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Relevance to Autism

Genetic association has been found between common SNPs near the HMGN1 gene and ASD in an AGRE cohort (Abuhatzira et al., 2011). In addition, that study also showed that HMGN1 functionally binds the human MECP2 promoter.

Molecular Function

Binds to the inner side of nucleosomal DNA, thus altering the interaction between the DNA and the histone octamer. May be involved in the process which maintains transcribable genes in an unique chromatin conformation. Inhibits the phosphorylation of nucleosomal histones H3 and H2A by RPS6KA5/MSK1 and RPS6KA3/RSK2.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice.
ASD

Rare

No Rare Variants Available

Common

Variant ID
Polymorphism
SNP ID
Allele Change
Residue Change
Population Origin
Population Stage
Author, Year
 GEN303C001 
 intergenic_variant 
 rs2410062 
  
 G/A 
 AGRE 
 Discovery 
 GEN303C002 
 intergenic_variant 
 rs2836716 
  
 A/G 
 AGRE 
 Discovery 
 GEN303C003 
 intergenic_variant 
 rs717871 
  
 C/T 
 AGRE 
 Discovery 
 GEN303C004 
 intergenic_variant 
 rs2142109 
  
 G/A 
 AGRE 
 Discovery 
 GEN303C005 
 intergenic_variant 
 rs2222994 
  
 C/A 
 AGRE 
 Discovery 
 GEN303C006 
 intergenic_variant 
 rs2836788 
  
 A/G 
 AGRE 
 Discovery 
 GEN303C007 
 intergenic_variant 
 rs6517502 
  
 G/T 
 AGRE 
 Discovery 
 GEN303C008 
 intergenic_variant 
 rs2836978 
 c.610-313A>G 
 C/T 
 AGRE 
 Discovery 
 GEN303C009 
 intergenic_variant 
 rs2837029 
 c.49G>A;c.-69+686G>A 
 T/C 
 AGRE 
 Discovery 
 GEN303C010 
 intergenic_variant 
 rs2837039 
 c.-100+7700T>C;c.234+1488T>C;c.-100+7531T>C;c.-100+7548T>C;c.-100+7737T>C;c.-100+800T>C 
 C/T 
 AGRE 
 Discovery 
 GEN303C011 
 intergenic_variant 
 rs2837066 
  
 T/C 
 AGRE 
 Discovery 
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
21
Duplication
 3
 
21
Duplication
 11
 
21
Duplication
 2
 
21
Deletion-Duplication
 1
 
21
Duplication
 4
 
21
Deletion
 2
 
21
Deletion
 3
 
21
Deletion
 3
 
21
Deletion-Duplication
 8
 
21
Deletion
 5
 

Model Summary

HMGN1 is an epigenetic factor that contributes to the development of neurodevelopmental disorders.

References

Type
Title
Author, Year
Primary
The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice.
Additional
The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice.

M_HMGN1_1_OE_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: .
Allele Type: Targeted (Overexpression)
Strain of Origin: Not Specified
Genetic Background: C57BL/6J
ES Cell Line: Not Specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_HMGN1_2_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: .
Allele Type: Targeted (Knock Out)
Strain of Origin: Not Specified
Genetic Background: C57BL/6J
ES Cell Line: Not Specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_HMGN1_1_OE_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Motor coordination and balance1
Increased
Description: Increased motor coordination and balance
Exp Paradigm: Parallel bar task
 Parallel bar test
 6-7 months
General locomotor activity1
Increased
Description: Increased locomotor activity indicative of hyperactivity and increased exploration
Exp Paradigm: Open field test
 Open field test
 6-7 months
Social interaction1
Decreased
Description: Decreased sociability indicated by no change in preference for unfamiliar mouse
Exp Paradigm: Automated sociability test
 Three-chamber social approach test
 6-7 months
Anxiety1
Decreased
Description: Decreased anxiety levels
Exp Paradigm: Elevated plus maze test
 Elevated plus maze test
 6-7 months
Gene expression1
Decreased
Description: Decreased levels of mecp2 transcript in brain
Exp Paradigm: Mecp2 mrna levels
 Quantitative pcr (qrt-pcr)
 8 weeks
Chromatin modification1
Increased
Description: Increased chromatin modification indicated by increased levels of heterochromatin marker h3k9me2 and decreased levels of h3k9ac, marker of transcriptional activity
Exp Paradigm: Chromatin modifications
 Chromatin immunoprecipitation sequencing (chip-seq)
 8 weeks
Chromatin modification1
Decreased
Description: Decreased accessibility to chromatin regulatory regions
Exp Paradigm: Chromatin regulatory region accessibility
 Formaldehyde-assisted isolation of regulatory elements (faire)/quantitative pcr (qpcr)
 8 weeks
Protein expression level evidence1
Decreased
Description: Decreased levels of mecp2 protein
Exp Paradigm: Mecp2 protein levels
 Western blot
 8 weeks
Social memory1
 No change
 Three-chamber social approach test
 6-7 months
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Immune response, Learning & memory, Maternal behavior, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure, Sensory

