張化鵬,張慶澤,何凡,祁夢(mèng)凡,符彬彬,李清春,李夢(mèng)尋,馬力鵬,劉乙,黃濤,2
梅山豬和杜洛克豬卵泡中差異表達(dá)lncRNA克隆鑒定及與miRNAs相關(guān)性分析
張化鵬1,張慶澤1,何凡1,祁夢(mèng)凡1,符彬彬1,李清春1,李夢(mèng)尋1,馬力鵬1,劉乙1,黃濤1,2
1石河子大學(xué)動(dòng)物科技學(xué)院,新疆石河子 832000;2新疆生豬種業(yè)工程技術(shù)研究中心,新疆昌吉 831100
【目的】通過(guò)克隆鑒定梅山豬和杜洛克豬卵泡期第4天M2卵泡中差異表達(dá)的lncRNA-ALDBSSCT0000005583,分析其在豬顆粒細(xì)胞與miRNAs表達(dá)量的相關(guān)性,為探究lncRNA調(diào)控miRNA在母豬卵泡發(fā)育過(guò)程中的作用提供理論依據(jù)。【方法】對(duì)課題組前期在梅山和杜洛克M2卵泡中篩選出的差異表達(dá)lncRNA-ALDBSSCT0000005583,進(jìn)行RT-qPCR驗(yàn)證,并利用RACE克隆其全長(zhǎng)序列;根據(jù)編碼潛力評(píng)估工具CPAT、CPC對(duì)該lncRNA的編碼能力進(jìn)行預(yù)測(cè),原核表達(dá)試驗(yàn)進(jìn)一步鑒定其編碼能力;核質(zhì)分離試驗(yàn)對(duì)lncRNA-ALDBSSCT0000005583進(jìn)行亞細(xì)胞定位,RT-qPCR檢測(cè)其在各組織中的表達(dá)水平;利用miRBase網(wǎng)站查找豬的miRNA數(shù)據(jù)庫(kù),結(jié)合RNAhybrid、miRanda在線軟件預(yù)測(cè)與lncRNA-ALDBSSCT0000005583有相互作用的物種間保守miRNA,使用TargetScan和miRanda預(yù)測(cè)與lncRNA-ALDBSSCT0000005583具有相互作用miRNA的靶基因,并對(duì)其靶基因進(jìn)行GO富集和KEGG信號(hào)通路分析;通過(guò)過(guò)表達(dá)以及干擾lncRNA驗(yàn)證其對(duì)miRNA表達(dá)量的影響。【結(jié)果】lncRNA- ALDBSSCT0000005583在杜洛克豬M2卵泡中的表達(dá)量顯著高于梅山豬,lncRNA 5'RACE和3'RACE片段大小為569 bp和546 bp,測(cè)序分析表明lncRNA-ALDBSSCT0000005583大小為588 bp。生物信息學(xué)預(yù)測(cè)其編碼潛能較低,同時(shí)原核表達(dá)試驗(yàn)結(jié)果進(jìn)一步證明其不編碼蛋白質(zhì)。組織表達(dá)譜分析表明,lncRNA-ALDBSSCT0000005583在腎上腺、脾肝和卵巢中表達(dá)量較高,在下丘腦和心臟中的表達(dá)量較低,亞細(xì)胞定位結(jié)果顯示該lncRNA主要存在于細(xì)胞質(zhì)中。生物信息學(xué)分析后共篩選出9個(gè)物種間保守的miRNA與lncRNA-ALDBSSCT0000005583具有潛在的相互作用,其中有兩個(gè)與卵巢發(fā)育相關(guān)的miRNA:miR-193a-5p、miR-361-3p;KEGG和GO富集分析顯示miR-193a-5p、miR-361-3p的靶基因與系統(tǒng)進(jìn)程和細(xì)胞與細(xì)胞信號(hào)傳導(dǎo)等生物學(xué)過(guò)程有關(guān),并顯著參與到催產(chǎn)素、Ras、NF-κB、促性腺激素釋放激素分泌等通路。隨后在顆粒細(xì)胞中過(guò)表達(dá)lncRNA-ALDBSSCT0000005583,經(jīng)RT-qPCR發(fā)現(xiàn)miR-193a-5p、miR-361-3p的表達(dá)量均顯著下調(diào)(<0.05),但干擾lncRNA-ALDBSSCT0000005583后無(wú)顯著影響?!窘Y(jié)論】lncRNA-ALDBSSCT0000005583是一個(gè)不具備編碼蛋白質(zhì)能力的lncRNA,在梅山與杜洛克豬中等卵泡間表達(dá)量有極顯著差異,在腎上腺、脾肝和卵巢中表達(dá)量較高,主要存在于顆粒細(xì)胞的細(xì)胞質(zhì)中,可能與miR-193a-5p、miR-361-3p相互作用,從而參與豬卵巢顆粒細(xì)胞的發(fā)育過(guò)程。
lncRNA-ALDBSSCT0000005583;豬;卵泡;顆粒細(xì)胞;miR-193a-5p;miR-361-3p
