KIRREL is differentially expressed in adipose tissue from “fertil+” and “fertil-” cows: in vitro role in ovary? Stéphanie Coyral-Castel, Christelle Ramé, Juliette Cognie, Jerôme Lecardonnel, Sylvain Marthey, Diane Esquerré, Christelle Hennequet-Antier, Sébastien Elis, Sébastien Fritz, Mekki Boussaha, et al.
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Stéphanie Coyral-Castel, Christelle Ramé, Juliette Cognie, Jerôme Lecardonnel, Sylvain Marthey, et al.. KIRREL is differentially expressed in adipose tissue from “fertil+” and “fertil-” cows: invitro role in ovary?. Reproduction -Cambridge- Supplement-, Society for Reproduction and Fertility, 2018, 155 (2), pp.181-196. 10.1530/REP-17-0649. hal-02625059
HAL Id: hal-02625059 https://hal.inrae.fr/hal-02625059 Submitted on 26 May 2020
HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Version postprint Page 1of49 Reproduction AdvancePublicationfirstpostedon23November2017asManuscriptREP-17-0649 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 11 11 18 18 17 16 15 14 13 12 10 10 23 23 25 25 19 19 21 21 22 22 5 5 4 4 3 3 2 1 6 6 9 9 8 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is Josas, France France Josas, France France France Dupont Esquerré Coyral Castel S vitro in 7 9 8 7 6 5 4 3 2 1 cows: “fertil-” and “fertil+” from tissue adipose in expressed differentially is KIRREL Short title: KIRREL in bovine adipose tissue and ovary tissueovary and adipose bovineKIRREL in title: Short 24 orsodn ato: r ole uot Uié e hsooi d l Rpouto e des et Reproduction la de Physiologie de Unité Dupont, Joëlle Dr author: Corresponding 20 opreet, nttt ainl e a ehrh Arnmqe 330 ozly France Nouzilly, 37380 Agronomique, Recherche la de National Institut Comportements, (email: (email: INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France Nouzilly, F-37380 Avicoles, Recherches UR83 INRA, F-78350Jouy-en- Intégrative, et AnimaleBiologie Génétique UMR1313 AgroParisTech, F-78350Jouy-en-Josas, Biologie etIntégrative, Animale Génétique UMR1313, INRA, France12, cedex 75595Paris Bercy,149 de rueGIPSIE, département del’Elevage, Institut France Nouzilly, F-37380 IFCE, Nouzilly,F-37380 desComportements, Reproduction et dela Physiologie UMR85 INRA, Université François Rabelais de Tours, F-37000 Tours, France France F-37000 Tours, deTours, Rabelais François Université FranceNouzilly, F-37380 UMR7247,CNRS, UNCEIA, 149 rue de Bercy, 75595 Paris cedex 12, France12, cedex75595 Paris deBercy, 149rue UNCEIA, ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
role in ovary? inovary? role 1,2,3,4 [email protected] 6,7 C Hennequet Antier C ,
Copyright ©2017 bythe Society for Reproduction and Fertility. 1,2,3,4,5 Comment citer cedocument: C Ramé C , ; Phone: 33 2 47 42 77 89 ; Fax: 33 2 47 42 77 43).4277247 33 Fax: 89; 42 77 2 47 Phone:33 ; 8
1,2,3,4 S Elis S , J Cognié J , 1,2,3,4 S Fritz S , 1,2,3,4 J Lecardonnel J , 9 M Boussaha M , 6,7 6,7 F Jaffrézic F , S Marthey S ,
6,7 n J and 6,7 , D D , 1
Version postprint Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 35 35 27 27 26 26 28 28 29 29 34 34 30 30 31 31 36 36 32 32 37 37 38 38 33 33 42 42 39 39 43 43 40 40 41 41 44 44 47 47 46 45 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is proliferation ( proliferation greater expressed in “fertil+” than in “fertil ”. “fertil ”. in than “fertil+” in expressed greater uniaie ri lcs fetn fml friiy oae o te oie hoooe three chromosome bovine the on located fertility female affecting locus trait quantitative Abstract (QTL F Fert BTA3) have a significantly lower conception rate and body weight after calving after weight body and rate conception lower significantly a have (QTL F Fert BTA3) than cows carrying the “fertil+” haplotype. “fertil+” the carrying cows than immunoblot we confirmed that adipose tissue tissue adipose that confirmed we immunoblot of genes included in the QTL F Fert BTA3 in “fertil+” and “fertil ” adipose tissue one week week one tissue adipose “fertil ” and “fertil+” in QTL F Fert BTA3 the in included genes of after calving when plasma non esterified fatty acid concentrations were greater in “fertil ” “fertil ” in greater were concentrations acid fatty esterified non plasma when calving after adipose tissue, pituitary, and ovary and detectable in hypothalamus and mammary gland. Its gland. mammary and hypothalamus in detectable and ovary and pituitary, tissue, adipose animals. animals. expression (mRNA and protein) is greater in kidney of “fertil+” than “fertil ” cows ( cows “fertil ” than “fertil+” of kidney in greater is protein) and (mRNA expression KIRREL (mRNA and protein) is also present in the different ovarian cells with a greater greater a with cells ovarian different the in present also is protein) and (mRNA KIRREL xrse i “etl” s oprd o fri cw ( cows “fertil ” to compared as “fertil+” in expressed to a rapidly increase in MAPK1/3 and MAPK14 phosphorylation in granulosa cells and to a a to and cells granulosa in phosphorylation MAPK14 and MAPK1/3 in increase rapidly a to xrsin n rnls cls f fri+ ta “etl” os I clue gauoa cells, granulosa cultured In cows. “fertil ” than “fertil+” of cells granulosa in expression erae n AK/ popoyain n oye Thus, oocyte. in phosphorylation MAPK1/3 in decrease recombinant KIRREL halved steroid secretion in basal state ( state basal in secretion steroid halved KIRREL recombinant metabolic messenger linking body composition and fertility. fertility. and composition linkingbody messenger metabolic ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
