Research Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes

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1 Research Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila =C E?D ) 5 K@AH V :E= K K= W ;K E C5DE W,=LE@,? AA ALE +=HHE? W E 6E JDO 9E I D 6 HA )@@HAIIAI K? A=H4A?AFJ H,EI? W +A K =HA E?I =N 5 EJD E A 4AIA=H?D6HE= C A2=H + %%' 75) V += >HE=E I?EA?AI A@B H@ )%! 75) 5O CA J=1? 4AIA=H?D6HE= C A2=H + %%' 75) + D 6 HA - =E J!$&(CI? Published: 24 July 2001 Genome Biology 2001, 2(8):research The electronic version of this article is the complete one and can be found online at Maglich et al., licensee BioMed Central Ltd (Print ISSN ; Online ISSN ) Abstract Background: The availability of complete genome sequences enables all the members of a gene family to be identified without limitations imposed by temporal, spatial or quantitative aspects of mrna expression. Using the nearly completed human genome sequence, we combined in silico and experimental approaches to define the complete human nuclear receptor (NR) set. This information was used to carry out a comparative genomic study of the NR superfamily. Results: Our analysis of the human genome identified two novel NR sequences. Both these contained stop codons within the coding regions, indicating that both are pseudogenes. One (HNF4γ-related) contained no introns and expressed no detectable mrna, whereas the other (FXR-related) produced mrna at relatively high levels in testis. If translated, the latter is predicted to encode a short, non-functional protein. Our analysis indicates that there are fewer than 50 functional human NRs, dramatically fewer than in Caenorhabditis elegans and about twice as many as in Drosophila. Using the complete human NR set we made comparisons with the NR sets of C. elegans and Drosophila. Searches for the >200 NRs unique to C. elegans revealed no human homologs. The comparative analysis also revealed a Drosophila member of NR subfamily NR3, confirming an ancient metazoan origin for this subfamily. Conclusions: This work provides the basis for new insights into the evolution and functional relationships of NR superfamily members. Background 6DA? F AJA CA E? IAGKA?AI B B KH AK =HO JE? HC= EI I D=LA >AA HAF HJA@,H I FDE = A = C=IJAH +=A HD=>@EJEIA AC= I 5=??D=H >E@ FIEIJD= E= = 6DAIACA AIAGKA?AID=LA>AA KIA@ IJH=JAJDAKJE EJO B? F=H=JELACA E C AL KJE =HO =I MA =I F IIE> A BK?JE = HA =JE IDEFI MEJDE FH JAE IKFAHB= E EAI 9EJDJDAHA?A J=@@EJE B JDA? F AJA DK = CA A IAGKA?A =L=E => A MEJDE JDA Received: 20 April 2001 Revised: 6 June 2001 Accepted: 20 June 2001 DK = CA AFH A?J@=J=>=IA '"IAGKA?A=L=E => A=I B A>HK=HO EJ EI M F IIE> A J >ACE? F=H=JELA CA E?IJK@EAIKIE CDK = IKFAHB= E O A >AHI 9A=HAF=HJE?K =H OE JAHAIJA@E JDA K? A=HHA?AFJ H 4? =II BFH JAE I 4I=FFA=HJ >AHAIJHE?JA@J AJ= = I E MDE?DJDAOD=LA AOH AIE E JACH=JE CJDA? F ANEJEAI BD A F A J! 1 CA AH= 4IBK? JE =I JH= I?HEFJE = HACK =J HI M H E C E??AHJ MEJD