【研究意義】長(zhǎng)鏈非編碼RNA(long non-coding RNA lncRNA)是長(zhǎng)度超過(guò)200個(gè)堿基的轉(zhuǎn)錄本,沒(méi)有蛋白質(zhì)編碼潛能[1]。越來(lái)越多的研究表明,lncRNA參與各種重要生物過(guò)程的調(diào)控,包括染色質(zhì)修飾、選擇性剪接、表觀遺傳修飾、充當(dāng)分子骨架、轉(zhuǎn)錄和轉(zhuǎn)錄后調(diào)控[2- 6]。lncRNA既可以充當(dāng)競(jìng)爭(zhēng)性內(nèi)源性RNA(ceRNA),也可以“吸附”miRNA或蛋白質(zhì),調(diào)節(jié)mRNA的翻譯[7]。母豬的繁殖力是養(yǎng)豬業(yè)的一個(gè)重要特征,梅山豬以其高繁殖力和較大的窩產(chǎn)仔豬數(shù)而聞名[8]。與杜洛克母豬相比,梅山母豬在卵泡期中后期可以維持較多的中型卵泡庫(kù),產(chǎn)生更多的排卵前卵泡,有可能排出更多的成熟卵子并生下更多的胎兒[9-10]。因此研究梅山豬和杜洛克豬M2卵泡中差異表達(dá)的lncRNA的具體功能及調(diào)控機(jī)制,對(duì)提高母豬的繁殖力具有重要意義?!厩叭搜芯窟M(jìn)展】近年來(lái)隨著高通量測(cè)序技術(shù)的發(fā)展,許多研究表明lncRNA可以調(diào)節(jié)卵泡發(fā)育,進(jìn)而影響母豬的繁殖力。HU等[11]鑒定了大白母豬在發(fā)情周期的卵泡期和黃體期的繁殖力相關(guān)的卵巢lncRNA,并發(fā)現(xiàn)卵巢中的lncRNA顯著影響豬的生育能力。LI等[10]通過(guò)轉(zhuǎn)錄組測(cè)序在梅山豬和杜洛克豬M2卵泡中共鑒定出3 554個(gè)lncRNA,其中與繁殖性狀有關(guān)的差異表達(dá)lncRNA有127個(gè)。LIU等[12]在杜洛克豬卵泡期的第0、2和4天鑒定了豬卵巢的lncRNA和mRNA表達(dá)譜,發(fā)現(xiàn)lncRNA- ENSSSCT00000034907可能在卵泡發(fā)育中發(fā)揮重要作用。【本研究切入點(diǎn)】前人研究表明,lncRNA在豬的卵巢中發(fā)揮著重要作用,但是關(guān)于豬卵巢lncRNA的研究只集中于篩選出卵巢中差異表達(dá)的lncRNA,并未進(jìn)行下一步驗(yàn)證?!緮M解決的關(guān)鍵問(wèn)題】本研究利用本課題組前期出在梅山和杜洛克豬M2卵泡篩選的差異表達(dá)lncRNA-ALDBSSCT0000005583進(jìn)行RACE克隆,并利用生物信息學(xué)對(duì)其靶向miRNA進(jìn)行預(yù)測(cè),結(jié)合組織表達(dá)譜分析其表達(dá)量,并驗(yàn)證其在顆粒細(xì)胞中的亞細(xì)胞定位,從而為豬lncRNA通過(guò)miRNA發(fā)揮功能的調(diào)控機(jī)制研究提供試驗(yàn)依據(jù)。
試驗(yàn)于2022—2023年在石河子大學(xué)動(dòng)物科技學(xué)院遺傳育種與繁殖實(shí)驗(yàn)室完成。
1.1.1 試驗(yàn)樣品來(lái)源 2023年8月,在石河子大學(xué)附屬獸醫(yī)站,選取體重接近、健康大白豬三頭,屠宰后采集心、胃、大腦、脾、腎上腺、肝、小腸、卵巢、子宮等組織,DEPC處理后,錫紙包裹于液氮中凍存,帶回實(shí)驗(yàn)室備用;梅山和杜洛克豬M2卵泡樣品為石河子大學(xué)動(dòng)物科技學(xué)院遺傳育種與繁殖實(shí)驗(yàn)室保存。細(xì)胞在石河子市綠源達(dá)康屠宰場(chǎng)中采集的豬卵巢,經(jīng)處理后凍存于液氮中的原代顆粒細(xì)胞。
1.1.2 主要試劑與儀器 主要試劑:pCDNA3.1(+)載體;pET-28a(+)載體;DH5α感受態(tài)細(xì)胞為實(shí)驗(yàn)室保留;siRNA oligos由上海吉瑪公司合成;lipofectamine? 3000(賽默飛);Trizol up(全式金);SMARTer?RACE cDNA Amplification Kit(TaKaRa);DAPI染色劑(碧云天);一抗,卵泡刺激素受體(FSHR),二抗,CY3-羊抗兔IgG;NE-PERTM細(xì)胞核和細(xì)胞質(zhì)提取試劑盒(賽默飛)等。
主要儀器:超低溫冰箱(-80℃)、CO2培養(yǎng)箱、高壓滅菌鍋、LightCycle 96實(shí)時(shí)熒光定量PCR儀、高速離心機(jī)、Nano-Drop ND 2000c Spectrophotometer、熒光倒置顯微鏡等。
根據(jù)TRIzolip up試劑盒說(shuō)明書提取樣本總RNA,用1%的瓊脂糖凝膠電泳和NanoDrop 2000進(jìn)行總RNA的完整性和純度檢驗(yàn)合格后備用。
按照TaKaRa反轉(zhuǎn)錄試劑盒PrimeScriptTM RT ReagentKit with gDNA Eraser(PerfectReal Time)說(shuō)明書進(jìn)行cDNA合成。
根據(jù)實(shí)驗(yàn)室之前二代測(cè)序結(jié)果中l(wèi)ncRNA- ALDBSSCT0000005583的部分已知核苷酸序列,使用Primer Primer 5.0軟件設(shè)計(jì)實(shí)時(shí)熒光定量PCR引物、5′RACE和3′RACE特異性引物。實(shí)時(shí)熒光定量PCR內(nèi)參基因選擇GAPDH,在用于RACE克隆的特異性引物(GSP)在5′端添加15 bp“GATTACGCCAA GCTT”的序列用于后續(xù)實(shí)驗(yàn)中的連接測(cè)序,所有引物見(jiàn)表1。所有引物均由生工生物工程(上海)股份有限公司合成。
通過(guò)編碼潛力評(píng)估工具CPAT(coding-potential assessment tool)、CPC(http://lilab.research.bcm.edu/)在線預(yù)測(cè)工具對(duì)lncRNA-ALDBSSCT0000005583進(jìn)行編碼潛能預(yù)測(cè)。
