Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs

摘要

AttheemDrosophilamelanogaster/embithoraxcomplex(BX-C)over330#xA0;kbofintergenicDNAisresponsiblefordirectingthetranscriptionofjustthreehomeotic(Hox)genesduringembryonicdevelopment.Anumberofdistinctenhanceremcis/em-regulatorymodules(CRMs)areresponsibleforcontrollingthespecificexpressionpatternsoftheHoxgenesintheBX-C.WhileithasprovenpossibletoidentifyorthologsofknownBX-CCRMsindifferentemDrosophila/emspeciesusingoverallsequenceconservation,thisapproachhasnotprovensufficientlyeffectiveforidentifyingnovelCRMsordefiningthekeyfunctionalsequenceswithinenhancerCRMs.Herewedemonstratethatthespecificspatialclusteringoftranscriptionfactor(TF)bindingsitesisimportantforBX-Cenhanceractivity.AbioinformaticsearchforcombinationsofputativeTFbindingsitesintheBX-Csuggeststhatsimpleclusteringofbindingsitesisfrequentlynotindicativeofenhanceractivity.However,throughmoleculardissectionandevolutionarycomparisonacrosstheemDrosophila/emgenuswediscoveredthatspecificTFbindingsiteclusteringpatternsareanimportantfeatureofthreeknownBX-Cenhancers.Sub-regionsofthedefinedIAB5andIAB7benhancerswerebothfoundtocontainanevolutionarilyconservedsignaturemotifofclusteredTFbindingsiteswhichiscriticalforthefunctionalactivityoftheenhancers.Together,theseresultsindicatethatthespatialorganizationofspecificactivatorandrepressorbindingsiteswithinBX-Cenhancersisofgreaterimportancethanoverallsequenceconservationandisindicativeofenhancerfunctionalactivity./p/div