Time course RNA-seq differential expression analysis of wild type and Jumonji (atjmjd5) mutant of arabidopsis thaliana

Abstract

Next generation sequencing technologies coupled with bioinformatics tools has reduced the cost of generating vast amounts of biological count data while enabling researchers to sequence and study genomes. Ribonucleic acid-sequencing (RNA-Seq), provides quality reads for use in genomics studies such as quantification of gene expressions and isoform transcripts in a manner superior than conventional methods. In Arabidopsis thaliana the Circadian rhythm has been shown to influence biological processes such as hypocotyl growth, hormone and stress responses and flowering time. Jumonji C Domain containing 5 (AtJMJD5/JUMONJI30) is involved in the circadian rhythm in Arabidopsis thaliana by acting together with Timing of CAB Expression1 (TOC1) to positively control Circadian Clock-Associated1 (CCA1) as well as Late elongated Hypocotyl (LHY) expression. This suggests that AtJMJD5 could be a key clock gene and thus could affect expression of circadian regulated genes as well as other clock genes. This study aimed at establishing the relationship between AtJMJD5 and 30 other clock genes obtained from published data, thereafter, establish the effects of mutating AtJMJD5 by exploring the differentially expressed genes and finally determine which gene networks are affected after mutating AtJMJD5. Illumina reads were analyzed at 16 time points by comparing the Wild Type (WT) and AtJMJD5 mutant to obtain expression profiles and later used Fragment Per Kilobase of exon Per million fragments Mapped (FPKM) data to obtain differentially expressed genes and finally mined for gene networks affected by AtJMJD5 mutation by utilizing public databases. The results obtained from this study complement the known interactions between AtJMJD5 and TOC1, LHY and CCA1 and further improve our understanding of its relationship to other genes that are either positively or negatively co-expressed with AtJMJD5. Furthermore, these findings suggest that AtJMJD5 probably does not affect or rather has no direct relationship with some other clock related genes. Novel clock genes were also discovered from our co-expression analysis, namely; Cycling factor3, Clock regulated 4, Clock regulated 3, Clock regulated1, Cold Regulated gene 27 and one unknown gene with AGI number of AT3G54500. This study however, could not conclusively depict the effects of AtJMJD5 mutation on most clock genes and we suggest coupling our study with chip data to establish any direct binding between AtJMJD5 and other co-expressed genes