Related Experiment Video
Updated: Jun 7, 2026
09:12
Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
Published on: February 27, 2026
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome
Daniel P Riordan1, Daniel Herschlag, Patrick O Brown
1Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA. driordan@stanford.edu
Nucleic Acids Research
|October 21, 2010
Summary
Researchers decoded RNA-protein interactions by analyzing mRNA sequences bound by RNA-binding proteins (RBPs) in yeast. This study identified novel RNA motifs crucial for post-transcriptional gene regulation and evolutionary conservation.
Area of Science:
- Molecular Biology
- Genetics
- Bioinformatics
Background:
- Post-transcriptional gene regulation governs mRNA fate (localization, translation, decay) but remains largely uncharacterized.
- Specific RNA-binding proteins (RBPs) mediate these processes, analogous to transcription factors in DNA binding.
- Understanding mRNA sequence encoding of regulatory programs is crucial.
Purpose of the Study:
- To decode regulatory programs encoded within mRNA sequences by analyzing specific mRNA-protein interactions.
- To identify novel RNA motifs recognized by RBPs and understand their functional significance.
Main Methods:
- Computational analysis of Saccharomyces cerevisiae mRNA sequences bound in vivo by 29 RBPs.
- Biochemical selection assays to identify RNA sequences recognized by 12 yeast RBPs.
- Sequence motif identification and evolutionary conservation analysis.
Main Results:
- Identified eight novel candidate RNA motifs and confirmed/extended six known recognition elements.
- Discovered novel motifs for Pin4, Nsr1, Hrb1, Gbp2, Sgn1, and Mrn1, and recovered known elements for Puf3, She2, Vts1, and Whi3.
- Uncovered RNA elements associated with coherent mRNA expression changes and conserved in related yeasts.
Conclusions:
- The identified RNA motifs are functionally important and evolutionarily conserved.
- This work provides insights into the sequence-based encoding of post-transcriptional regulatory programs.
- Establishes a foundation for decoding complex mRNA-RBP interactions.
Related Concept Videos
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
01:29Translational Regulation
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
02:53Ribosomal RNA Synthesis
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...