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Annemarie Eckes-Shephard

Forskare

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Ribosome Profiling in the Model Diatom Thalassiosira pseudonana

Författare

  • Monica Pichler
  • Andreas Meindl
  • Markus Romberger
  • Annemarie Eckes-Shephard
  • Carl Fredrik Nyberg-Brodda
  • Claudia Buhigas
  • Sergio Llaneza-Lago
  • Gerhard Lehmann
  • Amanda Hopes
  • Gunter Meister
  • Jan Medenbach
  • Thomas Mock
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Summary, in English

Diatoms are an important group of eukaryotic microalgae, which play key roles in marine biochemical cycling and possess significant biotechnological potential. Despite the importance of diatoms, their regulatory mechanisms of protein synthesis at the translational level remain largely unexplored. Here, we describe the detailed development of a ribosome profiling protocol to study translation in the model diatom Thalassiosira pseudonana, which can easily be adopted for other diatom species. To isolate and sequence ribosome-protected mRNA, total RNA was digested, and the ribosome-protected fragments were obtained by a combination of sucrose-cushion ultracentrifugation and polyacrylamide gel electrophoresis for size selection. To minimize rRNA contamination, a subtractive hybridization step using biotinylated oligos was employed. Subsequently, fragments were converted into sequencing libraries, enabling the global quantification and analysis of changes in protein synthesis in diatoms. The development of this novel ribosome profiling protocol represents a major expansion of the molecular toolbox available for diatoms and therefore has the potential to advance our understanding of the translational regulation in this important group of phytoplankton.

Avdelning/ar

  • Institutionen för naturgeografi och ekosystemvetenskap

Publiceringsår

2023-07-01

Språk

Engelska

Publikation/Tidskrift/Serie

Current protocols

Volym

3

Issue

7

Dokumenttyp

Artikel i tidskrift

Förlag

John Wiley & Sons Inc.

Ämne

  • Biochemistry and Molecular Biology

Nyckelord

  • diatoms
  • high-throughput sequencing
  • ribosome profiling
  • RNA
  • Thalassiosira pseudonana
  • translation

Status

Published

ISBN/ISSN/Övrigt

  • ISSN: 2691-1299