TY - JOUR

T1 - Utilizing high-resolution ribosome profiling for the global investigation of gene expression in Chlamydomonas

AU - Gotsmann, Vincent Leon

AU - Ting, Michael Kien Yin

AU - Haase, Nadin

AU - Rudorf, Sophia

AU - Zoschke, Reimo

AU - Willmund, Felix

N1 - Funding information: This work was supported by the Deutsche Forschungsgemeinschaft grant 437345987 (WI 3477/3-1, ZO 302/5-1, RU 2266/2-1 to F.W., R.Z. and S.R., respectively) and the Forschungsschwerpunkt BioComp to F.W.

PY - 2024/2/26

Y1 - 2024/2/26

N2 - Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5′ and 3′ sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.

AB - Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression. Extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq yields genome-wide insight into translational dynamics and post-transcriptional control of gene expression. Here, we provide details on the Ribo-seq method and the subsequent analysis with the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas) for generating high-resolution data covering more than 10 000 different transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5′ and 3′ sections of transcripts and characteristics of eukaryotic translation termination, which are fundamentally distinct for chloroplast translation. In chloroplasts, a heterogeneous RPF size distribution along the coding sequence indicates specific regulatory phases during protein synthesis. For example, local accumulation of small RPFs correlates with local slowdown of psbA translation, possibly uncovering an uncharacterized regulatory step during PsbA/D1 synthesis. Further analyses of RPF distribution along specific cytosolic transcripts revealed characteristic patterns of translation elongation exemplified for the major light-harvesting complex proteins, LHCs. By providing high-quality datasets for all subcellular genomes and attaching our data to the Chlamydomonas reference genome, we aim to make ribosome profiles easily accessible for the broad research community. The data can be browsed without advanced bioinformatic background knowledge for translation output levels of specific genes and their splice variants and for monitoring genome annotation.

KW - Chlamydomonas reinhardtii

KW - next-generation sequencing

KW - protein synthesis

KW - ribosome profiling

KW - ribosomes

KW - transcript accumulation

KW - translation

UR - http://www.scopus.com/inward/record.url?scp=85178433527&partnerID=8YFLogxK

U2 - 10.1111/tpj.16577

DO - 10.1111/tpj.16577

M3 - Article

AN - SCOPUS:85178433527

VL - 117

SP - 1614

EP - 1634

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 5

ER -