We have previously shown that dairy cows carrying the “fertil ” haplotype for one one for haplotype “fertil ” the carrying cows dairy that shown previously have We
We observed that thirty one genes were over expressed whereas twelve were under were twelve whereas over expressed were genes thirty one that observed We P <0.05) and and <0.05) Comment citer cedocument: oocyte maturation ( maturation oocyte vitro in
Here, we compared by tiling array tiling by compared we Here, KIRREL KIRREL P mRNA and protein were significantly were protein and mRNA mRNA is abundant in bovine kidney, kidney, bovine in abundant is mRNA <0.05). These results were associated associated were results These <0.05). P <0.05). By quantitative PCR and and PCR quantitative By <0.05). KIRREL KIRREL P <0.05). It also decreased cell cell decreased also It <0.05). ol b a potential a be could
the expression expression the P <0.05). <0.05). 2 Page 2of49 Version postprint Page 3of49 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 63 63 64 64 58 58 69 69 70 70 71 71 72 72 59 59 57 57 60 60 65 65 62 62 61 66 66 67 67 68 68 56 56 55 55 54 54 49 49 48 48 50 50 52 52 51 53 53 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is production, locomotion, maintenance or reproduction, are greater than the energy provided by by provided energythe than greater are reproduction, or maintenance locomotion, production, partially due to a lowest quality of the oocytes and consequently of pre implantation embryo embryo pre implantation of consequently and oocytes the of quality lowest a to due partially balance, but its magnitude and duration are quite variable (Butler variable quite are duration and magnitude its but balance, o, t s el nw ta eeg epniue fr hsooia fntos sc a milk as such functions, physiological for expenditures energy that known well is it cow, eeomn (Coyral Castel development ure 90 Shöe & tuebe 20) n cw my oe oy egt n body and weight body lose may cows and 2006) Staufenbiel & Schröder 1980, Currie odto. n al lcain cw my oiie bu 5 k o lpd Bua & Bruce & (Bauman lipid of kg 50 about mobilize may cows lactation, early In condition. Currie 1980) to support lactation. The use of body reserves accounts energetically for about for energetically accounts reserves body of use The lactation. support to 1980) Currie cows for food intake and eating behaviour, milk production, live weight and plasma plasma and weight live production, milk behaviour, eating and intake food for cows metabolites during the first lactation. Interestingly, the body weight of “fertil ” cows in the in cows “fertil ” of weight body the Interestingly, lactation. first the during metabolites feed intake. The maximum dry matter intake is reached about four to ten weeks after peak after weeks ten to four about reached is intake matter dry maximum The intake. feed al. weeks eight first ik Cpok 95. o hg ilig ar cw asm a eid f eaie energy negative of period a assume cows dairy high yielding So, 1985). (Coppock milk h eeg dfct bd rsre ae oiie (y nrae lplss (amn Bruce & (Bauman lipolysis) increased (by mobilized are reserves body deficit, energy the al. waves, length of oestrus cycle...) in “fertil+” and “fertil ” heifers and cows (Coyral Castel cows and heifers “fertil ” and “fertil+” in cycle...) oestrus of length waves, quantitative trait locus affecting female fertility located on the bovine chromosome 3 (QTL F 3 chromosome bovine the on located fertility female affecting trait locus quantitative Introduction Introduction Fert BTA3) had a greater conception rate 35 days after the first artificial insemination than insemination artificial first the after days 35 rate conception greater a had Fert BTA3) mapped (Druet mapped (Coyral Castel haplotype “fertil ” carrying those al. ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649 , 2013) suggesting a greater fat mobilization in “fertil ” animals. During early lactation in in lactation early During animals. “fertil ” in mobilization fat greater a suggesting 2013) , 2007) and explained 14% of the total genetic variance (Ben Jemaa(Benvariancetotalgenetic of 14%the 2007)explained and 2011). However, we have demonstrated that the lower fertility of “fertil ” females could be could females “fertil ” of fertility that the lower demonstrated have we However, 2011).