以杜洛克豬M2卵泡cDNA為模板,擴(kuò)增lncRNA全長(zhǎng),經(jīng)2 %的瓊脂糖凝膠電泳(120 V,40 min)檢測(cè)后,切取目的條帶,膠回收,經(jīng)雙酶切后與pcDNA3.1(+)載體進(jìn)行連接,轉(zhuǎn)化,測(cè)序。
將lncRNA-ALDBSSCT0000005583全長(zhǎng)和YY1的CDs區(qū)亞克隆到Pet-28a(+)載體的RⅠ和Ⅰ酶切位點(diǎn)上,獲得lncRNA-ALDBSSCT0000005583和YY1原核表達(dá)質(zhì)粒,轉(zhuǎn)化至BL21(DE3)感受態(tài)細(xì)胞,獲得重組質(zhì)粒后進(jìn)行酶切和測(cè)序鑒定。YY1為實(shí)驗(yàn)室保存的pcDNA3.1過(guò)表達(dá)載體,經(jīng)RⅠ和Ⅰ雙酶切后連接至Pet-28a(+)載體上,作為陽(yáng)性對(duì)照,空載體作為陰性對(duì)照。
經(jīng)測(cè)序鑒定成功的陽(yáng)性菌液,37 ℃搖床200 r/min培養(yǎng)至OD 0.6—0.8,以Pet-YY1為陽(yáng)性對(duì)照,空載體為陰性對(duì)照,各加入終濃度為1.0 mmol·L-1IPTG溶液,誘導(dǎo)表達(dá)4 h。取1 mL誘導(dǎo)后的菌液,12 000 r/min離心5 min,棄去上清,根據(jù)菌液沉淀的量,用50—100 μL PBS重懸沉淀,加入5×loading buffer上樣緩沖液,金屬浴中100 ℃10 min,保證菌體完全裂解,12 000 r/min離心5 min后,取10 μL用于SDS-PAGE電泳分析。SDS凝膠用考馬斯亮藍(lán)染色2 h,脫色液脫色后,在凝膠成像系統(tǒng)上觀察結(jié)果。
常規(guī)的細(xì)胞復(fù)蘇,向復(fù)蘇的細(xì)胞中加入10 mL完全培養(yǎng)基(DMEM,F(xiàn)BS,雙抗)輕柔吹勻,根據(jù)細(xì)胞密度合理鋪入6孔板中。將鋪好的細(xì)胞于37 ℃、5% CO2培養(yǎng)箱中,培養(yǎng)細(xì)胞,48 h后使用PBS清洗顆粒細(xì)胞。運(yùn)用免疫熒光的方法檢測(cè)細(xì)胞中卵泡刺激素受體(FSHR),以鑒定顆粒細(xì)胞。
試驗(yàn)采用豬顆粒細(xì)胞,按照NE-PER? 細(xì)胞核和細(xì)胞質(zhì)提取試劑盒說(shuō)明書進(jìn)行細(xì)胞核細(xì)胞質(zhì)RNA分離,通過(guò)qPCR檢測(cè)lncRNA-ALDBSSCT0000005583在豬顆粒細(xì)胞細(xì)胞核細(xì)胞質(zhì)中的表達(dá)量。
6孔板培養(yǎng)顆粒細(xì)胞待融合度達(dá)到70%—90%時(shí),使用Lipofectamine? 3000試劑盒將過(guò)表達(dá)載體pCDNA3.1-lncRNA-ALDBSSCT0000005583以及siRNA- ALDBSSCT0000005583轉(zhuǎn)染至豬顆粒細(xì)胞,以空質(zhì)粒pCDNA3.1及siRNA-NC作為對(duì)照。利用RT-qPCR檢測(cè)轉(zhuǎn)染處理48 h后的過(guò)表達(dá)/抑制的效率。
從miRBase(https://www.mirbase.org)獲得了豬的成熟miRNA序列,利用RNAhybrid(https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid)和miRanda(https://www.miranda-ng.org/en/)分別預(yù)測(cè)與lncRNA- ALDBSSCT0000005583存在相互作用的miRNA。對(duì)兩款軟件預(yù)測(cè)出的miRNA分別按照每款軟件的評(píng)分標(biāo)準(zhǔn)進(jìn)行篩選,取兩款軟件的交集作為最終的miRNA。使用TargetScan(v5.0)、miRanda(v3.3a)對(duì)篩選出的miRNA分別進(jìn)行靶基因預(yù)測(cè)。利用KEGG和GO數(shù)據(jù)庫(kù)進(jìn)行富集分析,用Cytoscape 3.6.0軟件構(gòu)建候選miRNA-mRNA相互作用的結(jié)果圖。
表1 RT-qPCR及載體構(gòu)建引物序列
F:上游引物;R:下游引物。表中加粗部分為保護(hù)堿基;下劃線部分為酶切位點(diǎn);酶切位點(diǎn)為R Ⅰ和Ⅰ;波浪線部分為添加的序列,用于后續(xù)試驗(yàn)中的無(wú)縫克隆。lncRNA-5583為lncRNA-ALDBSSCT0000005583縮寫,下同
F: Upstream primers; R: Downstream primers. The bold part in the table is the protective base; The underlined part is the enzyme cleavage site; The digestion sites wereR I. andI. The wavy portion is the added sequence for seamless cloning in subsequent experiments. lncRNA-5583 is an abbreviation for lncRNA-ALDBSSCT0000005583, The same as below
