{
 "key": "SAND",
 "name": "SAND domain (AIRE/SP100/GMEB)",
 "class": "SAND",
 "aka": [
  "SAND domain",
  "KDWK family",
  "GME (glucocorticoid modulatory element)",
  "PIF site",
  "parvovirus initiation factor site",
  "Sp100/AIRE/NucP41-75/DEAF1 domain"
 ],
 "definition": "GMEB1/2 (GRE-modulating), SP100, SP140, AIRE, DEAF1-like SAND factors.",
 "consensus": "ACGY-N(1-9)-RCGY",
 "dataConsensus": "TACGTAA",
 "motifCount": 15,
 "bySource": {
  "JASPAR": 2,
  "HOCOMOCO": 8,
  "CIS-BP": 2,
  "Vierstra": 3
 },
 "symbols": [
  "AIRE",
  "GMEB",
  "GMEB1",
  "GMEB2",
  "SP100",
  "SP140"
 ],
 "representative": "GMEB1.H14CORE.2.SM.B",
 "cohesion": 0.7,
 "short": "The SAND domain is a small DNA-binding fold named after the four proteins in which it was first recognized: Sp100, AIRE, NucP41/75 and DEAF1. Sequence-specific binding depends on a conserved KDWK motif on the domain's surface, and only some SAND proteins have it. The best-defined members are GMEB1 and GMEB2, which bind as a heterodimer, also known as parvovirus initiation factor, to two CpG-containing tetranucleotide half-sites with flexible spacing: ACGY-N(1-9)-RCGY, with an optimum spacer of six bases. Binding is abolished by methylation of the CpG in either half-site. AIRE and the speckled proteins SP100 and SP140 lack the KDWK motif and are recruited through chromatin rather than sequence, so motif models attributed to them should be treated as descriptions of where they were found.",
 "long": "## The factors\n\nSAND is a fold, not a functional group. The domain was named from Sp100, AIRE-1, NucP41/75 and\nDEAF1, and its NMR structure showed a novel alpha-beta fold whose DNA-binding activity maps to a\nconserved surface motif, KDWK, which gives the family its alternative name [PMID:11427895,10523663]. Human SAND proteins\nfall into distinct groups. GMEB1 and GMEB2 (p96 and p79) were identified twice over: as the\nheterodimer that binds the glucocorticoid modulatory element upstream of the tyrosine\naminotransferase gene [PMID:7665613], and as parvovirus initiation factor, the host factor required for\nminute virus of mice origin nicking [PMID:10523663]. They carry the KDWK motif, bind DNA cooperatively, and are\nubiquitously expressed [PMID:7665613,10523663,11743720]. DEAF1 (NUDR) is a related KDWK protein that binds TTCG-containing repeats [PMID:9773984];\nnotably, it has no motif in any of the four databases used here despite being named in this\nfamily's definition. The speckled proteins SP100, SP110, SP140 and SP140L are nuclear-body\ncomponents that combine a SAND domain with PHD fingers and bromodomains and act as chromatin\nreaders in immune cells [PMID:32386862]. AIRE, the autoimmune regulator, is the most important special case: its\nSAND domain lacks the KDWK residues required for sequence-specific DNA contact and instead mediates\nhomodimerization, while its two PHD fingers read histone H3, PHD1 binding H3 tails that are\nunmethylated at lysine 4 [PMID:18292755]. AIRE is essentially restricted to medullary thymic epithelial cells [PMID:12376594].\n\n## The motif\n\nFor GMEB1/GMEB2 the site is well defined and unusual. Degenerate oligonucleotide selection showed\nthat the heterodimer, and each homodimer, binds two tetranucleotide half-sites conforming to\nACGY-N(1-9)-RCGY, with an optimum spacer of six bases [PMID:11743720]; the spacing is genuinely flexible, so the\nelement is a pair of short half-sites at variable distance rather than a fixed-width motif [PMID:10523663,11743720]. The\ninvariant feature is the CpG in each half-site, and 5-methylation of those cytosines abolishes\nbinding completely [PMID:11743720], which makes GMEB an unusual example of a factor whose occupancy is directly\nmethylation-sensitive at its core. Because CpG is suppressed in vertebrate genomes, such sites\nshould be rare, yet over half of a sample of 100 human promoters contained at least one, often\nwithin 100 bases of the start site [PMID:11743720]. The models in these databases capture only part of this\ngrammar. Most GMEB matrices collapse the pair into a single half-site region: the representative\nmodel here is TACGTAA, and JASPAR's GMEB1 and GMEB2 matrices are tACGTa and TACGTAA. One CIS-BP\nmodel, M05735_2.00, does show the doubled form (TACGTACGGTACGTA), which