Transcriptome Analysis and Characterization of Long Non-Coding RNAs in Chicken Adipose Tissue

Boniface Muthuri Kimathi, Tennessee State University


Long non-coding RNAs (lncRNAs) are non-protein coding transcripts that are more than 200 nucleotides long. They lack an open reading frame of more than 100 amino acids and usually have one or two exons. Of all the transcripts from humans, approximately 2% code for proteins. Until recently, the non-coding transcripts were thought of as “junk DNA”. LncRNAs play crucial roles in transcriptional regulation of biological processes. The objective of this study was to identify and characterize lncRNAs from adipose tissue of chickens divergently selected for leanness from publicly available transcriptome data as well as in adipose tissue of chickens fed standard diet and high caloric diet. In total 1.39 billion paired-end sequence reads from adipose tissue of fat line (FL) and lean line (LL) were downloaded from National Center for Biotechnology Information’s (NCBI) SRA website. In addition, cDNA libraries were constructed from adipose tissue of chickens fed standard diet (SD) and high caloric diet (HC). Trim Galore which incorporates FastQc and cutadapt was used to analyze the quality of the reads and the high-quality reads were retained for further processing. HISAT2 was used to align the sequencing reads to the chicken reference genome and Cufflinks and CLC Genomics WorkBench software were used to assemble the transcripts and test for differential expression. Ingenuity Pathways Analysis (IPA®) was used to analyze the differentially expressed genes. The transcripts were then submitted to Flexible Extraction of long non-coding RNAs (FEELnc) software to distinguish non-coding from the coding transcripts. The filter module in FEELnc was used to remove all the protein-coding transcripts by comparing the transcripts to the nonredundant protein database, the codpot module was used to discriminate the long noncoding transcripts based on their size and protein-coding potential. A total of 472 putative lncRNAs from adipose tissue of the chicken selected for leanness were predicted. Of these, 276 were further classified as genic while 196 were classified as intergenic. For the SD and HC chicken, 483 lncRNA genes were predicted among which 202 genes were classified as intergenic and 281 genes as genic. The project adds to the database of chicken lncRNAs. A comparison between the expressions of lncRNAs will help in highlighting the specific lncRNAs that may have regulatory roles in adipogenesis. These will provide targets for further analysis into their mode of action. Differential expression analysis revealed over 2000 genes that were differentially expressed between the SD and HC chickens. Results from IPA suggested Oxidative phosphorylation, LXR/RXR activation, FXR/RXR activation, D-myo-inositol-5-phosphate Metabolism and Osteoarthritis Pathway as the Top canonical pathways. Molecular transport and lipid metabolism are reported as the functional groups with the highest number of differentially expressed genes under the molecular and cellular functions group.

Subject Area

Biology|Animal sciences|Molecular biology|Biochemistry|Physiology

Recommended Citation

Boniface Muthuri Kimathi, "Transcriptome Analysis and Characterization of Long Non-Coding RNAs in Chicken Adipose Tissue" (2020). ETD Collection for Tennessee State University. Paper AAI28154098.