實(shí)時(shí)熒光定量PCR以GAPDH作為內(nèi)參,RT-qPCR結(jié)果按使用2-ΔΔct法計(jì)算,用SPSS17.0軟件進(jìn)行顯著性分析。以GAPDH基因作為內(nèi)參基因?qū)z測(cè)的目的基因進(jìn)行歸一化,U6作為細(xì)胞核基因內(nèi)參。數(shù)據(jù)使用 Graph Pad Prism 8 進(jìn)行作圖,其中“*”(<0.05)為差異顯著,“**”(<0.01)為差異極顯著,“ns”(>0.05)表示差異不顯著。所有引物見(jiàn)表1。
通過(guò)qRT-PCR技術(shù)對(duì)lncRNA-ALDBSSCT0000005583在梅山豬和杜洛克豬的M2卵泡的表達(dá)情況進(jìn)行驗(yàn)證分析發(fā)現(xiàn),lncRNA-ALDBSSCT0000005583在杜洛克豬M2卵泡中的表達(dá)量極顯著高于梅山豬,結(jié)果與二代測(cè)序的結(jié)果相同(<0.01)(圖1),表明了二代測(cè)序結(jié)果的可靠性。
A:二代測(cè)序結(jié)果ALDBSSCT0000005583在M2卵泡中的表達(dá)水平;B:RT-qPCR驗(yàn)證ALDBSSCT0000005583的表達(dá)水平
根據(jù)SMARTer RACE 5'3' Kit 擴(kuò)增豬長(zhǎng)鏈非編碼lncRNA-ALDBSSCT0000005583,結(jié)果表明,3′RACE片段大小為546 bp(圖2-A),5′RACE片段大小為569 bp(圖2-B),根據(jù)3′RACE和5′ RACE測(cè)序序列結(jié)果拼接確定lncRNA-ALDBSSCT0000005583全長(zhǎng)為588 bp(圖2-C)。
利用在線軟件CPAT和CPC對(duì)長(zhǎng)鏈非編碼RNA lncRNA-ALDBSSCT0000005583的編碼能力進(jìn)行分析計(jì)算,結(jié)果lncRNA-ALDBSSCT0000005583的編碼能力分別為0.0122981(表2)、0.01716(表3),屬于非編碼RNA。
為了進(jìn)一步驗(yàn)證lncRNA-ALDBSSCT0000005583是否具有編碼能力,成功構(gòu)建了pET-28a-lncRNA- ALDBSSCT0000005583(圖3-A)、pET-28a-YY1(圖3-B)原核表達(dá)載體,通過(guò)原核表達(dá)試驗(yàn)發(fā)現(xiàn)lncRNA- ALDBSSCT0000005583與pET-28a(+)空質(zhì)粒的電泳條帶一致,而相同試驗(yàn)條件下陽(yáng)性對(duì)照pET- 28a-YY1則在69 kDa處有明顯的新增條帶(圖3-C)。綜合以上研究結(jié)果強(qiáng)調(diào)lncRNA-ALDBSSCT0000005583是一種真正的非編碼RNA。
表2 CPAT網(wǎng)站預(yù)測(cè)編碼潛能
表3 CPC網(wǎng)站預(yù)測(cè)編碼潛能的結(jié)果
顆粒細(xì)胞的鑒定結(jié)果如圖4所示,鑒于FSHR是卵巢中唯一表達(dá)FSHR的細(xì)胞,通過(guò)檢測(cè)細(xì)胞中FSHR的表達(dá)情況判斷是否是顆粒細(xì)胞,免疫熒光結(jié)果顯示,培養(yǎng)的細(xì)胞中FSHR陽(yáng)性率較高,判斷培養(yǎng)的細(xì)胞為顆粒細(xì)胞,可以用于進(jìn)行下一步試驗(yàn)。
利用豬的顆粒細(xì)胞進(jìn)行核質(zhì)分離試驗(yàn),確定了lncRNA-ALDBSSCT0000005583的亞細(xì)胞定位,結(jié)果顯示,lncRNA-ALDBSSCT0000005583主要存在于細(xì)胞質(zhì)中(圖5)。
試驗(yàn)利用RT-qPCR技術(shù),探究lncRNA- ALDBSSCT0000005583在豬不同組織中的表達(dá)情況。組織表達(dá)譜結(jié)果顯示,lncRNA-ALDBSSCT0000005583在心、下丘腦、胃、卵巢、脾、腎上腺、肝、小腸、子宮中均有不同程度表達(dá),在腎上腺、脾、肝和卵巢中表達(dá)量較高,在下丘腦和心中的表達(dá)量較低(圖6),以上研究表明lncRNA-ALDBSSCT0000005583在這些組織中可能均具備生物學(xué)功能。
根據(jù)miRbase 22數(shù)據(jù)庫(kù),下載豬的所有miRNAs,利用RNAhybrid和miRanda在線軟件分析與lncRNA-ALDBSSCT0000005583具有相互作用的miRNA,共發(fā)現(xiàn)9個(gè)在人、小鼠、大鼠、牛、豬等物種之間保守的miRNAs(圖7),利用TargetScan(v5.0)、miRanda(v3.3a)對(duì)這9個(gè)miRNA篩選出7 963個(gè)潛在的靶基因,借助Cytoscape軟件構(gòu)建了lncRNA- miRNA-mRNA靶向關(guān)系的網(wǎng)絡(luò)構(gòu)建圖(圖8)。
A:lncRNA- ALDBSSCT0000005583全長(zhǎng)擴(kuò)增和連接至pET-28a(+)載體Sanger DNA測(cè)序;B:pET-28a-YY1雙酶切結(jié)果及Sanger DNA測(cè)序;C:SDS-PAGE電泳分析