is the two half-sites\nresolved. The consequence for scanning is severe: a six- or seven-base ACGT-centered model sits in\nthe middle of the sequence space used by bZIP factors, since TACGTA, TGACGT and CACGTG all contain\nACGT [PMID:10523663], and the data reflect this directly. Two GMEB1 models have a higher similarity to their\nbest out-of-family neighbour than to any in-family motif, and the family's cohesion is only 0.70\nacross 15 motifs. The remaining models are not ACGT elements at all: the ChIP-derived GMEB models\nare GCGTCAGCGCG-like, the HOCOMOCO SP100 model is AACGGTTA and the SP140 model is GTCGTCACTA, each\nwith zero label agreement, and the Vierstra AIRE archetype (AC0160) is a CCAAT-containing element\nrather than anything resembling a SAND site.\n\n## Where it acts\n\nGMEB sites are promoter-proximal and, by construction, CpG-containing, so they concentrate in\nCpG-island promoters where their methylation sensitivity could make them responsive to DNA\nmethylation state. The glucocorticoid modulatory element itself modulates the sensitivity of a\nglucocorticoid-responsive promoter rather than driving it [PMID:7665613], so GMEB acts as a modifier of another\nfactor's output. AIRE acts in a completely different regime: in medullary thymic epithelial cells\nit associates with super-enhancers [PMID:28135252] and with thousands of promoters of tissue-restricted antigen\ngenes, and its principal mechanism is releasing stalled RNA polymerase II rather than recruiting it\nto a specific sequence [PMID:22203960]. SP140 occupies and maintains repressed loci in macrophages, including\nlineage-inappropriate developmental genes [PMID:32386862].\n\n## Biology and disease\n\nBiallelic loss-of-function mutations in AIRE cause autoimmune polyendocrinopathy-candidiasis-ectodermal\ndystrophy (APECED, also APS-1), a monogenic autoimmune disease [PMID:9398839]; Aire-deficient mice lose promiscuous\nexpression of thousands of tissue-restricted antigens in the thymus and develop multi-organ\nautoimmunity, which established the central-tolerance model of negative selection [PMID:12376594]. Missense\nmutations in the SAND domain of DEAF1 cause intellectual disability with severe speech impairment\nand behavioral problems [PMID:24726472]. Variants at SP140 and SP110 are associated with Crohn disease, multiple\nsclerosis and chronic lymphocytic leukemia, and SP110 mutations cause hepatic venoocclusive disease\nwith immunodeficiency [PMID:32386862]. GMEB proteins have no established monogenic disease link, but they are\nrequired for parvovirus DNA replication [PMID:10523663].\n\n## Reading a hit\n\nThe central caution is that this key mixes proteins that read sequence with proteins that do not. A\nmatch to a GMEB model is a real, if weak, claim: look for the second CpG half-site within nine bases\nand check the methylation state, because an unmethylated CpG is part of the site rather than\nincidental. A match to an AIRE, SP100 or SP140 model is much harder to interpret. The three are not alike. AIRE's SAND domain lacks the KDWK residues, and its only motif here is a Vierstra archetype that reads as a CCAAT-type element. SP100's SAND domain does carry KDWK, since the SAND structure itself was solved from Sp100b [PMID:11427895], and the SP100 and SP140 models are grade A in HOCOMOCO with in vitro selection support (HT-SELEX, GHT-SELEX and SMiLE-seq, plus PBM for SP140) as well as ChIP. Those two are measurements of direct binding, even though their nearest neighbours lie in other families. The general risk for the ACGT-centered GMEB models is\nconfusion with bZIP sites, which share the same four-base core and are far more abundant [PMID:10523663,7665613]; a TACGTA\nmatch in a promoter is more likely to be a CRE-like or MAF-like element than a GMEB site.",
 "caveats": "Split this family in two before trusting anything. GMEB1 and GMEB2 have the KDWK motif and a real, if unusual, site: two CpG-containing half-sites with a 1-9 base spacer, abolished by CpG methylation. But the matrices compress this to a six- or seven-base ACGT core that overlaps bZIP space, and two GMEB1 models here match an out-of-family motif better than any relative. AIRE is the real exception: its SAND domain lacks the KDWK residues and its only model is a Vierstra archetype that reads as a CCAAT-type element. The SP100 and SP140 models are grade A with in vitro selection support, so they do record sequences those proteins bind, but their nearest neighbours lie in other families. Treat the AIRE model as a record of where AIRE was found rather than of a sequence it reads. DEAF1 has no motif here at all.",