2 2 Genome Biology Vol 2 No 8 =C E?DAJ=? =?JEL=J HAFHAII HIJ CA A ANFHAIIE " 6DA JH= I?HEFJE = =?JELEJEAI B => KJ D= B B JDA 4I IJK@EA@ E DK = I =HA HACK =JA@ >O I = EF FDE E? MDAHA=I JDA JDAH I?= A@ HFD= HA?AFJ HI=M=EJ JEBE?=JE A?=KIA BJDAEHF JA JE= B =JE >O AN CA KI? F JDAEH?A JH= H AI E AJ=> EI JDAIA HA?AFJ HI =HA ANJHA A O E F HJ= JJ=HCAJIE DK )@@EJE = O 4IHAF HAIA J F IIE> A AM J=HCAJI B H JDA? JH B E LAHJA>H=JA FAIJIE =CHE?K JKHA 6DA =JJAH=FFH =?DM O FH EIE CEB?AHJ=E? =IIAI B 4I=HAID M J >AIFA?EBE? J IA A?JA@E LAHJA>H=JAIK>CH KFI + F=HEI B? F AJA IAJI B 4IBH AL KJE =HE O@ELAHCA J HC= EI IID JA KI HA=> KJJDABA=IE>E EJO BJDAIA=FFH =?DAI=IMA =I IDA@ ECDJ CA AH= FDO CA AJE? HA =JE IDEFI = C CIFA?EAI HJDAF=IJOA=H M 4IAJID=LAFHAIA JA@= E JAHAIJ E C FK A 9DA JDA + A AC= I CA A IAGKA?A M=I HAF HJA@ LAH 4 A >AHIMAHAB # GKA J IAGKA?A HA A=IAI D=LA >H KCDJ JDA K >AH B A AC= I 4CA AIJ %) 5 K FK> EIDA@@=J= =JE? E?HA=IA LAH JDA K >AH B?KHHA J O FK> EIDA@ DK = 4I "& A@ J IFA?K =JE JD=J JDA DK = 4IAJ? I =JE?= O $ 5KHFHEIE C O O J J= 4IMAHAB JDAHA?A J OHAF HJA@,H I FDE = CA AIAGKA?A % ) E JHECKE CGKAIJE MEIMDAJDAH JDAJ J= IAJ BDK = 4IME HAB A?JJDA@ELAHIEJOIAA E + A AC= I HE IJA=@ME F=H= A JD=JB I FDE = 9A A F OA@ =? >E A@ >E E B H =JE? A?K =H >E CO =FFH =?DJ = IMAHJDEIGKAIJE Results and discussion 9AD=LA@ALA FA@=CA E?IAGKA?A= = OIEIFEFA E AKJE E E C )56 IA=H?DAI & B MA@ >O =E = = OIEI ' J E@A JEBO 4 IAGKA?AI MEJDE JDA DK = CA A, =E = = OIEI M=I B=?E EJ=JA@ >O JDA M A@CA JD=J JDA 4 IKFAHB= E O EI K EBEA@ >O =H IJHK?JKHA ' A D= =H IJHK?JKHA JD=J?D=H=?JAHE AI JDA B= E OEI=, ) C@ =E,,?D=H=?JAHE A@>OJM +" JOFA E? BE CAHI? J=E A@ E JDA = E JAH E = D= B B JDA FH JAE I ) BA=JKHA JDA C@ =E, EIB NO JAH E KI J=E I = DECD O? IAHLA@ JH= I?HEFJE = JH= I=?JEL=JE BK?JE ) 6DA? F AJA M? F A A J BDK = 4IM=IKIA@=I=GKAHOIAJJ E@A LA 4 IAGKA?AI BH FK> E? DK = CA 1@A IAGKA?AI MAHA B MA@ KF MEJD HA@AJ=E A@>E E B H MDA M=HH= JA@ A?K =H>E CO= = OIEI 7IE CJDEI=FFH =?D MAE@A JEBEA@JM LA 4IAGKA?AI 6DA? IAIJD CI BJDAIAIAGKA?AI MAHAHAFHAIA JA@>O :4 "γ 4 ) 6DA :4 HA =JA@ CA A IAGKA?A :4 H M=I =FFA@ E IE E? J?DH I = F IEJE F! BH JDA?DH I =?=JE B :4 G! CIAGKA?A B :4 H M=I J? JECK KIMEJDE JDA CA A ) J J= B IALA E JH E? C=FI IAF=H=JA@ JDA HACE I C IE E =HEJO 1 JAHAIJE C O JDA F IEJE I B JDAE JH IMEJDE :4 H MAHA=JJDAI= AHA =JELAF IEJE I MEJDE C IAGKA?A =I E :4 IKCCAIJE C =? IA AL KJE =HOHA =JE IDEF>AJMAA JDAIAJM IAGKA?AI 6DA CIAGKA?A B :4 =OA@IE E =HEJOJ :4=?H II A=H OJDAA JEHA A CJD"&IAGKA?AE@A JEJO =JJDA= E =?E@ ALA >KJ? J=E A@ K JEF AIJ I ECKHA = 6DAIAGKA?AI B K JEF AIJ IMAHA? BEH A@>O2+4= F EBE?