圖4 顆粒細(xì)胞的鑒定
查閱文獻(xiàn)發(fā)現(xiàn)miR-193a-5p[13]、miR-361-3p[14]可能與卵巢的發(fā)育有關(guān)。根據(jù)TargetScan(v5.0)和miRanda(v3.3a)分別對(duì)miR-193a-5p、miR-361-3p篩選出1 152、3 026個(gè)潛在的靶基因,對(duì)這兩個(gè)miRNA的靶基因求交集共獲得298個(gè)靶基因。對(duì)這些靶基因進(jìn)行GO富集分析和KEGG信號(hào)通路分析,結(jié)果表明,這些miRNAs顯著富集到系統(tǒng)進(jìn)程和細(xì)胞與細(xì)胞信號(hào)傳導(dǎo)等生物學(xué)過(guò)程中(表4)。KEGG信號(hào)通路分析表明,這兩個(gè)miRNA顯著參與到催產(chǎn)素信號(hào)通路、Ras信號(hào)通路、NF-κB信號(hào)通路、促性腺激素釋放激素分泌通路等(表5)。
圖5 lncRNA- ALDBSSCT0000005583亞細(xì)胞定位
過(guò)表達(dá)lncRNA-ALDBSSCT0000005583有顯著的過(guò)表達(dá)效果(圖9-A),siRNA-ALDBSSCT0000005583有極顯著的抑制效果(圖9-B),結(jié)果表明過(guò)表達(dá)以及干擾lncRNA-ALDBSSCT0000005583的豬卵巢顆粒細(xì)胞模型構(gòu)建成功,可以進(jìn)行下一步試驗(yàn)。
圖6 lncRNA-ALDBSSCT0000005583在杜洛克豬不同組織中的表達(dá)情況
圖7 RNAhybrid和miRanda預(yù)測(cè)miRNA靶向lncRNA-ALDBSSCT0000005583
圖8 lncRNA-miRNA-mRNA網(wǎng)絡(luò)構(gòu)建
表4 與lncRNA-ALDBSSCT0000005583相互作用的miRNAs靶基因的GO富集條目
過(guò)表達(dá)lncRNA后顯著降低了miR-193a-5p和miR-361-3p的表達(dá)量(圖9-C、E),但干擾lncRNA后miR-193a-5p和miR-361-3p的表達(dá)量有升高的趨勢(shì)但不顯著(圖9-D、F),以上研究表明,lncRNA- ALDBSSCT0000005583在豬的卵巢顆粒細(xì)胞中可能通過(guò)調(diào)控miR-193a-5p、miR-361-3p基因的表達(dá),從而參與卵泡的發(fā)育過(guò)程。
母豬生產(chǎn)力作為影響生產(chǎn)效率的最重要因素之一,限制窩產(chǎn)仔豬數(shù)的主要因素是排卵率,排卵率越高,產(chǎn)仔數(shù)越多[12,15]。相對(duì)于杜洛克母豬,梅山豬的產(chǎn)仔數(shù)更大,以其高繁殖力聞名[16]。相關(guān)研究發(fā)現(xiàn),多產(chǎn)的梅山母豬和雜種大白母豬在卵泡期的中后期存在卵泡生長(zhǎng)動(dòng)力學(xué)差異,這種差異極大地促進(jìn)了排卵率[17]。此外,另一項(xiàng)研究表明,梅山母豬和杜洛克母豬在中等大小卵巢卵泡生長(zhǎng)調(diào)節(jié)和生理發(fā)育方面也存在顯著差異[18]。目前在動(dòng)物卵巢中的功能和分子機(jī)制的研究發(fā)現(xiàn)lncRNA對(duì)卵泡的生長(zhǎng)發(fā)育至關(guān)重要。但是關(guān)于豬卵巢lncRNA的研究主要集中于篩選出卵巢中差異表達(dá)的lncRNA,并未進(jìn)行下一步驗(yàn)證。因此本研究通過(guò)RACE技術(shù)獲取并鑒定了梅山豬和杜洛克豬M2卵泡中差異表達(dá)的lncRNA-ALDBSSCT0000005583,其全長(zhǎng)588 bp,經(jīng)原核表達(dá)試驗(yàn)驗(yàn)證,lncRNA-ALDBSSCT0000005583不具備編碼蛋白的能力,是一個(gè)真正的長(zhǎng)鏈非編碼RNA。中樞神經(jīng)系統(tǒng)中的神經(jīng)元對(duì)腎上腺和卵巢具有跨神經(jīng)支配[19],并且在母羊卵巢摘除后,其腎周圍脂肪組織中生長(zhǎng)激素受體(growth hormone receptor,GHR)表達(dá)量增加[20]。根據(jù)前人研究結(jié)果發(fā)現(xiàn)腎上腺和卵巢之間存在密不可分的關(guān)系。本研究通過(guò)組織表達(dá)譜分析,發(fā)現(xiàn)lncRNA在腎上腺中表達(dá)量最高,其次為肝、脾和卵巢,表明lncRNA-ALDBSSCT0000005583在這些組織中可能均具備生物學(xué)功能。
表5 與lncRNA-ALDBSSCT0000005583相互作用的miRNAs靶基因的信號(hào)通路
A. 過(guò)表達(dá)lncRNA-ALDBSSCT0000005583效率檢測(cè);B. siRNA-ALDBSSCT0000005583效率檢測(cè);C. 過(guò)表達(dá)lncRNA-ALDBSSCT0000005583對(duì)miR-193a-5p的影響;D. 過(guò)表達(dá)lncRNA- ALDBSSCT0000005583對(duì)miR-193a-5p的影響;E. 干擾lncRNA-ALDBSSCT0000005583對(duì)miR-361-3p的影響;F. 干擾lncRNA- ALDBSSCT0000005583對(duì)miR-1361-3p的影響