 "references": [
  {
   "cite": "Bottomley MJ, Collard MW, Huggenvik JI, et al. The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Nat Struct Biol 2001;8:626-33.",
   "pmid": "11427895",
   "url": "https://pubmed.ncbi.nlm.nih.gov/11427895/"
  },
  {
   "cite": "Christensen J, Cotmore SF, Tattersall P. Two new members of the emerging KDWK family of combinatorial transcription modulators bind as a heterodimer to flexibly spaced PuCGPy half-sites. Mol Cell Biol 1999;19:7741-50.",
   "pmid": "10523663",
   "url": "https://pubmed.ncbi.nlm.nih.gov/10523663/"
  },
  {
   "cite": "Burnett E, Christensen J, Tattersall P. A consensus DNA recognition motif for two KDWK transcription factors identifies flexible-length, CpG-methylation sensitive cognate binding sites in the majority of human promoters. J Mol Biol 2001;314:1029-39.",
   "pmid": "11743720",
   "url": "https://pubmed.ncbi.nlm.nih.gov/11743720/"
  },
  {
   "cite": "Oshima H, Szapary D, Simons SS Jr. The factor binding to the glucocorticoid modulatory element of the tyrosine aminotransferase gene is a novel and ubiquitous heteromeric complex. J Biol Chem 1995;270:21893-901.",
   "pmid": "7665613",
   "url": "https://pubmed.ncbi.nlm.nih.gov/7665613/"
  },
  {
   "cite": "Huggenvik JI, Michelson RJ, Collard MW, et al. Characterization of a nuclear deformed epidermal autoregulatory factor-1 (DEAF-1)-related (NUDR) transcriptional regulator protein. Mol Endocrinol 1998;12:1619-39.",
   "pmid": "9773984",
   "url": "https://pubmed.ncbi.nlm.nih.gov/9773984/"
  },
  {
   "cite": "Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, et al. Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems. Am J Hum Genet 2014;94:649-61.",
   "pmid": "24726472",
   "url": "https://pubmed.ncbi.nlm.nih.gov/24726472/"
  },
  {
   "cite": "Nagamine K, Peterson P, Scott HS, et al. Positional cloning of the APECED gene. Nat Genet 1997;17:393-8.",
   "pmid": "9398839",
   "url": "https://pubmed.ncbi.nlm.nih.gov/9398839/"
  },
  {
   "cite": "Anderson MS, Venanzi ES, Klein L, et al. Projection of an immunological self shadow within the thymus by the aire protein. Science 2002;298:1395-401.",
   "pmid": "12376594",
   "url": "https://pubmed.ncbi.nlm.nih.gov/12376594/"
  },
  {
   "cite": "Org T, Chignola F, Hetényi C, et al. The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep 2008;9:370-6.",
   "pmid": "18292755",
   "url": "https://pubmed.ncbi.nlm.nih.gov/18292755/"
  },
  {
   "cite": "Giraud M, Yoshida H, Abramson J, et al. Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells. Proc Natl Acad Sci U S A 2012;109:535-40.",
   "pmid": "22203960",
   "url": "https://pubmed.ncbi.nlm.nih.gov/22203960/"
  },
  {
   "cite": "Bansal K, Yoshida H, Benoist C, et al. The transcriptional regulator Aire binds to and activates super-enhancers. Nat Immunol 2017;18:263-273.",
   "pmid": "28135252",
   "url": "https://pubmed.ncbi.nlm.nih.gov/28135252/"
  },
  {
   "cite": "Fraschilla I, Jeffrey KL. The Speckled Protein (SP) Family: Immunity's Chromatin Readers. Trends Immunol 2020;41:572-585.",
   "pmid": "32386862",
   "url": "https://pubmed.ncbi.nlm.nih.gov/32386862/"
  },
  {
   "cite": "Kumar PG, Laloraya M, Wang CY, et al. The autoimmune regulator (AIRE) is a DNA-binding protein. J Biol Chem 2001;276:41357-64.",
   "pmid": "11533054",
   "url": "https://pubmed.ncbi.nlm.nih.gov/11533054/"
  }
 ],
 "timeline": [
  {
   "year": 1995,
   "finding": "The factor binding the glucocorticoid modulatory element (GME) far upstream of the tyrosine aminotransferase gene is a novel, ubiquitous complex of two proteins, GMEB1 and GMEB2, distinct from the CREB/ATF proteins that also bind the element.",
   "methods": "Partial protein purification, gel shift, size-exclusion chromatography",
   "confidence": "medium",
   "pmids": [
    "7665613"
   ],
   "open": "The proteins' sequences, family and recognition rules were unknown."