=JE JIAGKA?E C B :4 H CA E?, ) BH=C A JI IAA =JAHE= I 5AGKA?A = = OIEI JDKI JD=J JDEI CA AI B H = BK?JE = 4 EI E A O J >A = FIAK@ CA A 5KHFHEIE C O HA= JE AGK= JEJ=JELA @AJA?JA@HA =JELA ODECD ALA I BANFHAIIE B :4 H 4 )E JAIJEI@=J= JID M CJD=JJDEICA AEI =JH= I?HE>A@FIAK@ CA A LA 4CA A0 "γ HM=I =FFA@E IE E? J?DH I A F IEJE!G"!G"! K E A@ J JDA M 0 "γ CA A=JF IEJE G 6DA0 "γ H IAGKA?A ID MA@IAGKA?AIE E =HEJO=?H II A=H OJDAA JEHA A CJD B CHACE B0 "γ % "IAGKA?AE@A JEJO=JJDA = E =?E@ ALA E A :4 H 0 "γ C IAGKA?A? J=E A@ K JEF A IJ I ECKHA > JDKI = I =FFA=HI J HAFHAIA J = FIAK@ CA A E A BH= A IDEBJI MAHA A?AII=HOJ =E J=E JDA= E =?E@HA=@E CBH= AHA =JELA J 0 "γ 6DA FHA@E?JA@ 0 "γ H IAGKA?A M=I? BEH A@ >OIAGKA?A= = OIEI BDK = CA E?, )IAA =JAHE= I 6DA C IAGKA?A B 0 "γ H M=I? JECK KIMEJDE JDACA A? IEIJA JMEJDF IIE> A HAJH JH= IF IEJE E J JDA CA A 7 E A :4 H ANFHAIIE B 0 "γ H 4 ) E = O B JDA JEIIKAIAN= E A@@=J= JID M O A JDAH 4FIAK@ CA AD=I>AA HAF = FIAK@ CA AHA =JA@J JDA-44α HA?AFJ H 6DAE@A JEBE?= JE B :4 H 0 "γ H >HE CI JDA J J= DK = 4 FIAK@ CA A K >AH J JDHAA KHJDAH ALE@A?A JD=J JDAIA CA AI=HAFIAK@ CA AIE? K@AIJDAB=?JJD=J D CI B JDA 0 "γ H :4 H CA AI? >A B E =L=E => A KIA H=J KCK H,H I FDE = CA AIAGKA?AI 2IAK@ CA A IAGKA?AI M J >A ANFA?JA@ J >A? IAHLA@ >AJMAA CA AI ALA =I? IA O HA =JA@ =I DK = KIA 1 =@@EJE JH=IJJ JDAEH? IAIJBK?JE = CA AD CI0 " :4 0 "γ H H :4 =O? IAHL=JE BJDAEH= E =?E@IAGKA?AIHA =JELAJ JDAEH K? AE? =?E@ IAGKA?AI 6DEI HAIK J EI = I? IEIJA J MEJDJDAFIAK@ CA A?D=H=?JAHE =JE BJDAIAIAGKA?AI :4 H "γ H MAHAB CIA=H?DAIJD=JKJE E A@ JDAH M DK = 4I =I GKAHO IAGKA?AI +AHJ=E + A AC= I HA?AFJ HI? J=E,IAGKA?AIJD=J@EBBAHIEC EBE?= J OBH = = E=,I # 1JHA =E A@F IIE> A

3 (a) FXR1 FXR60 FXR117 FXR175 FXR232 FXR292 FXR352 FXR412 (b) HNF4γ 1 HNF4γ 61 HNF4γ 121 HNF4γ 181 HNF4γ 241 HNF4γ 301 HNF4γ ILPEQISYQLHDTHFKKSPYCQYSIAQFPPA-- +L EQ+ + L + + PY QYS QFP MGSKMNLIEHSHLPTTDEFSFSENL FGVLTEQVAGPLGQ-NLEVEPYSQYSNVQFPQVQP -LQSESLNHFNTYRLDPQD--SDGGQCGFSSRELNKPTYVVAHDAEDGYPGIKRSRPTY + S S ++ Y P++ S G + R + T P K+ R QISSSSYYSNLGFYPQQPEEWYSPGI---YELRRMPAETLYQGETEVAEMPVTKKPRMGA SSSRNKGQEEFCVVCGDKASPSPYHYNALTCEG CIGFFSMHQQNAVYSCRNGSHCEMDM S+ R KG +E CVVCGD+ AS YHYNALTCEGC GFF +NAVY C+NG +C MDM SAGRIKG-DELCVVCGDRASG--YHYNALTCEGC KGFFRRSITKNAVYKCKNGGNCVMDM YMRRKCQECRLKKYKAVGMLAE CLLTEIQCKLKRLQKNFKEKNHFYSNIKVEEEGVDHSF YMRRKCQECRL+K K +GMLAECLLTEIQCK KRL+KN K + H LDV+ + EG D YMRRKCQECRLRKCKEMGMLAE CLLTEIQCKSKRLRKNVKQ--HADQTVNEDSEGRDLRQ LSSTTRPIQESMELTEEEHQLINNIVAAHQKYTIPLEET NKILQEHTNPELSFLQLSETA ++STT+ +E ELT ++ L++ I+ ++ K +P E TNKIL+E + E +FL L+E A VTSTTKSCREKTELTPDQQTLLHFIMDSYNKQRMPQEITNK ILKEEFSAEENFLILTEMA VLHIRGLMNFTKGL PGFENLANEDQTALQKGSKTEVIFLHGAQLYSQKQSASE S H++ L+ FTK LPGF+ L +EDQ AL KGS E +FL A+++++K + S TNHVQVLVEFTKKL PGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEER LFYFYKRMSKLDVTNTEYALLAATIVFS GDRPCLKNKQYMENLEPV +F FYK ++L + T EYALL A ++ S DR +K+++ +E L EP+ IRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILS PDRQYIKDREAVEKLQEPL LQILYKYSKMYHPEDPHFAHLIWKHTELRTLNYNHSEILSTWKTKDPKLATLLSE L +L K K++ PE+P HFA L+ + TELRT N++H+E+L +W+ D K LL E LDV LQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ MNT NSLICLFAICESRATGKHCGASSCGGCKGFFRCSICKSNVYSCRFRRQCFVDKAK N + CL AIC RATGKH GAS+C GCKGFFR SI KS++YSCRF RQC