We observed no differences in ovarian activity (number of follicles and follicular follicular and follicles of (number activity ovarian in differences no observed We We have previously shown that primiparous cows carrying “fertil+” haplotype for one one for haplotype “fertil+” carrying cows primiparous that shown previously have We et al. et ot partum post Comment citer cedocument: 2008), was described to affect early reproductive events (Guillaume events reproductive early affect to described was 2008), e al. et was significantly lower than “fertil+” cows (Coyral Castel (Coyral Castel cows “fertil+” than lower significantly was
02. e ae lo hrceie fri+ n “fertil ” and “fertil+” characterized also have We 2012). et al. et 2011). This QTL F Fert BTA3, finely finely QTL F Fert BTA3, This 2011). et al. et et al. et 1981). As a result of result a As 1981). 2008). et et et et 3 Version postprint Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 81 81 80 80 82 82 83 83 84 84 78 78 77 77 79 79 85 85 86 86 73 73 87 87 74 74 88 88 75 75 76 76 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is and greater fat mobilization of “fertil ” cows, we compared by Tiling array the expression of expression the array Tiling by compared we cows, “fertil ” of mobilization fat greater and genes included in QTL F Fert BTA3 in the adipose tissue of “fertil+” and “fertil ” females females “fertil ” and “fertil+” of tissue adipose the in QTL F Fert BTA3 in included genes one week after calving. We then studied the distribution in bovine tissues of one candidate candidate one of tissues bovine in distribution the studied then We calving. after week one ee Kn f RE ie Doohl)lk ( (Drosophila) like like IRRE of Kin gene, o ert a ubr f omn ie opud ta rglts dpct dvlpet and development adipocyte regulates that compounds hormone like of number a secrete to 2008, Roche 2008, metabolic function (Ouchi function metabolic “fertil+” adipose tissue. Finally, we localized KIRREL by immunohistochemistry in bovine bovine in immunohistochemistry by KIRREL localized we Finally, tissue. adipose “fertil+” 3 o te ik rdcd n h frt ot o lcain Bua & rc Cri 1980). Currie Bruce & (Bauman lactation of month first the in produced milk the of 33% ovarian cells and investigated more precisely its its precisely more investigated and cells ovarian oiiain f a rsls n ees o nnetrfe fty cd (EA i bod which blood, in (NEFA) acids fatty non esterified of release in results fat of Mobilization steroidogenesis and proliferation and oocyte maturation by using recombinant KIRREL. recombinant using maturationby oocyte proliferation and and steroidogenesis were reviewed as indicators of energy status of ruminants (Bowden 1971). It is now well well now is It 1971). (Bowden ruminants of status energy of indicators as reviewed were 89 salse ta ngtv eeg blne mat erdcie ris t aiu lvl o the of levels various at traits reproductive impact balance energy negative that established yohlm iutr oaa ai (em Bte 19, Roche 1999, Butler & (Beam axis hypothalamo pituitary gonadal ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
In order to better understand the molecular mechanisms involved in the lower fertility fertility lower the in involved mechanisms molecular the understand better to order In et al. et 2009). Adipose tissue is not only an energy storage organ but it is also able also is it but organ storage energy onlyan isnot tissue Adipose 2009). Comment citer cedocument: et al.et ) but also fertility (Campos ) fertility but also
KIRREL fet o te rnls cell granulosa the on effects vitro in ), significantly greater expressed in in expressed greater significantly ), etal. 2008, Tersigni2008, t al. et 00 Leroy 2000, et al. et 2011). t al. et 4
Page 4of49 Version postprint Page 5of49 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 107 107 106 106 105 105 104 104 114 114 103 103 102 102 112 112 101 101 100 111 111 110 110 109 109 108 108 113 113 99 99 98 98 96 95 93 93 92 92 91 90 94 94 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is between the energy intake and the energy requirements for maintenance, milk production, and and production, milk maintenance, for requirements energy the and intake energy the between Animals Animals rgac. codn t h IR sse, h al rqieetfr aneac i 11 * 1.1 is maintenance for requirement daily the system, INRA the to According pregnancy. Ethics Ethics rtcl, hc wr cnitn wt te udlns rvdd y h Fec Cucl for Council French the by provided guidelines the with consistent were which protocols, after calving). Plasmas were stored at 20°C until assay. NEFA plasma concentrations were concentrations plasma NEFA assay. until 20°C at stored were Plasmas calving). after diet distribution, one week after calving and 5 months of pregnancy (about 7 and 8 months 8 and 7 (about pregnancy of months 5 and calving after week one distribution, diet heat detection with the semen of the same bull. Blood samples were taken from the tail