Abstract
This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented with 5% LSO or 5% SFO) of 28 days. Mammary gland biopsies were collected from each animal on day-14 (D-14, control period), D+7 (early treatment period) and D+28 (late treatment period) and were subjected to RNA-Sequencing and subsequent bioinformatics analyses. Functional enrichment of lncRNA was performed via potential cis regulated target genes located within 50 kb flanking regions of lncRNAs and having expression correlation of >0.7 with mRNAs. A total of 4955 lncRNAs (325 known and 4630 novel) were identified which potentially cis targeted 59 and 494 genes in LSO and SFO treatments, respectively. Enrichments of cis target genes of lncRNAs indicated potential roles of lncRNAs in immune function, nucleic acid metabolism and cell membrane organization processes as well as involvement in Notch, cAMP and TGF-β signaling pathways. Thirty-two and 21 lncRNAs were differentially expressed (DE) in LSO and SFO treatments, respectively. Six genes (KCNF1, STARD13, BCL6, NXPE2, HHIPL2 and MMD) were identified as potential cis target genes of six DE lncRNAs. In conclusion, this study has identified lncRNAs with potential roles in mammary gland functions and potential candidate genes and pathways via which lncRNAs might function in response to LSO and SFA.
Highlights
Advances in high throughput RNA sequencing technologies and computational prediction techniques have enabled the discovery of an abundant class of non-coding RNA species with emerging roles in gene regulation
We showed a reduction in milk fat yield of 30.38% and 32.42% in response to 5% linseed oil (LSO) aPnrdev5io%uSslFyO, w, reesspheocwtievdelay,readccuocmtiopnaniniemd iblky fiantcyreiealsdedofc3o0n.3ce8n%traantidon32s.o42f %soimneremspoonnosuentsoa5tu%raLtSeOd aanndd 5p%olSyFuOns,arteusrpaetcetdiveflayt,tyacacocimdspainniemd iblky,indcirfefearseendticaolncreengutrlaattiioonns ooff sgoemneesmwonitohunrsoalteusraintedliapnidd spyonlythuenssisa/tumraetteadbolfiastmty [5a3c]i,dsdififneremntiilakl, mdiiRffeNrAenteiaxlprreesgsiuolnati[o3n2] oafndgecnoe-sexpwreitshsiornolensetwinorklipoidf msyinRtNheAssis/[m52e]t.abInolitshme p[r5e3s]e, ndt isffteurdeyn,tiwale mhaiRveNcAhaerxapctreersiszieodn th[3e2]lnacRndNAcor-eepxeprrteosisrieonof nthetewboorvkinoef mmaiRmNmAasry[5g2la].ndIninthreespproensseenttosLtuSdOya, nwdeSFhOav.e characterized the long non-coding RNA (lncRNA) repertoire of the bovine mamAmtaortyalgolafn3d25inknreoswpnonasnedto46L3S0OnoanvdelSlnFcOR.NAs were identified in this study
Other notable pathways enriched for safflower oil (SFO) lncRNA cis target genes were cAMP and TGF-β signaling pathways. cAMP was recently identified as an enriched pathway for lncRNA target genes in the bovine mammary gland [24] while TGF-β signaling pathway, known to have important immune functions, was reported as an important pathway for lactation persistency [75] as well as an enriched pathway for target genes of differentially expressed (DE) miRNAs during a lactation curve [76]
Summary
Advances in high throughput RNA sequencing technologies and computational prediction techniques have enabled the discovery of an abundant class of non-coding RNA (ncRNA) species with emerging roles in gene regulation. Long non-coding RNA (lncRNA) generally considered as RNA molecules >200 nucleotides (nts) are known to participate in a diverse set of biological processes including genomic imprinting, X chromosome inactivation, cell differentiation and development, cancer metastasis, immunity, disease and ageing [1,2,3,4,5,6,7,8,9]. A recent study has suggested that some lncRNAs play a role in translation control of target mRNA (messenger RNA) during development of bovine early embryos [4] as well as development processes in calf gut at the early part of life [25]
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