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Updated: Jun 21, 2026
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
Published on: March 7, 2018
Short-read sequencing technologies for transcriptional analyses.
Stacey A Simon1, Jixian Zhai, Raja Sekhar Nandety
1Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.
Annual Review of Plant Biology
|July 7, 2009
Summary
Recent DNA sequencing advances have revolutionized gene expression analysis, shifting from hybridization to sequencing methods. This enables deeper transcript discovery and new insights into RNA dynamics and chromatin effects in plants.
Area of Science:
- Genomics and Molecular Biology
- Plant Science
- Bioinformatics
Background:
- Technological advancements in DNA sequencing have rapidly evolved over the past five years.
- Traditional hybridization-based methods for gene expression analysis are increasingly being replaced by sequencing-based approaches.
- Next-generation sequencing technologies offer unprecedented depth and capabilities for genomic studies.
Purpose of the Study:
- To review the impact of recent DNA sequencing technologies on gene expression analysis, particularly in plant biology.
- To highlight the shift from hybridization to sequencing-based methods.
- To discuss new opportunities for understanding RNA dynamics and chromatin influences on gene expression.
Main Methods:
- Application of next-generation sequencing for quantitative, tag-based gene expression studies.
- Utilizing deep sequencing for de novo transcript discovery, replacing traditional expressed sequence tag (EST) sequencing.
- Analysis of RNA generation, stability, and decay.
- Investigating the impact of chromatin differences on gene expression.
Main Results:
- Sequencing-based approaches have become dominant in gene expression analysis.
- Deep sequencing facilitates comprehensive de novo transcript discovery.
- New insights into RNA metabolism and chromatin regulation of gene expression are emerging.
Conclusions:
- Technological advances in DNA sequencing are fundamentally transforming plant genomics and gene expression studies.
- The pace of discovery is accelerating, promising deeper understanding of plant genomes.
- These methods are broadly applicable, with implications extending to animal systems.
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