miRNA和lncRNA通過(guò)識(shí)別序列相互作用,其中l(wèi)ncRNA充當(dāng)競(jìng)爭(zhēng)性內(nèi)源RNA(ceRNA)導(dǎo)致miRNA的隔離,并抑制miRNA對(duì)靶mRNA的調(diào)節(jié)作用[21-22]。ceRNA機(jī)制通常發(fā)生在細(xì)胞質(zhì)中,這與miRNA在細(xì)胞質(zhì)中起作用的觀點(diǎn)一致[23]。本研究通過(guò)核質(zhì)分離試驗(yàn)分析了lncRNA-ALDBSSCT0000005583的細(xì)胞定位,發(fā)現(xiàn)lncRNA主要存在于細(xì)胞質(zhì)中,為了研究lncRNA-ALDBSSCT0000005583是否可以作為ceRNA或miRNA的海綿發(fā)揮作用,我們使用生物信息學(xué)靶基因預(yù)測(cè)工具搜索了可以與lncRNA結(jié)合的miRNA,總共篩選到9個(gè)與lncRNA相互作用的miRNAs。其中,有研究表明miR-193a-5p可以調(diào)控RAB11A[13]、HOXA7[24]和CDK14[25]抑制卵巢癌細(xì)胞的增殖并促進(jìn)其凋亡;miR-361-3p可以抑制卵泡刺激素(FSH)的分泌[14],并且miR-361-3p也可以作為L(zhǎng)ncRNA-BBOX1-AS1[26]、LINC00922[27]的海綿對(duì)卵巢的生長(zhǎng)發(fā)育起到一定的調(diào)控作用。結(jié)合前人對(duì)miRNAs功能的研究篩選出兩個(gè)與卵巢發(fā)育相關(guān)的miRNA:miR-193a-5p和miR-361-3p。對(duì)這兩個(gè)miRNAs的靶基因通過(guò)GO富集和KEGG信號(hào)通路表明:這些miRNAs顯著富集到系統(tǒng)進(jìn)程和細(xì)胞與細(xì)胞信號(hào)傳導(dǎo)等生物學(xué)過(guò)程中。KEGG信號(hào)通路分析表明,這兩個(gè)miRNA顯著參與到催產(chǎn)素信號(hào)通路、Ras信號(hào)通路、NF-κB信號(hào)通路等。
眾所周知,miRNA通過(guò)與靶mRNA的3′-非翻譯區(qū)(3′UTR)結(jié)合,成為基因調(diào)控的主要參與者,隨后引起mRNA降解或翻譯抑制[28],miRNA也對(duì)卵泡發(fā)育具有一定的影響[29]。與miRNA結(jié)合的lncRNA具有極大的研究?jī)r(jià)值,因?yàn)樗鼈兛捎糜谡{(diào)控miRNA功能。到目前為止,只有少數(shù)lncRNA被發(fā)現(xiàn)與miRNA結(jié)合,這些lncRNA已經(jīng)過(guò)驗(yàn)證。例如,lncRNA-ZFAS1與miR-129結(jié)合進(jìn)而影響卵巢顆粒細(xì)胞的增殖和凋亡[30],lncRNA-NEAT1可以阻止miR-16、miR-483和miR-324-3p的表達(dá)來(lái)促進(jìn)卵巢顆粒細(xì)胞的增殖并阻止細(xì)胞凋亡[31],lncRNA-2300通過(guò)抑制miR-365-3p的促凋亡作用來(lái)減少豬顆粒細(xì)胞的凋亡[32],lncRNA- FDNCR靶向湖羊的miR-543-3p來(lái)促進(jìn)顆粒細(xì)胞凋亡[33],lncRNA-MEG3通過(guò)負(fù)反饋調(diào)控miR-23影響卵泡顆粒細(xì)胞的凋亡[34]。根據(jù)ceRNA假說(shuō),lncRNA應(yīng)與miRNA表達(dá)呈負(fù)相關(guān),lncRNA下調(diào)miRNA的表達(dá)水平,降低其對(duì)mRNA的抑制作用[35]。本研究通過(guò)過(guò)表達(dá)以及干擾lncRNA發(fā)現(xiàn)miR-193a-5p和miR- 361-3p的表達(dá)與lncRNA存在著顯著的負(fù)相關(guān)。由此可以推測(cè),lncRNA可能調(diào)控miR-193a-5p、miR-361-3p參與到卵巢的生長(zhǎng)發(fā)育,但是其具體的作用機(jī)制還需進(jìn)一步后續(xù)驗(yàn)證。
lncRNA-ALDBSSCT0000005583在杜洛克豬M2卵泡中的表達(dá)量極顯著高于梅山豬,是一個(gè)全長(zhǎng)588 bp的不具有翻譯蛋白質(zhì)功能的lncRNA,生物信息學(xué)分析發(fā)現(xiàn)lncRNA-ALDBSSCT0000005583可能與系統(tǒng)進(jìn)程和細(xì)胞與細(xì)胞信號(hào)傳導(dǎo)等生物學(xué)過(guò)程有關(guān);并參與到催產(chǎn)素、Ras、NF-κB、促性腺激素釋放激素分泌通路等通路;并且可能對(duì)miR-193a-5p、miR-361-3p的表達(dá)存在影響。本研究為進(jìn)一步探索lncRNA- ALDBSSCT0000005583在豬卵巢的生長(zhǎng)發(fā)育過(guò)程中提供了基礎(chǔ)數(shù)據(jù)。
