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Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.

Publication ,  Journal Article
Pastor, MM; Sakrikar, S; Rodriguez, DN; Schmid, AK
Published in: Biomolecules
May 2022

Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80-90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.

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Published In

Biomolecules

DOI

EISSN

2218-273X

ISSN

2218-273X

Publication Date

May 2022

Volume

12

Issue

5

Start / End Page

682

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA-Seq
  • RNA, Ribosomal
  • RNA, Messenger
  • Archaea
  • 3206 Medical biotechnology
  • 3102 Bioinformatics and computational biology
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology
 

Citation

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Pastor, M. M., Sakrikar, S., Rodriguez, D. N., & Schmid, A. K. (2022). Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. Biomolecules, 12(5), 682. https://doi.org/10.3390/biom12050682
Pastor, Mar Martinez, Saaz Sakrikar, Deyra N. Rodriguez, and Amy K. Schmid. “Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.Biomolecules 12, no. 5 (May 2022): 682. https://doi.org/10.3390/biom12050682.
Pastor MM, Sakrikar S, Rodriguez DN, Schmid AK. Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. Biomolecules. 2022 May;12(5):682.
Pastor, Mar Martinez, et al. “Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.Biomolecules, vol. 12, no. 5, May 2022, p. 682. Epmc, doi:10.3390/biom12050682.
Pastor MM, Sakrikar S, Rodriguez DN, Schmid AK. Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea. Biomolecules. 2022 May;12(5):682.

Published In

Biomolecules

DOI

EISSN

2218-273X

ISSN

2218-273X

Publication Date

May 2022

Volume

12

Issue

5

Start / End Page

682

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA-Seq
  • RNA, Ribosomal
  • RNA, Messenger
  • Archaea
  • 3206 Medical biotechnology
  • 3102 Bioinformatics and computational biology
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology