Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

Abstract

Background: Eimeria necatrix, the most highly pathogenic coccidian in chicken small intestines, can cause high morbidity and mortality in susceptible birds and devastating economic losses in poultry production, but the underlying molecular mechanisms in interaction between chicken and E. necatrix are not entirely revealed. Accumulating evidence shows that the long-non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are key regulators in various infectious diseases. However, the expression profiles and roles of these two non-coding RNAs (ncRNAs) during E. necatrix infection are still unclear. Methods: The expression profiles of mRNAs, lncRNAs and circRNAs in mid-segments of chicken small intestines at 108 h post-infection (pi) with E. necatrix were analyzed by using the RNA-seq technique. Results: After strict filtering of raw data, we putatively identified 49,183 mRNAs, 818 lncRNAs and 4153 circRNAs. The obtained lncRNAs were classified into four types, including 228 (27.87%) intergenic, 67 (8.19%) intronic, 166 (20.29%) anti-sense and 357 (43.64%) sense-overlapping lncRNAs; of these, 571 were found to be novel. Five types were also predicted for putative circRNAs, including 180 exonic, 54 intronic, 113 antisense, 109 intergenic and 3697 senseoverlapping circRNAs. Eimeria necatrix infection significantly altered the expression of 1543 mRNAs (707 upregulated and 836 downregulated), 95 lncRNAs (49 upregulated and 46 downregulated) and 13 circRNAs (9 upregulated and 4 downregulated). Target predictions revealed that 38 aberrantly expressed lncRNAs would cis-regulate 73 mRNAs, and 1453 mRNAs could be trans-regulated by 87 differentially regulated lncRNAs. Additionally, 109 potential sponging miRNAs were also identified for 9 circRNAs. GO and KEGG enrichment analysis of target mRNAs for lncRNAs, and sponging miRNA targets and source genes for circRNAs identified associations of both lncRNAs and circRNAs with host immune defense and pathogenesis during E. necatrix infection. Conclusions: To the best of our knowledge, the present study provides the first genome-wide analysis of mRNAs, lncRNAs and circRNAs in chicken small intestines infected with E. necatrix. The obtained data will offer novel clues for exploring the interaction mechanisms between chickens and Eimeria spp.

Comprehensive Analyses of circRNA Expression Profiles and Function Prediction in Chicken Cecums After Eimeria tenella Infection

“…(2020) reported that 27 differentially expressed circRNAs were involved in the immune response to infectious bursal infection in chickens. Fan et al. (2020) performed transcriptome sequencing on the small intestine tissues of chickens infected with E. necatrix .…”

Circular RNA ciRS-7 affects the propagation of Cryptosporidium parvum in HCT-8 cells by sponging miR-1270 to activate the NF-κB signaling pathway

“…In recent years, circRNAs, a novel RNA class, are being recognized to function in many kinds of physiological and pathological processes by regulating gene expression at the transcriptional and posttranscriptional levels [ 34 – 36 ]. Significantly aberrant expression of host circRNAs at the genome-wide level was also found during infections with a limited number of parasites [ 13 , 18 , 37 ], including Cryptosporidium [ 19 ]; however, the functions of these DE circRNAs are still unknown. In the present study, we performed microarray analysis of DE circRNAs in HCT-8 cells infected with the important zoonotic C. parvum and identified a total of 178 circRNAs (including 128 upregulated and 50 downregulated) that were abnormally expressed.…”

“…porcine endemic diarrhea virus, transmissible gastroenteritis virus), and parasites (e.g. Nosema ceranae , Toxoplasma gondii , Eimeria necatrix ) [ 13 – 18 ]. Using the RNA-seq technique without RNase R treatment, our group found 104 significantly differentially expressed circRNAs in tracheal tissues of chickens experimentally infected with C. baileyi .…”

Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System

“…One RNA sequence analysis of differentially expressed lncRNAs, circRNAs, and mRNAs has been performed in chicken small intestines during Eimeria necatrix infection. This RNA sequence analysis obtained 1543 DEmRNAs, 95 DElncRNAs, 13 DEcircRNAs [144]. Functional annotation for lncRNAs, miRNAs, and circRNAs were correlated with chicken host immune defense and pathogenesis during E. necatrix infection [144].…”

“…This RNA sequence analysis obtained 1543 DEmRNAs, 95 DElncRNAs, 13 DEcircRNAs [144]. Functional annotation for lncRNAs, miRNAs, and circRNAs were correlated with chicken host immune defense and pathogenesis during E. necatrix infection [144]. In addition, miRNA expression was compared between naturally or Eimeria maxima and Eimeria acervulina -infected Ross 308 broilers using RNA sequencing.…”