before tail the from taken were samples Blood bull. same the of semen the with detection heat was more variable. Animals were artificially inseminated from 55 60 d postpartum 12 h after h 12 postpartum d 55 60 from inseminated artificially were Animals variable. more was morning live body weight was used for weight analyses, because the afternoon body weight weight body afternoon the because analyses, weight for used was weight body live morning each milking, cows were automatically weighted (software RIC version RW1.7). Only the the Only RW1.7). version RIC (software weighted automatically were cows milking, each soybean, 15% concentrate, 10% dehydrated alfalfa, and 0.5% calcium oxide (CaO). After After (CaO). oxide calcium 0.5% and alfalfa, dehydrated 10% concentrate, 15% soybean, fed and yards acltd e w acrig o h IR feig ytm (NA 20) s h difference the as 2007) (INRA, systems feeding INRA the to according wk per calculated were monitored during their second lactation. Dairy cows were managed in straw bedded straw bedded in managed were cows Dairy lactation. second their during monitored were week after calving when the adipose biopsy was performed as described below. It was was It below. described as performed was biopsy adipose the when calving after week Care. Animal 97 corporation, Espoo, Finland). Energy balance (EB, expressed in Mcal/d) was calculated one calculated was Mcal/d) in expressed (EB, balance Energy Finland). Espoo, corporation, determined by enzymatic colorimetry on a multiparameter analyser (KONE instruments instruments (KONE analyser multiparameter a on colorimetry enzymatic by determined (CEEA VdL”)), protocol registered under ref. n° 2012 10 4) approved all experimental experimental all approved 2012 10 4) n° ref. under registered protocol VdL”)), (CEEA methods and Materials ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
Thirty six Holstein dairy cows (n=18 fertil+ and =18 fertil animals), born in 2006, 2006, in born animals), fertil =18 and fertil+ (n=18 cows dairy Holstein Thirty six nehc cmite(Cmt dEhqee Eprmnain nml a d Loire de Val Animale Expérimentation en d’Ethique (“Comité committee ethics An d libitum ad Comment citer cedocument: ih ttl ie rto cmoe o 6.% az slg, 10% silage, maize 64.5% of composed ration mixed total a with
5 Version postprint Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 118 118 116 116 121 121 120 120 131 131 115 115 119 119 130 130 129 129 128 128 133 133 127 127 132 132 138 138 137 137 136 126 126 123 124 124 122 122 135 135 134 134 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is Biopsy of subcutaneous adipose tissue tissue subcutaneous adipose of Biopsy Bovine fertility Tiling Array design Array Tilingfertility Bovine 117 Xylazine i.v. (Rompun; Bayer AG, Leverkusen, Germany) and an injection of 200 mg of of 200mg of injection an and Germany) Leverkusen, AG, Bayer (Rompun; i.v. Xylazine fasted for 12 h before surgery. Anesthesia was induced with injections of 12 to 14 mg of of mg 14 to 12 of injections with induced was Anesthesia surgery. before h 12 for fasted having a unique genome sequence match were selected with SSAHA (Ning SSAHA with selected were match sequence genome unique a having expressed in Mcal/d, where kg where Mcal/d, in expressed nml a 1kp oe ek otatm ad mg 5 ots f etto) Cw were Cows gestation). of months (5 5mpg and postpartum) week (one 1wkpp at animals Highly repeated elements in the genome were repeat masked. Concerning uniqueness, probes uniqueness, Concerning repeat masked. were genome the in elements repeated Highly .4 * kg * 0.041 fertility Tiling Array was designed and produced by Roche NimbleGen Inc. (Madison, USA). (Madison, Inc. NimbleGen Roche by produced and designed was Array Tiling fertility a gt rm CC aaae n c. 07 ees bsa4 nldn 3282 t The nt. 3627832 including bosTau4 release 2007 Oct. on database UCSC from got was for probe synthesis. Each probe overlapped its neighbour by about 40 bases. The arrays were arrays The bases. 40 about by neighbour its overlapped probe Each synthesis. probe for QTL F Fert BTA3. The sequence from position 9 887 417 to 13 515 249 on chromosome 3 chromosome on 249 515 13 to 417 887 9 position from sequence The QTL F Fert BTA3. isothermal format (Tm=76°C) and probe length constraint between 50 and 75 bp were used were bp 75 and 50 between constraint length probe and (Tm=76°C) format isothermal maskless process in which the synthesis of each probe is directed by a digital light processor. digitallight by a directed is each probe ofthe synthesis which in process maskless probes oligonucleotide the synthesized NimbleGen 2002). 125 dewlap. the from Lidocaine s.c. (Lurocaïne; Vétoquinol SA, Lure, France). Subcutaneous fat was collected collected was fat Subcutaneous France). Lure, SA, Vétoquinol (Lurocaïne; s.c. Lidocaine yteie o te ras y htltorpy (Singh Gasson photolithography by arrays the on synthesized manufactured by maskless array synthesis technology and the oligonucleotides were were oligonucleotides the and technology synthesis array maskless by manufactured ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
During the second lactation, biopsies of adipose tissue were collected from the same same the from collected were tissue adipose of biopsies lactation, second the During The 385k bovine fertility Tiling Array was designed in both orientations to cover the the cover to orientations both in designed was Array Tiling fertility bovine 385k The 0.75 ad h rqieet o ml pouto i 04 * ik rdcin E is EB production. milk * 0.44 is production milk for requirement the and , Comment citer cedocument: 0.75
indicates metabolic body weight (INRA, 2007). (INRA, weight2007). body metabolic indicates n situ in t al. et using a photo mediated, photo mediated, a using 99 Nuwaysir 1999, et al. et 2001). An 2001). t al. et 6
Page 6of49 Version postprint Page 7of49 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 153 153 162 162 144 144 150 150 149 152 152 143 143 148 148 161 161 159 159 158 160 160 147 147 154 154 142 142 163 163 141 141 146 146 145 145 157 157 140 140 156 156 139 139 155 155 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is pair. by aligning probe coordinates with annotation data from Ensembl database (release 56). The The 56). (release database Ensembl from data annotation with coordinates probe aligning by ae o Esml oprtv aayi, o ee wt kon tts n nte species another in status known with genes to analysis, comparative Ensembl on based bovine fertility Tiling Array platform has been submitted to the Gene Expression Omnibus Omnibus Expression Gene the to submitted been has platform Array Tiling fertility bovine several probes are available per exon and per gene. The model proposed is a mixed model mixed a is proposed model The gene. per and exon per available are probes several em ewe eo ad odto. Parameter condition. and exon between term transcript with a sequence match in a sequence repository external to Ensembl for the same same the for Ensembl to external repository sequence a in match sequence a with transcript Tiling Array data analysis analysis data Array Tiling 151 loci are classified three types: (1) known protein coding gene, known gene has at least one least at has gene known gene, coding protein known (1) types: three classified are loci genebuild transcript and the Vega manual annotation have the same sequence, for every base base every for sequence, same the have annotation manual Vega the and transcript genebuild omitted here as it is a gene by gene model: gene by gene hereisait as omitted where where (usually human genes). (3) Putative protein coding gene refers to genes where the Ensembl the where genes to refers gene coding protein Putative (3) genes). human (usually including a fixed exon and a random probe effects. In this study, our aim was to detect detect to was aim our study, this In effects. probe random a and exon fixed a including (GEO) repository and the accession number is GPL15186. Annotation of probes was obtained obtained was probes of Annotation GPL15186. is number accession the and repository (GEO) species. (2) Known by projection protein coding gene, refers to genes that are homologous, are that genes to refers gene, coding protein projection by Known (2) species. fet a be cniee fr ah gene each for considered been has effect A hierarchical mixed model with an exon within gene effect and a random probe within exon exon within probe random a and effect gene within exon an with model mixed hierarchical A n vrg eey lvn ae ad 5 6 rnol gnrtd rbs Al nomto of information All probes. generated randomly 961 45 and bases eleven every average on differentially expressed genes between “fertil+” and “fertil ” samples. samples. and “fertil ” genes“fertil+” between expressed differentially The array contained 343 162 50 75 mer oligonucleotides designed on both strands and tiled and strands both on designed oligonucleotides 50 75 mer 162 343 contained array The ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649 corresponds to an exon effect effect exon an to corresponds
We developed a new model to perform Tiling array analysis taking advantage that that advantage taking analysis array Tiling perform to model new a developed We corresponds to a condition effect with two levels ( levels two with effect condition a to corresponds Comment citer cedocument:
within gene gene within ( orsod t te rb efc k within k effect probe the to corresponds . For simplicity the index index the simplicity For . c =1.2 for =1.2for " ), and ),
fertil is the interaction the is +" and and " fertil will be be will " ), 7 Version postprint Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 188 188 187 187 186 186 185 185 184 184 183 183 179 179 182 182 180 178 178 169 169 177 177 166 166 176 176 174 174 175 175 173 173 172 172 171 171 168 168 170 170 167 167 165 165 164 164 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is sample. Tubes were waved for 15 seconds and left at room temperature for 5 minutes before minutes 5 for temperature room at left and seconds 15 for waved were Tubes sample. QIAzol lysis reagent (Qiagen, Courtaboeuf, France). Chloroform (0.2 ml) was added to each each to added was ml) (0.2 Chloroform France). Courtaboeuf, (Qiagen, reagent lysis QIAzol a etatd n c fo 20 g ftsu wt a utaua hmgnzr sn 8 l of ml 8 using homogenizer ultraturax an with tissue of mg 250 from ice on extracted was “fertil+” and 14 “fertil ”), frozen in liquid nitrogen and stored at 80°C until use. Total RNA Total use. until 80°C at stored and nitrogen liquid in frozen “fertil ”), 14 and “fertil+” (18 “fertil+” and 18 “fertil ”) one week after parturition and at 5 months of pregnancy (16 (16 pregnancy of months 5 at and parturition after week one “fertil ”) 18 and “fertil+” (18 Total RNA extraction extraction RNA Total 1.8).release (AmiGO website Ontology Gene 181 Genes were classified according to the Gene Ontology using NCBI, Ensembl, DAVID and the DAVID and Ensembl, NCBI, Ontology using Gene to the according classified were Genes ( Jaffrézic. We focused our study on known and known by projection protein coding genes. genes. coding protein projection by known and known on study our focused We Jaffrézic. variances variances alternative splicing. R functions implementing this model are available upon request from F. from request upon available are model this implementing functions R splicing. alternative Our model could also be used to detect differentially expressed exons and genes with with genes and exons expressed differentially detect to used be also could model Our strand. for the forward strand, and 4 379 probes matching to 62 genes and 352 exons for the reverse reverse the for exons 352 and genes 62 to matching probes 379 4 and strand, forward the for gene and exon information: 5 822 probes matching to 62 genes and 449 exons in the analysis analysis the in exons 449 and genes 62 to matching probes 822 5 information: exon and gene & Hochberg 1995). This model was applied on two datasets containing annoted probes with probes annoted containing datasets two on applied was model This 1995). Hochberg & hypothesis hypothesis adjusted by Benjamini Hochberg’s procedure to control the False Discovery Rate (Benjamini Rate Discovery False the control to procedure Benjamini Hochberg’s by adjusted In this model, testing for differentially expressed genes is equivalent to testing the null null the testing to equivalent is genes expressed differentially for testing model, this In independent and normally distributed such that: that: such distributed normally and independent exon exon that: c ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649 =1.2 for =1.2for "
Subcutaneous adipose tissue was sampled at the dewlap of 36 second lactation cows cows lactation second 36 of dewlap the at sampled was tissue adipose Subcutaneous ( fertil . Index . +" , with gene by gene variances variances gene by gene with , and and " Comment citer cedocument: . h poe fet s sue t b a adm fet such effect random a be to assumed is effect probe The ). represents the biological replicates biological the represents fertil , where where , " ). Taking into account multiple testing, testing, multiple account into Taking ).
n and Residuals . . . wt gene by gene with , for two conditions conditions two for are also assumed assumed also are P vle were values 8 Page 8of49 Version postprint Page 9of49 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 197 197 198 198 196 196 195 195 202 202 201 201 200 200 194 194 206 206 193 193 204 204 205 205 192 192 191 191 190 190 203 203 209 209 208 207 211 211 210 210 189 189 213 213 212 212 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is NanoDrop Spectrophotometer (Nyxor Biotech, Paris, France) and RNA quality with an an with quality RNA and France) Paris, Biotech, (Nyxor Spectrophotometer NanoDrop S1. Table 199 Massy, France). The RNA integrity number (RIN) for each RNA sample is shown in the the in shown is sample RNA each for (RIN) number integrity RNA The France). Massy, Agilent 2100 Bioanalyzer using a RNA 6000 Nano assay protocol (Agilent Technologies, Technologies, (Agilent protocol assay Nano 6000 RNA a using Bioanalyzer 2100 Agilent luhehue a etatd n c wt a utaua hmgnzr n TRIzol in homogenizer ultraturax an with ice on extracted was slaughterhouse ag flils > m) cru ltu, vra cre ad rnls cls from cells) granulosa and cortex ovarian luteum, corpus mm), 7 (> follicles large tissue, kidney, pituitary, lung, skeletal muscle, ovary, hypothalamus, small follicles (< 6 mm), mm), 6 (< follicles small hypothalamus, ovary, muscle, skeletal lung, pituitary, kidney, tissue, was extracted using 1 ml of TRIzol of ml 1 using extracted was System and stored at 80°C until cDNA synthesis. RNA quantity was assessed with a a with assessed was quantity RNA