Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle
Rumen acidosis is a widespread digestive disorder in livestock, causing inflammation and lowering animal performance. Unraveling its molecular mechanisms is vital for improving cattle health and welfare. Circular RNAs (circRNAs) are noncoding RNAs functioning as miRNA or protein sponges. This study...
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2025-05-01
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| author | Saeid Neysi Jamal Fayazi Hedayatollah Roshanfekr Ikhide G. Imumorin |
| author_facet | Saeid Neysi Jamal Fayazi Hedayatollah Roshanfekr Ikhide G. Imumorin |
| author_sort | Saeid Neysi |
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| description | Rumen acidosis is a widespread digestive disorder in livestock, causing inflammation and lowering animal performance. Unraveling its molecular mechanisms is vital for improving cattle health and welfare. Circular RNAs (circRNAs) are noncoding RNAs functioning as miRNA or protein sponges. This study employed high-throughput RNA sequencing to identify differentially expressed (DE) circRNAs in subacute rumen acidosis (SARA) in Holstein cattle, revealing 65 DE-circRNAs. We constructed a competitive endogenous RNA (ceRNA) network comprising 57 circRNAs, 14 miRNAs, and 22 mRNAs. Key hub nodes included circRNAs (8:69996068-69996853, 16:2614111-2615445, 5:109525933-109531380, 20:63115665-63116774), miRNAs (bta-miR-146b, bta-miR-181a, bta-miR-223, bta-miR-130b), and mRNAs (SLC2A3, SOCS3, DLC1, ARRDC4). Examination of hub circRNA host genes identified 30 DE transcription factors (TFs). Functional and pathway enrichment analysis pinpointed inflammation and immune response pathways, such as NF-kappa B and TNF signaling. This pioneering study offers the first circRNA expression profile and ceRNA network in SARA cattle, indicating circRNAs’ role in inflammation regulation, thus enhancing our understanding of SARA’s systems biology and potential treatment strategies. |
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| id | doaj-art-af561921795b45b2bf1e29f01f910f03 |
| institution | Kabale University |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-05-01 |
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| spelling | doaj-art-af561921795b45b2bf1e29f01f910f032025-08-20T03:47:52ZengMDPI AGAnimals2076-26152025-05-011510147210.3390/ani15101472Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein CattleSaeid Neysi0Jamal Fayazi1Hedayatollah Roshanfekr2Ikhide G. Imumorin3Department of Animal Science, Agricultural Sciences and Natural Resources, University of Khuzestan, Ahvaz 6341773637, IranDepartment of Animal Science, Agricultural Sciences and Natural Resources, University of Khuzestan, Ahvaz 6341773637, IranDepartment of Animal Science, Agricultural Sciences and Natural Resources, University of Khuzestan, Ahvaz 6341773637, IranCalifornia State University Biotechnology Program (CSUBIOTECH), College of Science, San Diego State University, San Diego, CA 92182-0001, USARumen acidosis is a widespread digestive disorder in livestock, causing inflammation and lowering animal performance. Unraveling its molecular mechanisms is vital for improving cattle health and welfare. Circular RNAs (circRNAs) are noncoding RNAs functioning as miRNA or protein sponges. This study employed high-throughput RNA sequencing to identify differentially expressed (DE) circRNAs in subacute rumen acidosis (SARA) in Holstein cattle, revealing 65 DE-circRNAs. We constructed a competitive endogenous RNA (ceRNA) network comprising 57 circRNAs, 14 miRNAs, and 22 mRNAs. Key hub nodes included circRNAs (8:69996068-69996853, 16:2614111-2615445, 5:109525933-109531380, 20:63115665-63116774), miRNAs (bta-miR-146b, bta-miR-181a, bta-miR-223, bta-miR-130b), and mRNAs (SLC2A3, SOCS3, DLC1, ARRDC4). Examination of hub circRNA host genes identified 30 DE transcription factors (TFs). Functional and pathway enrichment analysis pinpointed inflammation and immune response pathways, such as NF-kappa B and TNF signaling. This pioneering study offers the first circRNA expression profile and ceRNA network in SARA cattle, indicating circRNAs’ role in inflammation regulation, thus enhancing our understanding of SARA’s systems biology and potential treatment strategies.https://www.mdpi.com/2076-2615/15/10/1472RNA sequencingmiRNAtranscription factorsinflammation pathwaysSARA |
| spellingShingle | Saeid Neysi Jamal Fayazi Hedayatollah Roshanfekr Ikhide G. Imumorin Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle Animals RNA sequencing miRNA transcription factors inflammation pathways SARA |
| title | Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle |
| title_full | Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle |
| title_fullStr | Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle |
| title_full_unstemmed | Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle |
| title_short | Preliminary Study of Differential circRNA Expression and Investigation of circRNA–miRNA–mRNA Competitive Endogenous Network in Rumen Acidosis of Holstein Cattle |
| title_sort | preliminary study of differential circrna expression and investigation of circrna mirna mrna competitive endogenous network in rumen acidosis of holstein cattle |
| topic | RNA sequencing miRNA transcription factors inflammation pathways SARA |
| url | https://www.mdpi.com/2076-2615/15/10/1472 |
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