VDK K MNTTDNGVNCLCAICGDRATGKHYGASTCDGCKGFFRRSIRKSHIYS CRFSRQCVVDKDK RNQCRYSQLRKCFRAGMEKEVVHNECNRTSTRRSTCDGSNIPSINTLAQAEVLSCQISVS RNQCRY +LRKCFRAGM+KE V NE +R STRRST DGSNIPSINTLAQAEV S QISVS RNQCRYCRLRKCFRAGMKKEAVQNERDRISTRRSTFDGSNIPSINTLAQAEVRSR QISVS SLGASTDIHVKKSV--GDVCEFLKQQLLVLVEWAKYIPAFCQLPLDDKVALLRYHAGEHL S G+STDI+VKKS+ GDVCE +KQQLLVLVEWAKYIPAFC+LPLDD+VALLR HAGEHL SPGSSTDINVKKIASIGDVCESMKQQLLVLVEWAKYIPAFCELPLD DQVALLRAHAGEHL LPGAIKRSMMYKDILLLGNNYIIHCNSCEFEISSVISRVLVELVQPFQEIQ L GA KRSMMYKDILLLGNNY+IH NSCE EIS V +RVL ELV+PFQEIQ LLGATKRSMMYKDILLLGNNYVIHRNSCEVEISRVANRVLDELVRPFQEIQIDDNEYACL KAIVFFGPDVKGL-DPINIKNMQFQGRMGLENSVNDL-----GRFGELLLLLPTLLRIIW KAI FF PD KGL DP+ IKNM+FQ ++GLE+ +NDR GRFGELLLLLPTL I W KAIVFFDPDAKGLSDPVKIKNMRFQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSITW QMIEQI-FVKTFAV----HLLQEML-NGASNDSSHLHHPIHPHSSQDPLTGQTVLLGPMY QMIEQI FVK F + +LLQEML GASND SHLHHP+HPH SQDPLTGQT+LLGPM QMIEQIQFVKLFGMVKIDNLLQEMLL GGASNDGSHLHHPMHPHLSQDPLTGQTILLGPMS TLV------TPETPLPSPPQG--QEDYRTATNQASVISHQPLFKQKQL TLV TPETPLPSPPQG QE Y+ A NQASVISHQ L KQKQL TLVHADQISTPETPLPSPPQGSGQEQYKIAANQASVISHQHLSKQKQL Figure 1 Amino acid alignments of the novel NR sequences FXR-r and HNF4γ-r. (a) FXR-r amino acid alignment with FXR (NR1H4). The nucleotide sequences from complete and ordered clone AL contained eight fragments with amino acid sequence similarity with FXR (from 5-3 relative to FXR-r, nucleotide positions ; ; ; ; ; ; ; ). The positions of the intron gaps within FXR-r and FXR are boxed. Positions of termination codons within FXR-r are indicated by an asterisk. (b) HNF4γ-r amino acid alignment with HNF4γ (NR2A2). The complete and ordered clones AL and AL contained contiguous HNF4γ-r sequence. Seven frameshifts (indicated by asterisks) were required to preserve the reading frame of HNF4γ-r relative to HNF4γ. Intron locations in the HNF4γ gene are boxed. JDA JD=J 4,IAGKA?AIANEIJA@E JDADK = CA A JD=JHAFHAIA JA@D CI B + A AC= I 4I>KJMAHA J E@A JEBEA@KIE C = = E= 4I=I=GKAHOIAJ 6 =@@HAII JDEIGKAIJE MAI?= A@JDADK = CA AMEJDJDA? F AJA IAJI B + A AC= I I FDE = 4I -NJA IELA = = OIEI KIE C JDAIA HA?AFJ HI =I GKAHO J HALA= = IE C A LA = = E= D C B JDAIA IAGKA?AI )56 DEJI MEJD F L= KA H KH = = OIEI MA?? K@A JD=J JDA DK = 4 IAJ ME J >A HJD CIHAIA > E CJDA =HCA K >AH B 4I B + A AC= I 2DO CA AJE? = = OIEI B LAHJA>H=JA 4I A@ IEN =?AIJH= 4IK>B= E EAI! # ELA BJDAIK>B= E EAI=HA = I HAFHAIA JA@= C> JDJDA+ A AC= I I FDE = 4I ECKHA? IEIJA JMEJDJDAFH F IA@=?EA J AJ= = HECE B JDAIA IK>B= E EAI " 6DA A=H EAH = = OIEI E@A JEBEA@ =HJDH H A A >AHI B JDA 4! IK>B= E O IKCCAIJE C JD=J JDEI IK>B= E O ECDJ >A HA HA?A J IFA?EBE? J IJ A E A=CA " HA HA?A J O D MALAH JDA,H I FDE = CA A IAGKA?A D=I HALA= A@ = FHALE KI O K M 4 IAGKA?A +%"% JD=J B= I E J JDA 4! IK>B= E O ECKHAI! 6DA >IAHL=JE JD=J 4! EI HAFHAIA JA@ E > JD FH J IJ IJ AI JD=J 4! E AJDA JDAH = H 4IK>B= E EAI EI B= =?EA J AJ= = HECE J=> O JDA+ A AC= I CA A@ AI = A >AH BJDA 4!IK>B= E O 1JME >A BE JAHAIJJ A=H EB 4!EIHAFHAIA JA@E = O A =I=>IA?A B JDA 4!IK>B= E OBH A CA AH= M =OID=HA= AL KJE =HO DEIJ HO JD=J??KHHA@ =BJAH IAF=H=JE B JDA A E A=CA 5K?D= A=H O@ELAHCA?A BJDA A KJE =HO E A JMEJD=HA?A JDOF JDA IEI F =?E C A =HJDH E =? AL KJE =HO? =@A B JE C E LAHJA>H=JAI $ M >A HA? IEIJA JMEJDJDAJH=@EJE = F =?A A J B A = = E A=CAJD=J@ELAHCA@BH JDAH AJ= = I>AB HA IAF=H=JE B JDA = H FH J IJ IJ A E A=CAI % + A=H =JE?= J AL KJE =HO F=JDM=OI D=LA ID=FA@JDA 4IAJIE IAF=H=JAFDO CA AJE? E A=CAI 9EJDE JDA IEN = H 4 IK>B= E EAI B KH CH KFI B 4I =HA?KH HA J O M OE LAHJA>H=JAIJDOH E@D H AHA?AFJ HI 64 FAH NEI A FH EBAH=J H =?JEL=JA@ HA?AFJ H 22)4 HAJE E?=?E@HA?AFJ E@HA?AFJ HCH KF? J=E E C C K?? HJE? E@ HA?AFJ H 4 E AH=? HJE? E@ HA?AFJ HI 4 FH CAIJAH A HA?AFJ H 24 CA HA?AFJ HI )4 1 =@@EJE > JD E LAHJA>H=JA CA AI 4I JD=J =HA J? A=H O F =?A@ E A B JDA A@ 4IK>B= E EAI ECKHA )IFHALE KI O JA@! JDAJDHAA,H I FDE = A >AHI BJDA EHFICH KF@ABE A= K KIK=? =II B 4IJD=J =? IE E =HEJOJ JDA,I BJDA LAHJA>H=JA 4I IJ BJDA+ A AC= I 4I ## B JD IAB DK = EAI ECKHA 1J

4 4 Genome Biology Vol 2 No 8 =C E?DAJ= DmKnr DmKnrl DmEagle CeC33G8.10 CeNHR-50 CeF44C4.2 CeT09D3.4 CeNHR-84 CeNHR-44 CeNHR-18 CeNHR-55 CeNHR-56 CeNHR-28 CeNHR-57 CeNHR-108 CeNHR-11 CeZK697.2 CeC29G2.5 CeNHR-75 CeC14C6.4 CeNHR-89 CeY69H2.8 CeT07C5.5 CeT26E4.8 CeK06B4.8 CeF47C10.7 CeF16H9.2 CeDAF-12 CeNHR-48 CeNHR-8 DmHR96 HsPXR HsVDR HsCAR DmEcR HsFXR HsLXRα HsLXRβ CeFAX-1 DmCG16801 HsPNR DmTLL HsTLX DmDSF DmCG10296 HsCOUP-TF1 HsCOUP-TF2 DmSvp HsEAR-2 CeUNC-55 HsHNF4α HsTR2 HsTR4 CeNHR-41 DmHR78 HsRXRα HsRXRγ HsRXRβ HsTRα HsTRβ HsNGFIBγ HsNGFIBβ HsNGFIBα DmHR38 CeNHR-6 HsRARα HsRARβ HsRARγ HsHNF4γ DmHNF4 CeNHR-64 CeNHR-69 HsPPARα HsPPARβ HsPPARγ CeSEX-1 DmE78 HsREVERBα HsREVERBβ CeNHR-23 DmHR3 HsRORα HsRORβ HsRORγ CeNHR-91 DmHR4 HsGCNF HsGR HsMR HsERα HsERβ HsPR HsAR HsLRH-1 HsSF1 DmFTZ-F1 DmUSP CeNHR-25 DmHR39 NR1 NR4 DmE75 CeNHR-85 NR1 NR6 NR3 NR5 CeNHR-67 NR substitutions per 100 residues Figure 2 Relationships within the completed sets of NR superfamily members from humans, C. elegans and Drosophila. A neighborjoining tree of NR DNA-binding domain sequences was generated using the paupsearch feature of the GCG 10.1 program package (1,000 bootstrap replicates, midpoint rooting); analysis methods are described in detail in Sluder et al. [5]. Significant bootstrap support values are indicated by slashes on the appropriate branches: () 50-79%; () 80-94%; () 95%; branches also supported by parsimony analysis are marked by dots; subfamilies are boxed. All human (Hs) and Drosophila (Dm) NRs are included, except for the two human NRs that lack a canonical DBD (DAX-1 (NR0B1) and SHP (NR0B2)). The C. elegans (Ce) sequences include all members of the six major metazoan NR subfamilies as well as selected representatives of the major groupings of divergent C. elegans NRs evident in a larger tree containing all the nematode sequences.

5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MGLEMSSKDSPGSLDGRAWEDAQKPQSAWCGGRKTRVYATSSRRAPPSEGTRRGGAARPE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~MSSEDRHLGSSCGSFIKTEPSSP ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~MSNKDRHIDSSCSSFIKTEPSSP EAAEEGPPAAPGSLRHSGPLGPHACPTALPEPQVTSAMSSQVVGIEP...LYIKAEPASP ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~MSDGVSILHIKQEVDTPSASCFSPSSKSTA SSGIDALSHHSPSGSSD...ASGGFGMALGTHANGLDSP.PMFAGAG.LGGN.PCRKSYE ASLTDSVNHHSPGGSSD...ASGSYSSTMNGHQNGLDSP.PLYPSAPILGGSGPVRKLYD...DSPKGSSE...TE...TEPP.VALAPGPAPTRCLPGHKEEE TQSGTNGLKSSPSVSPERQLCSSTTSLSCDLHNVSLSNDGDSLKGSGTSGGNGGGGGGGT DCTSGIMEDSAIKCEYMLNAIPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEY DCSSTIVEDPQTKCEYMLNSMPKRLCLVCGDIASGYHYGVASCEACKASFKRKIQANIEY D.GEGAGPGEQGGGKLVLSSLPKRLCLVCGDVASGYHYGVASCEACKAFFKRTIQGSIEY SGGNATNASAGAGSGSVRDEL.RRLCLVCGDVASGFHYGVASCEACKAFFKRTIQGNIEY SCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRLDSEN... SCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYKRRIDAEN... SCPASNECEITKRRRKACQACRFTKCLRVGMLKEGVRLDRVRGGRQKYKRRPEVDP... TCPANNECEINKRRRKACQACRFQKCLLMGMLKEGVRLDRVRGGRQKYRRNPVSNSYQTM SPY...LSLQISPP...AKKPLTKIVSYLLV...SPY...LNPQLVQP...AKKPYNKIVSHLLV...LPF...PGPFPAGPL..AVAGGPRKTAAPVNALVSHLLV QLLYQSNTTSLCDVKILEVLNSYEPDALSVQTPPPQVHTTSITNDEASSSSGSIKLESSV AEPDKLYAMPPDDVPEGDIKALTTLCDLADRELVFLISWAKHIPGFSNLTLGDQMSLLQS AEPEKIYAMPDPTVPDSDIKALTTLCDCADRELVVIIGWAKHIPGFSTLSLADQMSLLQS VEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQS VTPNGTCIFQNNNNNDPN.EILSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQV AWMEILILGIVYRSLPYDDKLAYAEDYIMDEEHSRLVGLLELYRAILQLVRRYKKLKVEK AWMEILILGFVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEK VWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLER SWAEILTLQLTFRSLPFNGKLCFATDVWMDEHLAKECGYTEFYYHCVQIAQRMERISPRR EEFVMLKALALANSDSMYIENLEAV.QKLQDLLHEALQDYELSQR...HEEPRRAGKLL EEFVTLKAIALANSDSMHIEDVEAV.QKLQDVLHEALQDYEAGQH...MEDPRRAGKML EEYVLLKALALANSDSVHIEDEPRLWSSCEKLLHEALLEYEAGRAGPGGGAERRRAGRLL EEYYLLKALLLANCDIL.LDDQSSL.RAFRDTILNSLNDVVYLLRHSSAVSHQQ...QLL LTLPLLRQTAAKAVQHFY.SVKLQGKVPMHKLFLEMLEAK~~ MTLPLLRQTSTKAVQHFY.NIKLEGKVPMHKLFLEMLEAKVC LTLPLLRQTAGKVLAHFY.GVKLEGKVPMHKLFLEMLEAMM~ LLLPSLRQ.ADDILRRFWRGIARDEVITMKKLFLEMLEPLAR Figure 3 Amino acid alignment of Drosophila CG7404 with the sequences of human ERRα, ERRβ, and ERRγ. exhibits similarity to the human ERRs in both DNA- and ligand-binding domain sequences. Block boxes indicate residues identical in at least two of the four sequences; gray boxes indicate similar residues. Expression of CG7407 as mrna and the splicing pattern has been confirmed by the recovery and sequencing of cdna (K.K. et al., unpublished data).

6 6 Genome Biology Vol 2 No 8 =C E?DAJ= EIK? A=HMDAJDAHJDAIA@ELAHCA J A 4IHAFHAIA J AMIK>B= E EAI & H=HADECD O@ELAHCA@ A >AHI B A H HA BJDAIENHA? C E A@IK>B= E EAI 1? JH=IJJ JDA IEJK=JE MEJDJDAE IA?J EHFICH KF = = OIAI BF JA JE= IJHK?JKHAI JD=J JDA = HEJO B J + A AC= I HA?AFJ HI=HAFHA@E?JA@J? J=E JDA?= E?= = JEF=H= A α DA EN IJHK?JKHA?D=H=?JAHEIJE? B HACK =JA@ 4I) C= + =E = E= + DA ;= = J 5 K@AH K FK> EIDA@@=J= JDA ANJA E IAGKA?A B = O + A AC= I, IAGKA?AI JDAO =HA K EBEA@ >O =? IJHK?JKH= F IIE> OHAB A?JE CJDAHAGKEHA A JB HE JAH =?JE MEJD=? HAIAJ B 4? B=?J HI ' 5E?AJDA M IJHK?JKHAI B 4,I? J=E =DO@H FD >E?? ABJE MDE?D CA KID H A =HA> EJEI E A OJD=J IJ EB J= HFD= HA?AFJ HIME >A= A => =JE >OI = A?K AI 1 IK MA D=LA B = IJHE E >AJMAA DK = I,H I FDE = A AC= I MEJDHAIFA?JJ JDAEH 4 IAJI 6DAHA EI = BE EJA F IIE>E EJO JD=J JDA =IJ # B JDA DK = CA A IAGKA?A? D=H> H = =@@EJE = LA 4 IAGKA?A >KJ JDEI EI K E A O CELA JD=J JDEI # EI A HE?DA@ E HAFAJEJELA DAJAH?DH =JE? IAGKA?A 5K?D = CM J?D= CAJDACA AH=?? KIE JD=JJDAHA =HAIJHE E C@EBBAHA?AI>AJMAA JDAJDHAACA AI M A@CA B= JDA A >AHI BA=?D 4IAJ@ABE AIJDAK EGKA H =JE LE@AI=>=IEIB H A@ FDO CA AJE? IJK@EAI KHJDAH HA IK?D = MD A CA A? F=HEI K >AHI BCA AI O HAB A?JI A ALA B 4? F ANEJO E = HC= EI 6DA E F=?J B JH= I?HEFJE = F IJ JH= I?HEFJE = FH?AII E CALA JI J J= 4BK?JE A=?DFH JA A ME >A=IK> A?JB HBKJKHAIJK@EAI Materials and methods Computational identification of human NR sequences 2H JAE D COIA=H?DAIMAHAFAHB H A@KIE A >AHI B JDA 4 B= E O? F=HA@ =C=E IJ JDA DK = CA 06 IA?JE BH A = KIE C 6 )56 & 4AIK JI B= IAGKA?ADEJIMAHAIJ HA@E = E D KIA H=? 0 C KI IAGKA?AI JD IA MEJD = )56 ANFA?J=JE L= KA B H MAH MAHA JDA? F=HA@MEJDJDAA JEHAGKAHO 4@=J=IAJKIE C )56 & O?D IE C JDA?HEJAHE= JDA >=IEI B =KJ =JA@ =IIAII A J B H '# IAGKA?A E@A JEJO LAH >=IA F=EHI >F=JJDA K? A JE@A ALA MA? =FJDAIADEJIJ LE@K= A >AHI B JDA FH JAE B= E O [>E I\ 6D IA IAGKA?ADEJIJD=J? J=KJ =JE?= O>AF =?A@E >E I JDA >=IEI B JDA IA A?JA@?HEJAHE= MAHA AEJDAH =FFA@ J JDAHFH JAE B= E EAIEBJDAEHIAGKA?AI =J?DA@= M CA A E A =? IE@AHA@ =I F JA JE= O LA 4 IAGKA?AI MDA =E I MAHA FHAIA J A@ EHHA AL= J =J?DJ = OJDE C 9AJDA =FF EA@0E@@A =H I 0 I >KE J =E I KIE C JDA 0-4 F=? =CA ' J JDAIA F JA JE= LA IAGKA?AI 6DA I MAHA KIA@ B H BKHJDAH IK>IJ= JE=JE HB HHK E C KJF JA JE= LA DEJI +H II IFA?EAI? F=HEI IMAHAFAHB H A@KIE CJDAB M E C = = OIAI EHIJ JDA B H 4,, B +" D BH =E M=I KIA@ J IA=H?D JDA + A AC= I FH =IIA > A@ E D KIA BH A = KIE C JDA 0-4 F=? =CA ' E@A JEBEA@ # + A AC= I IAGKA?AI 6DAIA # + A AC= I IAGKA?AI MAHA? F=HA@J JDADK = CA E?IAGKA?A@=J=>=IA>O JDA IA=H?D => LA LA DK = 4I MAHAB JDAIAIA=H?DAI JDA=> LAFH?AII M=IHAFA=JA@B HJDA,H I FDE = CA LA DK = 4IAGKA?AIMAHAB 6DEH@ JDA = HEJO BJDA + A AC= I 4IMAHACH KFA@E J JA IK>B= E EAI>=IA@? F=H=JELAIAGKA?A= = OIEI BJDA, ) C@ =E IAGKA?AI ) J ID M 6DAIA IK>B= E EAI MAHA KIA@ J 0 I 6DAIA 0 I MAHA JDA KIA@ J IA=H?DJDA@=J=>=IA BFHA@E?JA@,H I FDE = FH JAE IAIJ=> EIDA@ E D KIA >O ANJH=?JE C BH A = MEJD JDA 0-4 F=? =CA 6DA IEC EBE?= J DEJI I? HA MAHA? F=HA@ MEJD JDA M,H I FDE = 4I LA,H I FDE = 4IAGKA?AIMAHAB 9EJDA=?D AMKF@=JA BJDADK = CA E?@=J=>=IA JDA IOIJA E EJE=JA@= AMH BIA=H?DE JAHE C?=F JKHE C = IAGKA?AI JD=J MAHA D C KI KIE C = =IJAH >E EIJ J BE JAH KJ IAGKA?AI JD=J D=@ >AA = J=JA@E =FHALE KI?O? A 6DEIA E E =JA@JDA AA@J IAF= H=JA KJ = AM IAGKA?AI E =J A=?D KF@=JA 6DA= = OIEIA CE AM=IMHEJJA E 2AH ) =L==FF AJM=I KIA@=IJDAKIAH\I =E E JAHB=?AJ JDA= = OIEIA CE JDA OE C H=? 1J M=I A >A@@A@ E = 06 F=CA BH MDE?D KIAHI? LEAM JDA IAGKA?A HA? H@ >O E E C J JDA E D KIA FK> =I MA =I= =E = EC A JI )IL= E@= JE B KH >E E B H =JE? IA=H?D J I "& B JDA "' M 4 IAGKA?AI E JDA CA A E? K@E C JDA -44 FIAK@ CA A MAHA B 6DA CA A HAFHAIA JE C JDA +)4 4 41! EI IJE =>IA J BH DECD JDH KCDFKJ CA E? IAGKA?A@=J=>=IAI Genomic DNA analysis of novel human NR sequences + BEH =JE BE IE E? K? A JE@AIAGKA?AM=IFAHB H A@ >OIAGKA?E C :4 H "γ H CA E?, )BH=C A JI = F EBEA@>O FHE AHIMAHA@AIEC A@KIE CA = =??AIIE K >AHI )!#&!% :4 H )!&''% 0 "γ H :4 H # 66)6)))66))! 6)))666+)))6! A#$$ >F 0 "γ H # )+ 66 )66 66 ) ! # ) ))! IE A # >F 6DAIAFHE AHIMAHAKIA@J = F EBO C+ JA?DCA E?, ) KIE C ) F 2- E IOIJA I KIE C 2+4 = F I, ) IAGKA?E C M=I FAH B H A@>OJDA =N 5 EJD E A? HAIAGKA?E CB=?E EJO

