Elsevier

Genomics

Volume 111, Issue 3, May 2019, Pages 398-406
Genomics

Genome-wide analysis of long non-coding RNAs in Pichia pastoris during stress by RNA sequencing

https://doi.org/10.1016/j.ygeno.2018.02.016Get rights and content
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Highlights

  • 208 novel long non-coding RNAs were identified and analyzed.

  • The potential trans-target genes and cis-regulated genes of 39 differential lncRNAs were analyzed.

  • The differential expression of lncRNAs was validated by qRT-PCR.

  • The potential functions of three lncRNAs were evaluated by knockdown their expression.

Abstract

Long non-coding RNAs play significant roles in many biological processes. The roles of lncRNAs in Pichia pastoris remain unclear. In this work, we focused on the identification of lncRNAs in P. pastoris and exploration of their potential roles in stress response to PLA2 overexpression and methanol induction. By strand specific RNA sequencing, 208 novel long non-coding RNAs were identified and analyzed. Bioinformatic analysis showed potential trans-target genes and cis-regulated genes of 39 differential lncRNAs. Functional annotation and sequence motif analysis indicated that lncRNAs participate in pathways related to methanol degradation and production of the recombinant protein. The differential expression of lncRNAs was validated by qRT-PCR. Lastly, the potential functions of three lncRNAs were evaluated by knockdown of their expression and analysis of the expression levels of target genes. Our study identifies novel lncRNAs in P. pastoris induced during use as a bioreactor, facilitating future functional research.

Keywords

Pichia pastoris
Long non-coding RNA
RNA sequencing
Recombinant protein production
Methanol induction

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