synthesis. cDNA until 80°C at stored and System sur Yvette, France). A treatment with DNaseI using the DNA the using DNaseI with treatment A France). Yvette, sur technologies were evaporated without heating during 1.5 hours in a Thermo Savant SPD1010 SpeedVac SPD1010 Savant Thermo a in hours 1.5 during heating without evaporated were RNase free DNaseI (Qiagen) was performed. After elution with RNase free water, samples water, free RNase with elution After performed. was (Qiagen) DNaseI RNase free according to the manufacturer’s recommendations. During purification, a treatment with a a with treatment a purification, During recommendations. manufacturer’s the to according according to manufacturer’s recommendation (Invitrogen recommendation manufacturer’s to according cDNA synthesis and labeling, array hybridization, washing and scanning scanning and washing hybridization, array and labeling, synthesis cDNA Spectrophotometer. NanoDrop with a nn “etl” n nn “etl” oe ek fe clig ht s sae f nes adipose intense of stage a is that calving after week one “fertil ”) nine and “fertil+” (nine tao 7% vv. hn oa RA a prfe uig RNeasy a using purified was RNA total Then (v:v). 70% ethanol centrifugation (5000 g, 15 minutes, 4°C). Each aqueous phase was mixed to equal volume of volume equal to mixed was phase aqueous Each 4°C). minutes, 15 g, (5000 centrifugation tissue mobilization. Samples were prepared, labelled and hybridized according to the the to according hybridized and labelled prepared, were Samples mobilization. tissue ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
For RT PCR, total RNA from bovine tissues (Liver, mammary gland, heart, adipose adipose heart, gland, mammary (Liver, tissues bovine from RNA total RT PCR, For Array hybridation was performed using cDNA of adipose tissue from eighteen animals eighteen from tissue adipose usingof cDNA performed was Array hybridation ) was performed on the total RNAs. Total RNA from granulosa cells in culture culture in cells granulosa from RNA Total RNAs. total the on performed was ) Comment citer cedocument:
reagent by scratching wells. RNA quantity was assessed was quantity RNA wells. scratching by reagent by Life technologies Life by free Kit Midi Kit (Qiagen) (Qiagen) Kit Midi
(Ambion , Villebon , reagent by Life Life by 9
Version postprint Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 238 238 235 236 236 234 234 233 233 232 232 231 231 230 230 229 229 228 228 227 227 217 217 222 222 216 216 215 221 221 225 225 220 220 226 226 219 219 218 218 214 214 224 224 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is Real-time quantitative PCR (qPCR) (qPCR) PCR quantitative Real-time bromide. bromide. NimbleGen, Inc.). Hybridization solution was prepared from the NimbleGen Hybridization Hybridization NimbleGen the from prepared was solution Hybridization Inc.). NimbleGen, NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.2. cDNAs were synthesized synthesized were cDNAs v3.2. Analysis Expression Gene Guide: User’s Arrays NimbleGen Reverse Transcription and Polymerase Chain Reaction Chain andPolymerase Transcription Reverse KIRREL France). (Charbonnières les Bains, 237 eois Geol, rne. T n PR osmbe wr prhsd rm Promega from purchased were consumables PCR and RT France). (Grenoble, Genomics codn t te auatrrs rcdr. N ws eune b Bcmn Coulter Beckman by sequenced was DNA procedure. manufacturer’s the to according e uig h EN mcolt Gl xrcin i (W, otnysu os France) Fontenay sous Bois, (VWR, kit Extraction Gel microelute EZNA the using gel at 72°C. PCR products were visualized in a 1.5% (w:v) agarose gel stained with ethidium ethidium with stained gel agarose (w:v) 1.5% a in visualized were products PCR 72°C. at minute at 94°C, 1 minute at 58°C, 1 minute at 72°C), with a final extension step of 7 minutes 7 of step extension final a with 72°C), at minute 1 58°C, at minute 1 94°C, at minute described mixture (Coyral Castel mixture described technologies 223 Samples were labelled with Cy3 with a NimbleGen One Color DNA Labeling Kit (Roche (Roche Kit Labeling DNA One Color NimbleGen a with Cy3 with labelled were Samples Technologies 0µ mxue s rvosy ecie (Coyral Castel described previously as mixture µl 20 Inc.). NimbleGen, (Roche software NimbleScan theRoche wereData extracted with nm. i (oh NmlGn n..Ary wr sand ih GnPx40B cne t 532 at Scanner 4000B GenePix a with scanned were Arrays Inc.). NimbleGen, (Roche Kit 42°C for 18 hours. Finally, arrays were washed with solutions of the NimbleGen Wash Buffer Buffer Wash NimbleGen the of solutions with washed were arrays Finally, hours. 18 for 42°C Kit (Roche NimbleGen, Inc.) and Cy3 labeled samples were hybridized on the 385K array at array 385K the on hybridized were samples Cy3 labeled and Inc.) NimbleGen, (Roche Kit (Invitrogen Kit Synthesis cDNA Double Stranded Superscript Invitrogen an using ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
