Silent and expressed sister Mup genes are located within distinct chromatin domains: analysis by pulsed-field gel electrophoresis and polymerase chain reaction-supplemented DNase I digestion.

We haverecently described asubfamily oftwogenes, Mup-1.5a andMup-1.5b, whichexist asanonallelic pair inmostinbred strains ofmice. TheMup-1.5a andMup-1.5b genes aremorethan99.91% homologous, yetthey are differentially expressed. WhiletheMup-1.5a geneisexpressed atahighlevel inthesubmaxillary gland, the Mup-1.5b genedoesnotappear tobeexpressed either inthis orinanyother tissue. TheMup-1.5b genecan, however, beexpressed asatransgene withthetissue specificity ofits sister gene, Mup-1.5a. Wehaveshownbefore that boththeMup-1.5a andMup-1.Sb genes arelocated onchromosome 4,closely linked totheMup-)locus. In this report, wedemonstrate thetwogenes arelocated within distinct chromosomal domains, separated byatleast 150to200kbofDNA.Using anovel method, detailed inthis report, weshowthat inthesubmaxillary gland, the Mup-1.5a geneisfive- tosixfold moresusceptible toDNaseIdigestion thanistheMup-1.5b gene. Thisfinding suggests that theinactivity oftheMup-1.Sb geneisbrought about bylong range-acting mechanisms that establish achromatin structure inthevicinity ofthis geneincompatible withtranscription. Themousemajorurinary protein (Mup)genefamily consists ofca.35to40genes, mostorallofwhichare located intheMup-1locus onchromosome 4(2,3).However, intheBALB/cstrain, despite anextensive sequencing effort, thereisevidence forthesynthesis ofonlyeight species ofMUP mRNAs,MUP Ithrough VI(13, 14), p1057 (9), andpMUP11(5). MUP I,MUP II,MUP III, p1057, and pMUP11aresynthesized predominantly intheliver, MUP IVissynthesized inthelachrymal gland, MUP V issynthesized inthesubmaxillary gland, andMUP VIissynthesized intheparotid gland. We haverecently suggested thatthe nonexpressed genesinclude, inaddition topseudogenes, silent genes, i.e., genesthat arepotentially active butare rendered nonfunctional through long-range position effects (16). Inthisreport, we present datathatsupport this hypothesis. IntheBALB/cByJ strain, thegeneencoding theMUP V mRNA isamemberofasubfamily oftwohighly homologous genes, Mup-1.Sa andMup-1.5b (15, 16). TheMup-1.Sa and Mup-1.Sb genesarenearly identical throughout their entire 4-kbtranscription units. Intheexons, thetwogenesdiffer onlyatoneposition, inthe3'untranslated region, byan A-to-C substitution. Intheintrons, thetwogenesdiffer at twopositions; there isaT-Ctransition inintron IIanda deletion of(GT)3 inaGT-rich region ofintron III. Intheca. 0.6kbof5'flanking and0.3kbof3'flanking sequences, the Mup-1. 5aandtheMup-1.Sb genes areidentical (16). Thetwo genesexhibit identical restriction patterns, indicating that thesimilarity between themextends overmorethan20kb into both5'and3'flanking sequences (16). However, despite their virtual identity, theMup-1.Sa andtheMup-1.Sb genes aredifferentially expressed. Usingspecific oligonucleotides thatencompass theA-Csubstitution inthe3'untranslated region, wehaveshownthat theMup-1.5a geneisexpressed atahighlevel, predominantly inthesubmaxillary gland, while theMup-1.Sb geneisnotexpressed (16).