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Cloning and Identification of Differentially Expressed lncRNAs in Follicles of Meishan Pigs and Duroc Pigs with Their Correlation Analysis with miRNAs
ZHANG HuaPeng1, ZHANG QingZe1, HE Fan1, QI MengFan1, FU BinBin1, LI QingChun1, LI MengXun1, MA LiPeng1, LIU Yi1, HUANG Tao1, 2
1College of Animal Science and Technology, Shihezi University, Shihezi 832000, Xinjiang;2Xinjiang Pig Seed Industry Engineering Technology Research Center, Changji 831100, Xinjiang
【Objective】 The objective of this study was to clone and identify the differentially expressed lncRNA-ALDBSSCT0000005583in M2 follicles on the fourth day of follicular stage in Meishan pigs and Duroc pigs, and to analyze the correlation between the expression of miRNAs in porcine granulosa cells, so as to provide a theoretical basis for exploring the role of lncRNAs in the development of follicles in sows by regulating miRNAs. 【Method】Based on the differentially expressed lncRNA- ALDBSSCT0000005583 screened in Meishan and Duroc M2 follicles in our early research, the full-length sequence of ALDBSSCT0000005583 was verified by RT-qPCR and cloned by RACE; the coding ability of this lncRNA was predicted by the coding potential assessment tool of CAPT and CPC, which was further identified by the primary expression test; the coding ability of this lncRNA was identified by the primary expression test; the subcellular coding ability of NA-ALDBSSCT0000005583 was identified by the nucleoplasmic separation experiment and tested to identify its coding ability; the subcellular localization of lncRNA-ALDBSSCT0000005583 by nucleoplasmic isolation assay and its expression level in various tissues were detected by RT-qPCR; miRBase website was used to locate the miRNA database of pigs, and the combination of RNAhybrid and miRanda online software was used to predicte the relationship with the lncRNA-ALDBSSCT0000005583. The inter-species conserved miRNAs that interacted with lncRNA-ALDBSSCT0000005583 were predicted by TargetScan and miRanda, the target genes that interacted with lncRNA-ALDBSSCT0000005583 were predicted by TargetScan and miRanda, and their target genes were subjected to GO enrichment and KEGG signaling pathway analyses; the effects of target genes on miRNA expression were verified by overexpression as well as interference with lncRNA. 