M_HMGN1_2_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
General locomotor activity1
Decreased
Description: Decreased locomotor activity indicative of hypoactivity and decreased exploratory activity
Exp Paradigm: Open field test
 Open field test
 6-7 months
Social memory1
Decreased
Description: Decreased social memory indicated by equal time spent with strangers 1 and 2
Exp Paradigm: Automated sociability test
 Three-chamber social approach test
 6-7 months
Protein expression level evidence1
Increased
Description: Increased levels of mecp2 protein
Exp Paradigm: Mecp2 protein levels
 Western blot
 8 weeks
Gene expression1
Increased
Description: Increased levels of mecp2 transcript in brain
Exp Paradigm: Mecp2 mrna levels
 Quantitative pcr (qrt-pcr)
 8 weeks
Chromatin modification1
Increased
Description: Increased histone acetylation
Exp Paradigm: Histone acetylation
 Chromatin immunoprecipitation sequencing (chip-seq)
 Unreported
Chromatin modification1
Decreased
Description: Decreased accessibility to chromatin regulatory regions
Exp Paradigm: Chromatin regulatory region accessibility
 Formaldehyde-assisted isolation of regulatory elements (faire)/quantitative pcr (qpcr)
 8 weeks
Anxiety1
 No change
 Elevated plus maze test
 6-7 months
Motor coordination and balance1
 No change
 Parallel bar test
 6-7 months
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Immune response, Learning & memory, Maternal behavior, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure, Sensory





Download HMGN1's Cytoscape file

Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
BTG2 BTG family, member 2 7832 P78543 ChIP; in silico target prediction; Protein-fragment complementation assay
Cuddapah S , et al. 2010
CHD8 chromodomain helicase DNA binding protein 8 57680 Q9HCK8 CHIP-seq
Cotney J , et al. 2015
EP300 E1A binding protein p300 2033 Q9Y6B2 IP/WB; MS; in vitro acetylation assay
Bergel M , et al. 2001
ERCC6 excision repair cross-complementing rodent repair deficiency, complementation group 6 2074 Q03468 IP/WB
Anindya R , et al. 2010
ERCC8 excision repair cross-complementing rodent repair deficiency, complementation group 8 1161 Q13216 IP/WB
Fousteri M , et al. 2006
ESR1 estrogen receptor 1 2099 P03372 GST; IP; WB
Zhu N and Hansen U 2007
FMR1 fragile X mental retardation 1 2332 G8JLE9 PAR-CLIP; RNA immunoprecipitation (RIP)
Ascano M Jr , et al. 2012
HDGF hepatoma-derived growth factor 3068 P51858 LC-MS/MS
Zhao J , et al. 2011
HMGN1 high mobility group nucleosome binding domain 1 3150 P05114 2-D gel electrophoresis
Postnikov YV , et al. 1995
HMGN2 high mobility group nucleosomal binding domain 2 3151 P05204 2-D gel electrophoresis
Postnikov YV , et al. 1995
LIG4 ligase IV, DNA, ATP-dependent 3981 P49917 Y2H
Woods NT , et al. 2012
MECP2 methyl CpG binding protein 2 (Rett syndrome) 4204 P51608 ChIP
Abuhatzira L , et al. 2011
NFE2 nuclear factor, erythroid 2 4778 Q16621 M2H
Ravasi T , et al. 2010
NFIX nuclear factor I/X (CCAAT-binding transcription factor) 4784 Q14938 Y2H
Singh U , et al. 2009
POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 5430 P24928 IP/WB
Fousteri M , et al. 2006
PPIP5K1 diphosphoinositol pentakisphosphate kinase 1 9677 Q6PFW1 LC-MS/MS
Havugimana PC , et al. 2012
PPP1CC protein phosphatase 1, catalytic subunit, gamma isozyme 5501 P36873 Y2H
Esteves SL , et al. 2012
PRKACA protein kinase, cAMP-dependent, catalytic, alpha 5566 P17612 IP; WB
Prymakowska-Bosak M , et al. 2001
PRKACG protein kinase, cAMP-dependent, catalytic, gamma 5568 P22612 IP; WB
Prymakowska-Bosak M , et al. 2001
PRKCA protein kinase C, alpha 5578 P17252 IP; WB
Prymakowska-Bosak M , et al. 2001
RPS6KA3 ribosomal protein S6 kinase, 90kDa, polypeptide 3 6197 P51812 IP; WB
Thomson S , et al. 1999
RPS6KA4 ribosomal protein S6 kinase, 90kDa, polypeptide 4 8986 O75676 IP; WB
Soloaga A , et al. 2003
RPS6KA5 ribosomal protein S6 kinase, 90kDa, polypeptide 5 9252 O75582 IP; WB
Thomson S , et al. 1999
SLC38A3 solute carrier family 38, member 3 10991 Q99624 Y2H
Wang J , et al. 2011
SPP1 secreted phosphoprotein 1 6696 P10451 Y2H
Long P , et al. 2012
SRF serum response factor (c-fos serum response element-binding transcription factor) 6722 P11831 GST; IP; WB
Zhu N and Hansen U 2007
TERF2 telomeric repeat binding factor 2 7014 Q9NYB0 IP/WB; Protein-fragment complementation assay
Lee OH , et al. 2010
UBC ubiquitin C 7316 P63279 MS/MS; Protein-fragment complementation assay
Kim W , et al. 2011
YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide 7534 P63104 GST; IP; WB
Prymakowska-Bosak M , et al. 2002
ZNF219 zinc finger protein 219 51222 Q9P2Y4 EMSA
Sakai T , et al. 2003
Khdrbs3 KH domain containing, RNA binding, signal transduction associated 3 13992 Q9R226 RNA-Seq
Traunmller L , et al. 2016
PARP1 poly (ADP-ribose) polymerase family, member 1 11545 Q921K2 IP/WB
Masaoka A , et al. 2012
PCNA proliferating cell nuclear antigen 18538 P17918 IP/WB
Postnikov YV , et al. 2012
SLC6A9 solute carrier family 6 (neurotransmitter transporter, glycine), member 9 14664 P28571 ChIP
Barkess G , et al. 2011
TLR4 toll-like receptor 4 21898 Q9QUK6 IP/WB
Yang D , et al. 2011

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