  },
  {
   "year": 1999,
   "finding": "Parvovirus initiation factor is cloned as the p96/p79 heterodimer (GMEB1/GMEB2), placed in the KDWK family, and shown to bind two PuCGPy half-sites that can be spaced 1 to 15 nucleotides apart.",
   "methods": "cDNA cloning, recombinant protein, DNA-binding and promoter assays",
   "confidence": "medium",
   "pmids": [
    "10523663"
   ],
   "open": "The exact consensus and spacing optimum."
  },
  {
   "year": 2001,
   "finding": "NMR structure of the Sp100b SAND domain defines a new alpha/beta DNA-binding fold, with the conserved KDWK motif on a positively charged helical surface that mutagenesis and chemical-shift mapping identify as the DNA-binding surface; the NUDR (DEAF1) SAND domain alone suffices for DNA binding.",
   "methods": "NMR spectroscopy, mutagenesis, chemical-shift perturbation",
   "confidence": "high",
   "pmids": [
    "11427895"
   ]
  },
  {
   "year": 2001,
   "finding": "Selection and dissociation-rate analysis define the GMEB consensus as ACGY-N(1-9)-RCGY with an optimal spacer of six; CpG methylation of the half-sites abolishes binding, yet over half of 100 human promoters carry a site.",
   "methods": "Degenerate-oligonucleotide selection, dissociation kinetics, gel shift",
   "confidence": "medium",
   "pmids": [
    "11743720"
   ],
   "open": "Whether methylation regulates GMEB occupancy in cells."
  },
  {
   "year": 2001,
   "finding": "AIRE is reported to be a sequence-specific DNA-binding protein whose dimers and tetramers bind ATTGGTTA and TTATTA motifs.",
   "methods": "Gel shift and competition assays with recombinant protein",
   "confidence": "low",
   "pmids": [
    "11533054"
   ],
   "open": "The motifs were not tied to AIRE target genes in thymic epithelium."
  },
  {
   "year": 2002,
   "finding": "Aire-deficient mice lose ectopic expression of peripheral tissue-restricted antigens in medullary thymic epithelial cells and develop autoimmunity that depends on Aire in thymic stroma, establishing AIRE's role in central tolerance.",
   "methods": "Knockout mice, expression profiling, thymic transplantation",
   "confidence": "high",
   "pmids": [
    "12376594"
   ]
  },
  {
   "year": 2012,
   "finding": "In medullary thymic epithelial cells AIRE binds essentially all Pol II-rich start sites and activates its targets by releasing stalled RNA polymerase II, not by recognizing specific promoter sequences. This is at odds with the earlier report of sequence-specific AIRE binding.",
   "methods": "Transcript mapping with mRNA-spanning probes, ChIP-seq for AIRE and Pol II",
   "confidence": "medium",
   "pmids": [
    "22203960"
   ]
  }
 ],
 "openQuestions": [
  "Whether CpG methylation regulates GMEB binding in cells is open: methylating the half-site CpGs abolishes binding in vitro, but the proposal that this controls occupancy in vivo rests on that biochemistry.",
  "Whether AIRE has any intrinsic sequence preference is disputed: an early in vitro study reported AIRE oligomers binding ATTGGTTA and TTATTA motifs, and the Vierstra AIRE archetype AC0160 carries ATTGGTTA on its reverse strand, whereas genome-wide work finds AIRE at essentially all Pol II-rich start sites, acting by releasing stalled polymerase rather than by sequence recognition.",
  "Whether SP100 and SP140 bind DNA directly through their SAND domains is unsettled: their HOCOMOCO models are grade A and supported by in vitro assays (HT-SELEX, GHT-SELEX and SMiLE-seq, plus PBM for SP140) as well as ChIP, yet the motifs (AACGGTTA, GTCGTCACTA) share little with the GMEB half-site beyond a CpG, and their nearest neighbours lie in other families.",
  "The permitted GMEB half-site spacing differs between studies: the cloning work reported spacings of 1 to 15 nucleotides, whereas selection combined with dissociation-rate analysis gave 1 to 9 with an optimum of six."
