Supplementary Table 1. Validation BEAF-32 at Genes Identified with Fly Enhancer That Had

Supplementary Table 1. Validation BEAF-32 at genes identified with Fly Enhancer that had a binding cluster <1 kb from the TSS. ChIP-chip data (GEO Accession: GSE15661) was used to confirm that BEAF-32 was physically bound to each gene (*). A. gamibae orthologs (if present) are also listed in addition to whether the same Drosophila motif was identified and its relationship to the TSS.

D. melanogaster A. gambie ortholog genes identified A. gambiae BEAF-32 ChIP- identified with with Fly Enhancer Ortholog chip peak Mosquito Enhancer CG31174(-) - - - Spx(+) AGAP001538 * - Atx2(+) - * - CG11151(+) AGAP003092 - - nito(+) AGAP005127 * - CG5284(+) AGAP005777 * - AGAP010224, KdelR(+) AGAP012756 * - U2A(-) AGAP007670 * - osa(-) AGAP001786 * - CG10616(+) AGAP006119 * - CG6151(-) AGAP011546 * - CG1667(+) - * - CG15770(+) - * - CG5360(+) AGAP005115 * - CkIIalpha-i1(+) AGAP005569 * - su(s)(+) AGAP011127 * * downstream Tango2(+) AGAP002962 * - CG15743(+) AGAP001396 * - CG31195(-) AGAP001418 * - CG9253(+) AGAP009809 * - Acyp2(+) - * - CG6982(+) - * - CG8228(+) AGAP003980 * - AGAP010018, Psf2(-) AGAP012743 * - smt3(-) AGAP001701 * - sec63(+) AGAP007361 * * totally inside Vap-33-1(+) AGAP000626 * - Uhg1(+) - * - CG14820(+) - - - CG4452(+) AGAP005928 * - CG5500(+) - * - CG7600(+) AGAP002874 * - CkIalpha(+) AGAP000627 * - CG7845(-) AGAP010453 * - CG10971(-) AGAP004801 * - Pi3K92E(-) AGAP000018 * - l(1)G0168(+) - * - CG5235(-) AGAP011450 * - CG4813(-) AGAP003744 * - Gr98a(+) - - - SmB(-) AGAP005523 * - wuho(+) - * - hang(+) - * - bys(+) AGAP002923 * - CG18292(+) - * - CG3774(+) AGAP011493 * - CG17475(-) - - - CG9715(+) AGAP006128 * - CG13957(+) - * - CG11417(+) AGAP003294 * * 279 bp upstream Hira(+) AGAP009488 * - CG5399(+) - - - CG10566(+) AGAP006627 - - CG2182(-) - * - CG16890(-) AGAP010729 * - rev7(+) AGAP001326 * - CG17723(+) AGAP005918 * - CG7872(+) AGAP000831 * - CG32582(+) - * - CG7222(+) AGAP012058 * - CG32573(+) - * - CG3939(+) - - - Dredd(-) - * - up(-) AGAP002350 - - rg(+) AGAP000017 * - As(-) AGAP012366 * - su(w[a])(+) AGAP003635 * * totally inside drongo(-) AGAP010189 * - swm(+) AGAP009601 * - CR32657(+) - - - CG4699(+) - * - CG2694(+) - * - CG6650(+) AGAP006394 * - CG1599(-) AGAP000700 * - CG9866(+) - * - ras(+) AGAP011133 * - CG6299(+) - * - CG1663(+) - * - shtd(-) AGAP000374 * - PGRP-LE(-) - * - ATP7(+) - * - CG11847(+) AGAP002680 * - inv(+) - - - CG17180(+) - * - mei-9(-) AGAP002805 * * totally inside CG7326(-) - * - CG6907(+) AGAP010407 * - CG7466(+) AGAP008185 * - CG11857(+) AGAP011996 * - CG13933(-) AGAP006608 * - CG18811(-) - * - ave(+) AGAP012177 * - chico(-) - * - CG12018(+) AGAP008910 * - CG3563(+) AGAP000146 * - CG10238(-) AGAP004290 * - CG5098(+) - * - CG11975(+) AGAP012792 * - chrw(-) AGAP006159 * - CalpA(+) AGAP012069 * - CG1172(+) AGAP002354 * - CG14224(+) AGAP004294 * - Tps1(+) AGAP008227 * - smid(+) AGAP006205 * - CG6597(+) AGAP002513 * - eIF-4E(-) AGAP007172 * - CG9393(-) AGAP003981 * - CG33347(+) - - - CG9904(+) AGAP003143 * * downstream par-6(+) AGAP010494 * * @ end and overlaps GATAd(+) - * - CG14478(+) - * - Scsalpha(+) AGAP001312 * - CG31922(+) AGAP010248 * - Hsp60(+) AGAP004002 * * downstream mRpS5(+) - - - tomboy20(-) - - - Srp54(+) AGAP002265 * - CG8979(-) AGAP007418 * - CG17574(-) AGAP007609 * - CG31431(+) AGAP004218 * - CG12016(+) AGAP006740 * - CG15220(-) AGAP010177 * - HDAC4(-) AGAP000410 * - Hsromega(+) - * - CG15627(-) - - - Art9(-) - - - GABA-B-R3(+) AGAP009514 - - Cortactin(-) AGAP004625 * - CG11664(+) - - - CG10051(+) AGAP007676 - - Tak1(-) - * - Brd8(+) AGAP003845 * - CG8199(+) AGAP003136 * - aur(+) AGAP001793 * - CG3409(-) AGAP005394 * * 8912 bp upstream flw(+) AGAP003114 * - CG1623(-) - * - NFAT(+) - * - snoRNA:Psi28S- 2648(-), - - - ms(3)K81(+) - * - MAPk-Ak2(-) AGAP011890 * - CG2941(+) - * - Pros35(+) AGAP010253 * - CG10086(+) - - - CG12115(-) - - - CG4930(+) - * - Deaf1(+) AGAP004905 * - CG10232(-) - - - CG11105(-) AGAP004258 - * totally inside CG1826(+) AGAP006714 * - a6(-) - * - CG14205(+) - - - CG2641(+) - - - CG13260(+) - - - nmo(+) AGAP005898 * - gbb(+) AGAP000824 * - CG2446(-) AGAP004286 * * 25320 upstream lqf(+) AGAP007396 * * totally inside CG2982(+) - * - disco-r(-) AGAP001106 - - CG32243(-) - * - SMC1(+) AGAP002947 * - mei-217(-) - * - mei-S332(+) - * - CG8121(+) AGAP008322 * - cul-5(-) AGAP002404 * - AnnIX(+) AGAP003790 * - Psf3(-) AGAP011132 * - CG6125(-) AGAP001531 * - alpha-Man-IIb(+) AGAP004020 * - Pep(-) AGAP004864 * - CG8630(+) - - - CG8979(-) AGAP007418 * - Hsc70Cb(+) AGAP010331 * * 91625 upstream Cpr12A(+) - - - CG10664(+) AGAP008727 * - CG11357(+) - * - CG8436(+) - * - nuf(+) AGAP010445 * - CG1461(+) AGAP000327 - - CG33679(+) - * - CG2926(-) AGAP010697 * - CG6841(+) AGAP005640 * * 7643 upstream rtet(+) AGAP001391 * - ncm(-) AGAP007874 * - pxt(+) - * - exd(+) AGAP004696 * * downstream Rab40(-) AGAP000841 * - CG17788(+) - * - CG3252(-) - - - Ppn(-) - - - bic(+) AGAP006614 * - CG3253(+) - * - spas(+) AGAP002334 * - CG2662(+) AGAP010081 * - CG9849(+) - * - CG8290(+) AGAP011746 * - Aats-asp(+) AGAP005576 * - Rad51D(+) AGAP006734 * - dj-1beta(+) AGAP000705 * - CG1837(+) AGAP000044 * - CG15362(+) AGAP007577 * - CG7849(+) AGAP002077 * - CG15611(+) - - - CG15245(-) - - - Sep5(-) - * - Anxb11(-) - * - CG4949(+) - * - CG2807(+) AGAP000178 * - CG9743(-) AGAP003051 - - CG3262(+) AGAP000577 * - Ntf-2(+) AGAP000498 * - Anp(+) - * - syt(-) AGAP007942 - - CG5169(+) AGAP009961 * - CG15626(-) AGAP008107 * - snoRNA:Psi28S- 2626(-), - * - tth(-) - * - Rab10(+) AGAP000671 * - Rad51C(+) - * - CG12926(-) - - - CG31731(+) AGAP001523 * - Rab11(+) AGAP004559 * - CG15251(-) AGAP000696 - - Pfrx(+) AGAP012010 * - CG10418(+) AGAP005136 * * downstream CG4239(+) AGAP000393 * CG6923(-) - * - CG2556(+) AGAP010972 * - CG1109(+) AGAP001362 * - CG3773(+) - * - CG11404(+) - - - Nrg(+) AGAP000720 * - CG6788(+) - * - CG9072(-) - - - lic(+) AGAP000310 * - Rrp46(+) AGAP002177 * - eIF-5A(+) AGAP011284 * - CG5941(+) AGAP003344 * - CG3056(+) - * - CG15735(+) AGAP002167 * - Amph(+) AGAP005076 * * totally inside rdgBbeta(-) AGAP004469 * - CG12194(+) AGAP009523 * - CG9203(-) AGAP004082 * - CG4078(+) AGAP000634 * - CG13865(+) - * - Act57B(+) - - - CG12057(+) - - - Rst(1)JH(+) - * - CG14030(+) - * - Galpha49B(+) AGAP005079 * - CG13151(+) AGAP002349 * - CG32543(+) - - - Tsp42Ec(+) - - - mys(+) AGAP000815 * - CG31495(-) - * - CG11873(+) - * - CG8097(+) AGAP003132 * - lrrk(+) - * - CG31477(+) AGAP000260 - - fal(+) AGAP006056 * * 86 bp upstream AGAP001169, * (AGAP001170, no Gr93a(+) AGAP001170 - other information) CG14457(+) AGAP000750 - - CG5116(+) AGAP003969 * - CG10062(+) AGAP007676 - - CG16817(+) AGAP011157 * - CG7800(+) - * - Rpt3(+) AGAP003008 * - ey(+) AGAP000063 * - CG3008(+) AGAP009993 * - Dot(+) - * - crl(+) AGAP002169 * - Gtp-bp(-) AGAP010894 * *17833 upstream CG8083(+) AGAP005988 - * 1136 bp upstream CG7045(+) - * - CG12728(+) - * - CG18749(+) - * - CG11268(+) AGAP001310 * - CG8974(-) AGAP006041 * - CG3363(+) - * - RpS10b(+) AGAP000739 * - M6(+) AGAP012018 * - Dap160(-) AGAP009037 * - CG4764(+) AGAP002338 * - ctp(+) AGAP001335 * - CG1847(+) AGAP012255 * - l(2)37Ce(+) - * - eIF6(-) AGAP001380 * - unc-13(-) AGAP000065 * - pan(+) AGAP012389 * - mRpL17(+) AGAP001865 * - CHOp24(+) AGAP004743 * - Sas(+) AGAP002579 * - sec23(+) AGAP001759 * - shi(+) AGAP003018 * - BCL7-like(+) AGAP000566 * - tRNA:CR32525(+) - - - snf(+) AGAP011637 * - CG32767(-) - * - CG40006(-) AGAP002738 - - Sgt(+) AGAP003052 * * 20952 upstream