Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase. (December 2016)

• Record Type: Journal Article
• Authors: Cho, Yoo-Bok; Lee, Eun; Cho, Suhyung; Kim, Tae; Park, Jin; Cho, Byung-Kwan
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 12
• Publication Date: 2016-12
• Subjects: Kluyveromyces marxianus -- Non-coding RNA -- Long antisense ncRNA -- RNA-seq -- Pervasive transcription -- Metabolism; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2474-z
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such asKluyveromyces marxianus that is widely used in the field of industrial biotechnology. Results In this study, we measured changes in transcriptome at three time points during the exponential growth phase ofK. marxianus by using strand-specific RNA-seq. We found that approximately 60 % of the transcriptome consists of ncRNAs transcribed from antisense and intergenic regions of the genome that were transcribed at lower levels than mRNA. In the transcriptome, a substantial number of long antisense ncRNAs (lancRNAs) are differentially expressed and enriched in carbohydrate and energy metabolism pathways. Furthermore, this enrichment is evolutionarily conserved, at least in yeast. Particularly, the mode of regulation of mRNA/lancRNA pairs is associated with mRNA transcription levels; the correlation between the pairs is positive at high mRNA transcriptional levels and negative at low levels. In addition, significant induction of mRNA and coverage of more than half of the mRNA sequence by a lancRNA strengthens the positive correlation between mRNA/lancRNA pairs. Conclusions Transcriptome sequencing ofK. marxianus in the exponential growth phase reveals pervasive transcription of ncRNAs with evolutionarily conserved functions. Studies of the mode of regulation of mRNA/lancRNA pairs suggest that induction of lancRNA may be associated with switch-like behavior of mRNA/lancRNA pairs and efficient regulation of the carbohydrate and energy metabolism pathways in the exponential growth phase ofK. marxianus being used in industrial applications.