 ],
 "members": [
  {
   "id": "M05735_2.00",
   "source": "CIS-BP",
   "consensus": "cTACGTAcggTACGTA",
   "bits": 21.2,
   "prov": {
    "inferred": false
   }
  },
  {
   "id": "AC0268:GMEB:SAND",
   "source": "Vierstra",
   "consensus": "ACGTGgTtACGT",
   "bits": 12.4
  },
  {
   "id": "GMEB2.H14CORE.2.SM.B",
   "source": "HOCOMOCO",
   "consensus": "gTACGTaAcG",
   "bits": 12,
   "prov": {
    "evidence": "SM",
    "grade": "B"
   }
  },
  {
   "id": "GMEB1.H14CORE.2.SM.B",
   "source": "HOCOMOCO",
   "consensus": "TACGTAA",
   "bits": 11.7,
   "prov": {
    "evidence": "SM",
    "grade": "B"
   }
  },
  {
   "id": "GMEB2.H14CORE.0.P.C",
   "source": "HOCOMOCO",
   "consensus": "GCGTcagcGCG",
   "bits": 10.3,
   "prov": {
    "evidence": "P",
    "grade": "C"
   }
  },
  {
   "id": "AC0160:AIRE:SAND",
   "source": "Vierstra",
   "consensus": "taaCCaatawaACC",
   "bits": 10.1
  },
  {
   "id": "GMEB1.H14CORE.1.P.C",
   "source": "HOCOMOCO",
   "consensus": "gCGTcagcGCGc",
   "bits": 10,
   "prov": {
    "evidence": "P",
    "grade": "C"
   }
  },
  {
   "id": "GMEB2 (MA0862.1)",
   "source": "JASPAR",
   "consensus": "TACGTAA",
   "bits": 9.9
  },
  {
   "id": "SP140.H14CORE.0.PSGIB.A",
   "source": "HOCOMOCO",
   "consensus": "GtCGtCAcTa",
   "bits": 9.5,
   "prov": {
    "evidence": "PSGIB",
    "grade": "A"
   }
  },
  {
   "id": "GMEB2.H14CORE.1.P.C",
   "source": "HOCOMOCO",
   "consensus": "tGCGTgag",
   "bits": 9.2,
   "prov": {
    "evidence": "P",
    "grade": "C"
   }
  },
  {
   "id": "GMEB1.H14CORE.0.P.C",
   "source": "HOCOMOCO",
   "consensus": "TGCGTg",
   "bits": 9,
   "prov": {
    "evidence": "P",
    "grade": "C"
   }
  },
  {
   "id": "SP100.H14CORE.0.PSGI.A",
   "source": "HOCOMOCO",
   "consensus": "aaCGGTtA",
   "bits": 9,
   "prov": {
    "evidence": "PSGI",
    "grade": "A"
   }
  },
  {
   "id": "AC0272:GMEB:SAND",
   "source": "Vierstra",
   "consensus": "tACGTA",
   "bits": 8.9
  },
  {
   "id": "Gmeb1 (MA0615.2)",
   "source": "JASPAR",
   "consensus": "tACGTa",
   "bits": 7.2
  },
  {
   "id": "M02460_2.00",
   "source": "CIS-BP",
   "consensus": "aCGt",
   "bits": 5,
   "prov": {
    "inferred": false
   }
  }
 ],
 "url": "https://motif.zhoulab.io/families/sand/",
 "generated": "2026-10-21",
 "provenance": "Entry text drafted by a language model reading the primary literature; every cited PMID verified against PubMed. Computed fields derive from JASPAR 2024, HOCOMOCO v14, CIS-BP and the Vierstra archetypes. See https://motif.zhoulab.io/families/methods/"
}