3 heterodimer and possesses ATP-dependent nucleosome-remodeling activity. Within the complex, the heterodimer with POLE3 interacts with SMARCA5/SNF2H; the interaction is direct and enhances nucleosome sliding activity by the SMARCA5/SNF2H and BAZ1A/ACF1 interaction. Within the complex, the heterodimer with POLE3 interacts with BAZ1A/ACF1; the interactions are direct.

Subcellular location. Nucleus.

Tissue specificity. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.

RefSeq proteins (1): NP_059140* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003958	CBFA_NFYB_domain	Domain
IPR009072	Histone-fold	Homologous_superfamily
IPR050568	Transcr_DNA_Rep_Reg	Family

Pfam: PF00808

UniProt features (10 total): modified residue 3, sequence variant 2, initiator methionine 1, chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRG0-F1	85.85	0.71

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 (3): 2, 102, 124

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): PAL_PRMT5_TARGETS_UP, GOMF_DNA_POLYMERASE_ACTIVITY, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GOBP_DNA_BIOSYNTHETIC_PROCESS, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, FISCHER_DREAM_TARGETS, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_CHROMATIN_REMODELING, GOBP_DNA_REPLICATION, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOCC_DNA_POLYMERASE_COMPLEX, GOCC_CHROMOSOMAL_REGION, GOCC_TRANSFERASE_COMPLEX, GOCC_PERICENTRIC_HETEROCHROMATIN, GOCC_ATPASE_COMPLEX

GO Biological Process (5): DNA-templated DNA replication (GO:0006261), regulation of DNA replication (GO:0006275), nucleosome assembly (GO:0006334), chromatin remodeling (GO:0006338), DNA biosynthetic process (GO:0071897)

GO Molecular Function (6): DNA binding (GO:0003677), DNA-directed DNA polymerase activity (GO:0003887), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (4): nucleus (GO:0005634), pericentric heterochromatin (GO:0005721), epsilon DNA polymerase complex (GO:0008622), CHRAC (GO:0008623)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA replication	2
chromatin organization	2
regulation of DNA metabolic process	1
nucleosome organization	1
protein-DNA complex assembly	1
DNA metabolic process	1
nucleic acid biosynthetic process	1
nucleic acid binding	1
DNA polymerase activity	1
protein dimerization activity	1
binding	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
intracellular membrane-bounded organelle	1
chromosome, centromeric region	1
heterochromatin	1
nuclear chromosome	1
DNA polymerase complex	1
nuclear protein-containing complex	1
ISWI-type complex	1

Protein interactions and networks

STRING

706 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHRAC1	POLE3	Q9NRF9	998
CHRAC1	BAZ1A	Q9NRL2	991
CHRAC1	SMARCA5	O60264	963
CHRAC1	SMARCA1	P28370	912
CHRAC1	RSF1	Q96T23	763
CHRAC1	BAZ1B	Q9UIG0	714
CHRAC1	NFYB	P25208	702
CHRAC1	WASHC5	Q12768	684
CHRAC1	TRAPPC9	Q96Q05	667
CHRAC1	POLE2	P56282	644
CHRAC1	BAZ2A	Q9UIF9	598
CHRAC1	DR1	Q01658	565
CHRAC1	POLE	Q07864	564
CHRAC1	H2AC19	P20670	552
CHRAC1	H2AC20	Q16777	552

IntAct

52 interactions, top by confidence:

A	B	Type	Score
POLE3	CHRAC1	psi-mi:“MI:0915”(physical association)	0.830
CHRAC1	POLE3	psi-mi:“MI:0915”(physical association)	0.830
FAM9B	CHRAC1	psi-mi:“MI:0915”(physical association)	0.780
CHRAC1	FAM9B	psi-mi:“MI:0915”(physical association)	0.780
CAPN6	UBA6	psi-mi:“MI:0914”(association)	0.530
FSD1	UBFD1	psi-mi:“MI:0914”(association)	0.530
TAS2R41	YKT6	psi-mi:“MI:0914”(association)	0.530
PJA1	SMC5	psi-mi:“MI:0914”(association)	0.530
SMARCA5	RBBP4	psi-mi:“MI:0914”(association)	0.530
LRRTM4	AP3B1	psi-mi:“MI:0914”(association)	0.530
POLE3	SMARCA5	psi-mi:“MI:0914”(association)	0.530
CHRAC1	ACTC1	psi-mi:“MI:0915”(physical association)	0.400
BAZ1A	CHRAC1	psi-mi:“MI:0915”(physical association)	0.400
MCF2L2	CDK6	psi-mi:“MI:0914”(association)	0.350
SLC35G2	DDX23	psi-mi:“MI:0914”(association)	0.350
	ARID1A	psi-mi:“MI:0914”(association)	0.350
H2AZ1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
HMGA1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
HMGN5	SMCHD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (123): CHRAC1 (Two-hybrid), FAM9B (Two-hybrid), CHRAC1 (Co-fractionation), POLE3 (Co-fractionation), CHRAC1 (Two-hybrid), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), CHRAC1 (Affinity Capture-MS), TRAPPC13 (Negative Genetic), NPRL3 (Negative Genetic), VPS51 (Negative Genetic)

ESM2 similar proteins: A3QVV1, A8MT69, B0X2G0, B3M123, B3MJ61, B3P239, B4GDU3, B4I3S1, B4JGX4, B4KBI4, B4LZ60, B4NJR8, B4PUG5, B4QVL3, C6Y4D0, G2TRL2, O60076, O74807, O74896, O75843, O88796, P06353, P0DJH7, P36611, P78346, Q295I4, Q2KNB4, Q2KNB7, Q2KNB9, Q2NKU0, Q3E829, Q3E835, Q42525, Q54CN8, Q5E9L5, Q5RBU1, Q6NZB1, Q6P9U3, Q7QD36, Q7ZW33