7 mrna expression analysis 0K = JEIIKAIMAHA@AHELA@BH I =FBH A IKHCE?= IFA?E A I,K A 7 ELAHIEJO,KHD= + 6 J= 4 ) M=I ANJH=?JA@KIE C3E=CA 4 A=IO EJI=?? H@E CJ JDAIKFF E AH\IFH J? 5 AJ J= 4 )IMAHA >J=E A@BH? AH?E= HI IK?D =I + JA?D 2= ) J +) A E 4AIA=H?D6HE= C A2=H + 6 =NE E AJDAIA IEJELEJO B JDAGK= JEJ=JE BJH= I?HEFJI EJM=I?HEJE?= J A IKHAJD=J JDAHA M=I? J= E =JE C CA E?, ) 6DA 4 ) M=I JHA=JA@MEJD, =IAKIE C) >E 4 =IA BHAA, =IA -BBA? JELA AII BJDA, =IAJHA=J A JM=I? BEH A@>OHK E C 2+4MEJDDK = β =?JE FHE AHIE JDA=>IA?A BHALAHIA JH= I?HEFJ=IA J A IKHA IEC = 6DA 4 ) M=IJDA GK= JEJ=JA@KIE CJDA4 ) IFA?EBE?4E> A?K =H2H >AI # C= EGK JA@E J ='$ MA F =JA B H =J 6 GK= JEJ=JA 4 )ANFHAIIE M=IFAH B H A@ KIE C = ) %% 5AGKA?A,AJA?JE 5OIJA E IJHK A BJM=HA2-)FF EA@E IOIJA A A IFA?EBE? FHE AHI MAHA IO JDAIE A@ AOIJ A += =HE +) B H JDA IAGKA?AI :4 H =??AI IE K >AH )!#&!% 0 "γ H =??AIIE K >AH )!&''% References 1. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al.: Comparative genomics of the eukaryotes. Science 2000, 287: The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408: Giguere V: Orphan nuclear receptors: from gene to function. Endocr Rev 1999, 20: McKenna NJ, Lanz RB, O Malley BW: Nuclear receptor coregulators: cellular and molecular biology. Endocr Rev 1999, 20: Sluder AE, Mathews SW, Hough D, Yin VP, Maina CV: The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Res 1999, 9: Enmark E, Gustafsson J: Nematode genome sequence dramatically extends the nuclear receptor superfamily. Trends Pharmacol Sci 2000, 21: Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al.: The genome sequence of Drosophila melanogaster. Science 2000, 287: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: Eddy SR: Hidden Markov models. Curr Opin Struct Biol 1996, 6: Danielian PS, White R, Lees JA, Parker MG: Identification of a conserved region required for hormone dependent transcriptional activation by steroid hormone receptors. EMBO J 1992, 11: Tchenio T, Segal-Bendirdjian E, Heidmann T: Generation of processed pseudogenes in murine cells. EMBO J 1993, 12: Sladek R, Beatty B, Squire J, Copeland NG, Gilbert DJ, Jenkins NA, Giguere V: Chromosomal mapping of the human and murine orphan receptors ERRalpha (ESRRA) and ERRbeta (ESRRB) and identification of a novel human ERRalpha-related pseudogene. Genomics 1997, 45: Laudet V, Hanni C, Coll J, Catzeflis F, Stehelin D: Evolution of the nuclear receptor gene superfamily. EMBO J 1992, 11: Laudet V: Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor. J Mol Endocrinol 1997, 19: Escriva H, Safi R, Hanni C, Langlois MC, Saumitou-Laprade P, Stehelin D, Capron A, Pierce R, Laudet V: Ligand binding was acquired during evolution of nuclear receptors. Proc Natl Acad Sci USA 1997, 94: Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA: Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997, 387: Fitch DHA, Thomas WK: Evolution. In C. elegans II. Edited by Riddle DL, Blumenthal T, Meyer BJ and Priess JR. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1997; The Nuclear Receptors Committee: A unified nomenclature system for the nuclear receptor superfamily. Cell 1999, 97: Robyr D, Wolffe AP, Wahli W: Nuclear hormone receptor coregulators in action: diversity for shared tasks. Mol Endocrinol 2000, 14: Gibson UE, Heid CA, Williams PM: A novel method for real time quantitative RT-PCR. Genome Res 1996, 6: Heid CA, Stevens J, Livak KJ, Williams PM: Real time quantitative PCR. Genome Res 1996, 6:

Rick Van Kooten, Indiana Univ., FNAL Users Meeting, HEPAP Session, June 27, 2000

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