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    HMGN1 high mobility group nucleosome binding domain 1 [ Homo sapiens (human) ]

    Gene ID: 3150, updated on 2-Nov-2024

    Summary

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    Official Symbol
    HMGN1provided by HGNC
    Official Full Name
    high mobility group nucleosome binding domain 1provided by HGNC
    Primary source
    HGNC:HGNC:4984
    See related
    Ensembl:ENSG00000205581 MIM:163920; AllianceGenome:HGNC:4984
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HMG14
    Summary
    The protein encoded by this gene binds nucleosomal DNA and is associated with transcriptionally active chromatin. Along with a similar protein, HMG17, the encoded protein may help maintain an open chromatin configuration around transcribable genes. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in bone marrow (RPKM 44.3), lymph node (RPKM 41.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HMGN1 in Genome Data Viewer
    Location:
    21q22.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (39342315..39349088, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (37726869..37733757, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (40714241..40721014, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene bromodomain and WD repeat domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13326 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:40686351-40687046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:40687047-40687741 Neighboring gene BRWD1 antisense RNA 2 Neighboring gene BRWD1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:40704110-40704610 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18467 Neighboring gene uncharacterized LOC105372804 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:40723570-40723774 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:40731973-40732197 Neighboring gene ring finger protein 6 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Chromosomal protein HMG-14. Identification, characterization, and chromosome localization of a functional gene from the large human multigene family. Landsman D, et al. J Biol Chem, 1989 Feb 25. PMID 2563381
    2. Identification of novel in vivo phosphorylation sites in high mobility group N1 protein from the MCF-7 human breast cancer cells. Zou Y, et al. Biochemistry, 2004 May 25. PMID 15147216
    3. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Farley SJ, et al. Epigenetics Chromatin, 2022 Dec 3. PMID 36463299, Free PMC Article
    4. Chromosomal protein HMG-14. Complete human cDNA sequence and evidence for a multigene family. Landsman D, et al. J Biol Chem, 1986 Dec 5. PMID 3782107
    5. HMGN1 modulates estrogen-mediated transcriptional activation through interactions with specific DNA-binding transcription factors. Zhu N, et al. Mol Cell Biol, 2007 Dec. PMID 17938209, Free PMC Article

    See all (101) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HMGN1 plays a significant role in CRLF2 driven Down Syndrome leukemia and provides a potential therapeutic target in this high-risk cohort.
      Title: HMGN1 plays a significant role in CRLF2 driven Down Syndrome leukemia and provides a potential therapeutic target in this high-risk cohort.
    2. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain.
      Title: Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain.
    3. Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome.
      Title: Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome.
    4. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context.
      Title: Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression.
    5. Studies indicate that high mobility group nucleosome binding domain 1 (HMGN1) preferentially promotes Th1-type immunity, which makes it relevant for the fields of vaccinology, autoimmunity, and oncoimmunology [Review].
      Title: High-mobility group nucleosome binding domain 1 (HMGN1) functions as a Th1-polarizing alarmin.
    6. HMGN1 and HMGN 2 remodel core and linker histone tail domains within chromatin.
      Title: HMGN1 and 2 remodel core and linker histone tail domains within chromatin.
    7. RNA-seq evidence of biallelic expression of HMGN1 and 10 neighboring genes in at least one primary human tissue tested indicates that the expression of HMGN1 is uncoupled from the control of the maternally inherited 5mCpG imprints at the WRB differentially methylated region (DMR) in disomic controls or trisomy (Down syndrome) individuals.
      Title: Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners.
    8. HMGN1 can serve as a useful clinical parameter for evaluating disease progression and predicting the outcomes for early-stage patients with non-small cell lung cancer .
      Title: High-mobility group nucleosome-binding protein 1 is a novel clinical biomarker in non-small cell lung cancer.
    9. nucleosome binding protein HMGN1 as a new PCNA-interacting protein that enhances the binding of PCNA to chromatin
      Title: The nucleosome binding protein HMGN1 interacts with PCNA and facilitates its binding to chromatin.
    10. extracellular HMGN1 acts as a novel alarmin critical for LPS-induced development of innate and adaptive immune responses.
      Title: High-mobility group nucleosome-binding protein 1 acts as an alarmin and is critical for lipopolysaccharide-induced immune responses.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat specifically associates with HMGN1 promoter to upregulate HMGN1 expression in T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ27265, FLJ31471, MGC104230, MGC117425

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleosomal DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription, elongation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in post-embryonic camera-type eye morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pyrimidine dimer repair by nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of development, heterochronic IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to UV-B IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to UV-C IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription-coupled nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in female germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    non-histone chromosomal protein HMG-14
    Names
    high mobility group nucleosome-binding domain-containing protein 1
    high-mobility group (nonhistone chromosomal) protein 14
    high-mobility group nucleosome binding 1
    nonhistone chromosomal protein HMG-14

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_004965.7 → NP_004956.5  non-histone chromosomal protein HMG-14

      See identical proteins and their annotated locations for NP_004956.5

      Status: REVIEWED

      Source sequence(s)
      AL582106, BC070154, BE779939
      Consensus CDS
      CCDS33559.1
      UniProtKB/Swiss-Prot
      P05114, Q3KQR8
      UniProtKB/TrEMBL
      Q6NSG7
      Related
      ENSP00000370125.5, ENST00000380749.10
      Conserved Domains (1) summary
      pfam01101
      Location:1 → 94
      HMG14_17; HMG14 and HMG17

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      39342315..39349088 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440757.1 → XP_047296713.1  non-histone chromosomal protein HMG-14 isoform X1

    2. XM_047440758.1 → XP_047296714.1  non-histone chromosomal protein HMG-14 isoform X1

      Related
      ENST00000492280.5

    3. XM_024452071.2 → XP_024307839.1  non-histone chromosomal protein HMG-14 isoform X1

      UniProtKB/TrEMBL
      Q96N32

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      37726869..37733757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324457.1 → XP_054180432.1  non-histone chromosomal protein HMG-14 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P05114.3 GenPept UniProtKB/Swiss-Prot:P05114

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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