Diamond homologs: A0JPP1, A6BLW4, A6QQ14, B0XTT5, C6Y4D0, O17072, P40096, P70353, P79007, Q02516, Q10315, Q13952, Q14919, Q2YDP3, Q4PSE2, Q4X095, Q54DA1, Q557I1, Q58CM8, Q5E9X1, Q5RA23, Q62725, Q655V5, Q6BX14, Q6C6M5, Q6CLM5, Q8L4B2, Q8LCG7, Q9CQ36, Q9D6N5, Q9FGP6, Q9FGP7, Q9FGP8, Q9FMV5, Q9JKP8, Q9NR33, Q9NRG0, Q9SMP0, Q9W256, Q9XE33

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	7	41.6×	1e-07
nucleosome assembly	6	19.6×	1e-04
chromatin remodeling	7	11.9×	3e-04
chromatin organization	5	11.5×	4e-03
DNA damage response	7	8.7×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	16
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
686106	GRCh37/hg19 8q24.23-24.3(chr8:139188797-146295771)x3	Pathogenic

SpliceAI

479 predictions. Top by Δscore:

Variant	Effect	Δscore
8:140511617:G:GT	donor_gain	1.0000
8:140511619:GGC:G	donor_gain	0.9900
8:140511620:GCG:G	donor_gain	0.9900
8:140511644:ACGG:A	donor_loss	0.9900
8:140511647:G:GA	donor_loss	0.9900
8:140511647:G:GG	donor_gain	0.9900
8:140511648:T:A	donor_loss	0.9900
8:140514429:A:T	donor_gain	0.9900
8:140514491:TGCAG:T	donor_loss	0.9900
8:140514493:CAGGT:C	donor_loss	0.9900
8:140514494:AGGT:A	donor_loss	0.9900
8:140514495:G:GA	donor_loss	0.9900
8:140514496:GTA:G	donor_loss	0.9900
8:140514497:T:G	donor_loss	0.9900
8:140515124:A:G	acceptor_gain	0.9900
8:140512417:G:GT	donor_gain	0.9800
8:140514368:GGA:G	acceptor_gain	0.9800
8:140511601:GTCC:G	donor_gain	0.9700
8:140511617:GAGGC:G	donor_gain	0.9700
8:140514363:TTCTA:T	acceptor_loss	0.9700
8:140514364:TCTA:T	acceptor_loss	0.9700
8:140514365:CTA:C	acceptor_loss	0.9700
8:140515125:G:GG	acceptor_gain	0.9700
8:140515125:GAT:G	acceptor_gain	0.9700
8:140511627:TGCTC:T	donor_gain	0.9600
8:140511629:C:CG	donor_gain	0.9600
8:140514367:A:AG	acceptor_gain	0.9600
8:140514368:G:GG	acceptor_gain	0.9600
8:140512427:GAACT:G	donor_gain	0.9400
8:140514361:T:A	acceptor_loss	0.9400

AlphaMissense

865 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:140511641:G:C	A48P	0.999
8:140511642:C:A	A48D	0.999
8:140514379:T:A	V53D	0.999
8:140514486:T:C	F89L	0.999
8:140514488:T:A	F89L	0.999
8:140514488:T:G	F89L	0.999
8:140511579:T:A	I27N	0.998
8:140511635:G:C	A46P	0.998
8:140514390:G:C	A57P	0.998
8:140514391:C:A	A57D	0.998
8:140514487:T:C	F89S	0.998
8:140515134:C:T	P95S	0.998
8:140515150:C:A	A100D	0.998
8:140511582:T:A	M28K	0.997
8:140511636:C:A	A46D	0.997
8:140514490:T:A	L90H	0.997
8:140515134:C:A	P95T	0.997
8:140515135:C:A	P95Q	0.997
8:140511566:C:A	R23S	0.996
8:140511579:T:C	I27T	0.996
8:140511579:T:G	I27S	0.996
8:140511582:T:C	M28T	0.996
8:140511582:T:G	M28R	0.996
8:140511630:T:C	L44P	0.996
8:140514388:T:C	L56P	0.996
8:140514451:T:C	L77S	0.996
8:140514490:T:C	L90P	0.996
8:140515132:T:C	L94S	0.996
8:140515134:C:G	P95A	0.996
8:140515135:C:T	P95L	0.996

dbSNP variants (sampled 300 via entrez): RS1000079419 (8:140512063 C>G,T), RS1000404144 (8:140510526 C>T), RS1000414246 (8:140510264 G>A), RS1000536307 (8:140511879 C>G,T), RS1001281777 (8:140515946 A>G), RS1001387539 (8:140511371 T>A,C,G), RS1001521946 (8:140512996 T>A), RS1001733049 (8:140515646 T>C), RS1002314683 (8:140516999 G>A), RS1002390423 (8:140512171 C>A,G,T), RS1002537759 (8:140510876 C>G), RS1002596529 (8:140510724 GA>G,GAA), RS1002627975 (8:140517417 T>G), RS1003452306 (8:140512989 G>T), RS1003535321 (8:140515241 C>T)

Disease associations

OMIM: gene MIM:607268 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006944_8	Experiencing mood swings	1.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008475	mood instability measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cisplatin	affects expression, affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
trichostatin A	affects expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Decitabine	affects expression	1
Cadmium	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Ketoconazole	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
Sodium Selenite	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.