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7 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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CRAMP1
cramped chromatin regulator 1
Chromosome 16 · 16p13.3
NCBI Gene: 57585Ensembl: ENSG00000007545.17HGNC: HGNC:14122UniProt: A7MD53
22PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
positive regulation of DNA-templated transcriptionDNA-binding transcription factor activityhistone locus bodychromatin bindingplacenta praeviaAbnormality of the skeletal systemcleft palate-lateral synechia syndromeepilepsy
✦AI Summary

CRAMP1 is a transcription factor that specifically drives expression of linker histone H1 genes (H1-2, H1-3, H1-4, H1-5, and H1-10/H1x) 123. The protein localizes to histone locus bodies and promoters of H1 genes, where it positively regulates transcription by binding together with cofactors NPAT and GON4L, particularly through PAH domain interactions with GON4L 34. CRAMP1 selectively controls linker histone biogenesis without affecting core histone expression 4. Mechanistically, CRAMP1 maintains linker histone H1 supply, which is essential for Polycomb repressive complex 2 (PRC2)-mediated epigenetic repression. H1 preferentially localizes to H3K27me3-marked chr16 loci and enables proper chr16 compaction at PRC2 targets 1. Additionally, CRAMP1-dependent H1 biogenesis confers tolerance to topoisomerase II inhibitors by maintaining adequate H1 pools, preventing unscheduled TOP2 activity in low-accessibility chr16 regions 2. Clinically, CRAMP1 mutations have been identified in metastatic oral squamous cell carcinoma patients 5, suggesting potential roles in cancer progression. The specific manipulation of linker histone supply through CRAMP1 targeting presents therapeutic opportunities for cancer treatment and addressing H1 deficiency-associated pathologies.

Sources cited
1
CRAMP1 drives linker histone H1 expression and is required for PRC2-mediated repression of H3K27me3-marked chromatin
PMID: 40516528
2
CRAMP1 defines a histone H1 biogenesis factor that promotes TOP2i tolerance by maintaining H1 supply
PMID: 40516529
3
CRAMP1 is a selective regulator of linker histone H1 expression, recruited to histone locus bodies and physically associates with GON4L
PMID: 39829857
4
CRAMP1 specifically regulates H1 gene expression through promoter binding and GON4L interaction without affecting core histones
PMID: 41663757
5
CRAMP1 mutations were identified as novel somatic mutations in metastatic oral squamous cell carcinoma patients
PMID: 37373553
Disease Associationsⓘ20
placenta praeviaOpen Targets
0.12Weak
Abnormality of the skeletal systemOpen Targets
0.11Weak
cleft palate-lateral synechia syndromeOpen Targets
0.09Suggestive
epilepsyOpen Targets
0.08Suggestive
maculopapular eruptionOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.08Suggestive
triple-negative breast cancerOpen Targets
0.07Suggestive
esophageal squamous cell carcinomaOpen Targets
0.07Suggestive
orofacial cleft 11Open Targets
0.07Suggestive
orofacial cleft 10Open Targets
0.07Suggestive
orofacial cleft 1Open Targets
0.07Suggestive
orofacial cleft 5Open Targets
0.07Suggestive
Ankyloblepharon filiforme adnatum - cleft palateOpen Targets
0.06Suggestive
ankyloblepharon filiforme adnatum-cleft palate syndromeOpen Targets
0.06Suggestive
sialolithiasisOpen Targets
0.06Suggestive
spinal cord injuryOpen Targets
0.06Suggestive
van der Woude syndromeOpen Targets
0.06Suggestive
cleft palateOpen Targets
0.06Suggestive
cleft palate with or without ankyloglossia, X-linkedOpen Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HOXB1Shared pathway100%NPATProtein interaction73%GON4LProtein interaction70%SS18L2Protein interaction70%RFNGShared pathway33%MFNGShared pathway33%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
88%
Lung
63%
Liver
49%
Heart
39%
Brain
34%
Gene Interaction Network
Click a node to explore
CRAMP1HOXB1NPATGON4LSS18L2RFNGMFNG
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q96RY5
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.68LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.53 [0.42–0.68]
RankingsWhere CRAMP1 stands among ~20K protein-coding genes
  • #13,633of 20,598
    Most Researched22
  • #5,066of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedCRAMP1
Sources retrieved7 papers
Response time—
📄 Sources
7▼
1
CRAMP1 drives linker histone expression to enable Polycomb repression.
PMID: 40516528
Mol Cell · 2025
1.00
2
CRAMP1-dependent histone H1 biogenesis is essential for topoisomerase II inhibitor tolerance.
PMID: 40516529
Mol Cell · 2025
0.86
3
Identification of Somatic Mutations in Plasma Cell-Free DNA from Patients with Metastatic Oral Squamous Cell Carcinoma.
PMID: 37373553
Int J Mol Sci · 2023
0.71
4
Distinct Control of histone H1 expression within the Histone Locus body by CRAMP1.
PMID: 39829857
bioRxiv · 2025
0.57
5
CRAMP1's surprising grip on linker histones.
PMID: 40614702
Mol Cell · 2025
0.43