Reverse transcription (RT) of total RNA (1 µg) was performed for 1 hour at 37°C in a a in 37°C at hour 1 for performed was µg) (1 RNA total of (RT) transcription Reverse and and ACTR3 Tbe ) oyeaecan ecin PR ws are ot n previously a in out carried was (PCR) reaction chain Polymerase 2). Table , ). They were then purified using a MinElute Reaction Cleanup Kit (Qiagen). (Qiagen). Kit Cleanup Reaction MinElute a using purified then were They ). ACTR3 was used as positive control. Finally, DNA was extracted from the agarose agarose the from extracted was DNA Finally, control. positive as used was Comment citer cedocument: ee mlfe wt seii pies (Invitrogen primers specific with amplified were
et al. et 2010) for 30 ( 30 for 2010) ACTR3 et al. et 00.Snl tadcNs of cDNAs Single strand 2010). ) or 40 ( 40 or ) KIRREL ) PCR cycles (1 cycles PCR ) y Life by by Life by 10 Page 10of49 Version postprint Page 11of49 Coyral-Castel, S.,Ramé, C.,Cognié, J.,Lecardonnel, J.,Marthey, S.,Esquerré,D., Hennequet 253 253 252 252 263 263 262 262 261 261 251 251 260 260 250 250 259 259 249 249 255 255 248 248 254 254 247 247 258 258 256 246 246 245 245 244 244 243 243 242 242 239 239 241 241 240 240 differentially expressed in adipose tissue from“fertil+” and “fertil-” cows: invitro rolein Antier, C., Elis,S.,Fritz, S.,Boussaha, M.,Jaffrézic, F.,Dupont,J. (2018).KIRREL is o h goerc en f PA n EFA (h ms sal cmiain floig the following combination) stable most (the EEF1A1 and PPIA of mean geometric the to changes between « fertil+ » and « fertil » tissues or cells. Therefore, the data were normalized were data the Therefore, cells. or tissues «fertil » »and «fertil+ between changes rne, eiiln 10 Im, A lbrtre, e Mrax Fac) srpoyi (0.1 streptomycin France), Mureaux, Les laboratories, PAA UI/ml, (100 penicillin France), Euromedex, Souffelweyersheim, France), L glutamine (3 mM, Eurobio, Courtaboeuf, Courtaboeuf, Eurobio, mM, (3 L glutamine France), Souffelweyersheim, Euromedex, fiiny n C : expression=E : Cq and efficiency mm) in McCoy’s 5A culture medium enriched with bovine serum albumin (BSA 0.1% (w:v), (w:v), 0.1% (BSA albumin serum bovine with enriched medium culture 5A McCoy’s in mm) E11 wr eaie. o ec gn, xrsin a cluae acrig o primer to according calculated was expression gene, each For examined. were EEF1A1– saline up to the laboratory. Granulosa cells were isolated by puncturing small follicles (< 6 (< follicles small puncturing by isolated were cells Granulosa laboratory. the to up saline the expressions of four housekeeping genes – PPIA (cyclophilin A), RPL19, ACTR3 and and ACTR3 RPL19, A), (cyclophilin PPIA – genes housekeeping four of expressions the normalization factor (Vandesompele (Vandesompele factor normalization serial dilutions of a pool of obtained cDNA and ranged from 1.80 to 2.16. For normalization, normalization, For 2.16. to 1.80 from ranged and cDNA obtained of pool a of dilutions serial report that suggests the geometric mean of multiple housekeeping genes as an accurate accurate an as genes housekeeping multiple of mean geometric the suggests that report following by the acquisition of the melting curve. Primers’ efficiency (E) was performed from performed from was (E) efficiency Primers’ curve. melting the of acquisition bythe following Granulosa cell collection and primary culture culture primary and collection cell Granulosa 257 ujce t 4 cce (0 eod a 9°, 0 eod a 6°, 0 eod a 72°C), at seconds 30 60°C, at seconds 30 95°C, at seconds (30 cycles 40 to subjected incubation for 2 minutes at 50°C and a denaturation step of 10 minutes at 95°C, samples were samples 95°C, at minutes 10 of step denaturation a and 50°C at minutes 2 for incubation with water, instead of cDNA, was performed systematically as a negative control. After After control. negative a as systematically performed was cDNA, of instead water, with were tested in duplicate on the same plate and the CVs was less than 5% . PCR amplification PCR . 5% than less was CVs the and plate same the on duplicate in tested were wkpp and thirty animals (n=16 “fertil+” and =14 “fertil ” animals) at 5 months of pregnancy of months 5 at animals) “fertil ” =14 and “fertil+” (n=16 animals thirty and wkpp (Invitrogen primers specific of nM 250 and France) Coquette, la Marnes (Bio Rad, adipose tissue, samples from thirty six animals (n=18 “fertil+” and =18 “fertil ” animals) at 1 1 at animals) “fertil ” =18 and “fertil+” (n=18 animals six thirty from samples tissue, adipose technologies ovary? . Reproduction, 155 (2), 181-196. , DOI : 10.1530/REP-17-0649
Targeted cDNAs were quantified by real time PCR using SYBR Green Supermix Supermix Green SYBR using PCR real time by quantified were cDNAs Targeted Bovine ovaries were collected at the slaughterhouse and transported in physiological in transported and slaughterhouse the at collected were ovaries Bovine Tbe ) n oa vlm o 2 µ i a yQ yl dvc (i a) For (Bio Rad). device Cycle MyiQ a in µl 20 of volume total in 1) Table , Comment citer cedocument: