title: Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.
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 as Kluyveromyces 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 of K. 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 of K. 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 of K. marxianus being used in industrial applications.
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. newman73@gmail.com.
authors.forename: Yoo-Bok
authors.initials: YB
authors.lastname: Cho
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. lej7510@kaist.ac.kr.
authors.forename: Eun Ju
authors.initials: EJ
authors.lastname: Lee
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. shcho95@gmail.com.
authors.forename: Suhyung
authors.initials: S
authors.lastname: Cho
authors.affiliation: Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea. ty76.kim@samsung.com.
authors.forename: Tae Yong
authors.initials: TY
authors.lastname: Kim
authors.affiliation: Biomaterials Lab., Samsung Advanced Institute of Technology (SAIT), 130 Samsung-ro, Yeongtong-gu, Suwon, 443-803, Republic of Korea. jh111.park@samsung.com.
authors.forename: Jin Hwan
authors.initials: JH
authors.lastname: Park
authors.affiliation: Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Republic of Korea. bcho@kaist.ac.kr.|Intelligent Synthetic Biology Center, Daejeon, 305-701, Republic of Korea. bcho@kaist.ac.kr.
authors.forename: Byung-Kwan
authors.initials: BK
authors.lastname: Cho
mesh_terms: D016373:DNA, Antisense / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D007716:Kluyveromyces / Q000235:genetics* / Q000254:growth & development; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D016373:DNA, Antisense; D021901:DNA, Intergenic; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated