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| 1 | Methylome and transcriptome data integration reveals potential roles of DNA methylation and candidate biomarkers of cow Streptococcus uberis subclinical mastitis显示文摘Background:Mastitis caused by different pathogens including Streptococcus uberis(S.uberis)is responsible for huge economic losses to the dairy industry.In order to investigate the potential genetic and epigenetic regulatory mecha‑nisms of subclinical mastitis due to S.uberis,the DNA methylome(whole genome DNA methylation sequencing)and transcriptome(RNA sequencing)of milk somatic cells from cows with naturally occurring S.uberis subclinical mastitis and healthy control cows(n=3/group)were studied.Results:Globally,the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and introns.The DNA methylation levels at the promoter,first exon and first intron regions were nega‑tively correlated with the expression level of genes at a whole‑genome‑wide scale.In general,DNA methylation level was lower in S.uberis‑positive group(SUG)than in the control group(CTG).A total of 174,342 differentially methylated cytosines(DMCs)(FDR<0.05)were identified between SUG and CTG,including 132,237,7412 and 34,693 DMCs in the context of CpG,CHG and CHH(H=A or T or C),respectively.Besides,101,612 methylation haplotype blocks(MHBs)were identified,including 451 MHBs that were significantly different(dMHB)between the two groups.A total of 2130 differentially expressed(DE)genes(1378 with up‑regulated and 752 with down‑regulated expression)were found in SUG.Integration of methylome and transcriptome data with MethGET program revealed 1623 genes with signifi‑cant changes in their methylation levels and/or gene expression changes(MetGDE genes,MethGET P‑value<0.001).Functional enrichment of genes harboring≥15 DMCs,DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to S.uberis infection,especially cytokine activities.Furthermore,discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers,including 6 DE genes,15 CpG‑DMCs and 5 dMHBs that discriminated between SUG and CTG.Conclusion:The integration of methylome and transcriptome of milk somatic cells suggests the possible involve‑ment of DNA methylation changes in the regulation of the host immune response to subclinical mastitis due to S.uberis.The presented genetic and epigenetic biomarkers could contribute to the design of management strategies of subclinical mastitis and breeding for mastitis resistance. | Mengqi Wang Nathalie Bissonnette Mario Laterriere Pier‑Luc Dudemaine David Gagne Jean‑Philippe Roy Xin Zhao Marc‑Andre Sirard Eveline M.Ibeagha‑Awemu | 2023 | Journal of Animal Science and Biotechnology2023，14，2： | 2 |
| 2 | Effect of cycloheximide, 6- DMAP, roscovitine and butyrolactone I on resumption of meiosis in porcine oocytes 显示文摘 | Beux G L Richard F J Sirard M A | 2003 | Theriogenology2003，60，： | 1 |
| 3 | A cell initiating human acute myeloid leukaemia after transplantation into SCID mice显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，6464： | 1 |
| 4 | A cell initiating human acute myeloid leukaemia after transplantation into SCID mice显示文摘 | Lapidot T Sirard C Vormor J | 1994 | Nature1994，367，6464： | 1 |
| 5 | Relaxation dynamics of CO2 diffusion, sorption, and polymer swelling for plasticized polyimide membranes显示文摘 | Wind J D Sirard S M Paul D R | 2003 | Macromolecules2003，36，17： | 1 |
| 6 | An environmentally relevant mixture of organochlorines, their metabolites and effects on preimplantation development of porcine embryos显示文摘 | Campagna C Ayotte P Sirard MA | 2008 | Reprod Toxicol2008，25，3： | 1 |
| 7 | A eell initiating human acute myeloid leukaemia after transplantation into SCID mice 显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，： | 1 |
| 8 | A cell initiating human acute myeloid leukaemia after transplantation into SCID mice显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，： | 1 |
| 9 | 显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，： | 1 |
| 10 | Live attenuated salmonella:a paradigm of mucosal vaccines显示文摘 | Sirard JC Niedergang F Kraehenbuhl JP | 1999 | Immunol Rev1999，171，： | 1 |
| 11 | Effect of eycloheximide,6-DMAP,roscovitine and butyrolactone I on resumption of meiosis in porcine oocytes显示文摘 | Beux G L Richard F J Sirard M A | 2003 | Theriogenology2003，60，6： | 1 |
| 12 | Cumulus cell gene expression following the LH surge in bovine preovulatory follicles:potential early markers of oocyte competence 显示文摘 | Assidi M Dieleman SJ Sirard MA | 2010 | Reproduction2010，140，： | 1 |
| 13 | Carbon dioxide-induced plasticization of polyimide membranes: pseudo-equilibrium relationships of diffusion, sorption, and swelling显示文摘 | Wind J D Sirard S M Paul D R | 2003 | Macromolecules2003，36，17： | 1 |
| 14 | Relationships between en ergy balance knowledge and the home environment 显示文摘 | Slater M E Sirard J R Laska M N | 2011 | J Am Diet Assoc2011，111，4： | 1 |
| 15 | A cell initiating human acute myeloid leukaemia after transplantation into SCID mice 显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，6464： | 1 |
| 16 | Birth of caves after in vitro fertilization using laparoscope and rabbit oviduct incubation of zygotes显示文摘 | Sirard MA | 1986 | Vet Res1986，119，： | 1 |
| 17 | A cell initiating human acute myeloid leukemia after transplantation into SCID mice 显示文摘 | Lapidot T Sirard C Vormoor J | 1994 | Nature1994，367，6464： | 1 |
| 18 | Direct neural fate specification from embryonic stem cells: a primitive mammalian neural stem cell stage acquired through a default mechanism显示文摘 | Tropepe V Hitoshi S Sirard C | 2001 | Neuron2001，30，1： | 1 |
| 19 | In vitro inhibition of oocyte nuclear maturation in the bovine显示文摘 | SIRARD M A LAMBERT R D | 1988 | Biol Reprod1988，39，： | 1 |
| 20 | Temporal expression of factors involved in chromatin remodeling and in gene regulation during early bovine in vitro embryo development 显示文摘 | MCGRAW S VIGNEAULT C SIRARD M A | 2007 | Reproduction2007，133，3： | 1 |
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