【Result】The expression level of lncRNA-ALDBSSCT0000005583 in M2 follicles of Duroc pigs was significantly higher than that in Meishan pigs, and the size of lncRNA 5′RACE and 3′RACE fragments was 569 bp and 546 bp, respectively, and the sequencing analysis showed that the size of lncRNA-ALDBSSCT0000005583 was 588 bp. Bioinformatics predicted that the encoding potential was low, and the results of prokaryotic expression assay further proved that it did not code for proteins. Tissue expression profiling showed that lncRNA-ALDBSSCT0000005583 was expressed in the adrenal gland, spleen, liver and ovaries, and low in the hypothalamus and heart, while the subcellular localization results showed that the lncRNA was mainly present in the cytoplasm. After bioinformatics analysis, a total of 9 conserved miRNAs were screened for potential interaction with lncRNA-ALDBSSCT0000005583, including two miRNAs related to ovarian development: miR-193a-5p and miR-361-3p. KEGG and GO enrichment analysis showed that the target genes of miR-193a-5p and miR-361-3p were related to phylogenetic processes and biological processes such as cell-to-cell signaling. It was also significantly involved in oxytocin, Ras, NF-κB gonadotropin- releasing hormone secretion and other pathways. Subsequently, lncRNA-ALDBSSCT0000005583 was overexpressed in granulosa cells, and the expressions of miR-193a-5p and miR-361-3p were significantly down-regulated by RT-qPCR (<0.05), but there was no significant effect after interference with lncRNA-ALDBSSCT0000005583. 【Conclusion】lncRNA-ALDBSSCT0000005583 was a lncRNA that did not have the ability to code for proteins. There was a significant difference in the expression level between the medium follicles of Meishan and Duroc pigs, and the expression level was higher in the adrenal glands, spleen, liver and ovaries, which is mainly found in the cytoplasm of granulosa cells, and might be involved in the development of porcine ovarian granulosa cells by interacting with miR-193a-5p and miR-361-3p.
lncRNA-ALDBSSCT0000005583; pig; follicle; granulosa cells; miR-193a-5p; miR-361-3p
10.3864/j.issn.0578-1752.2024.09.014
2023-11-06;
2024-01-11
國(guó)家自然科學(xué)基金(31960645)、新疆維吾爾自治區(qū)天山英才青年科技拔尖人才項(xiàng)目(2022TSYCCX0047)、新疆維吾爾自治區(qū)第七師胡楊河市“揭榜掛帥”項(xiàng)目(QS2023010)
張化鵬,E-mail:914566978@qq.com。通信作者黃濤,E-mail:taohuang100@sina.com
(責(zé)任編輯 林鑒非)