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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Related Experiment Video

Updated: Jun 14, 2025

Investigating Tissue- and Organ-specific Phytochrome Responses using FACS-assisted Cell-type Specific Expression Profiling in Arabidopsis thaliana
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Transcriptional Modulation during Photomorphogenesis in Rice Seedlings.

Parul Gupta1, Pankaj Jaiswal1

  • 1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.

Genes
|August 29, 2024
PubMed
Summary
This summary is machine-generated.

Light significantly impacts rice gene expression and splicing. This study reveals light-induced changes in protein-coding genes and novel long noncoding RNAs (lncRNAs), particularly affecting the MEP pathway crucial for chloroplast development.

Keywords:
MVA and MEP pathwaysRNA-Seqalternative splicingcircadian clocklncRNAphotomorphogenesisricetranscriptome

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Area of Science:

  • Plant molecular biology
  • Transcriptomics
  • Plant development

Background:

  • Light is a critical regulator of plant gene expression, metabolism, and development.
  • Understanding light's role in transcript splicing is essential for plant science.

Purpose of the Study:

  • To investigate light-induced alterations in gene expression and alternative splicing in rice.
  • To identify differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs).
  • To associate these changes with specific biological pathways.

Main Methods:

  • RNA-Seq-based transcriptome analysis comparing etiolated (dark-grown) and green (light-treated) rice seedlings.
  • Differential gene expression analysis.
  • Alternative splicing event detection.
  • Identification of novel long noncoding RNAs (lncRNAs).

Main Results:

  • Identified 14,766 differentially expressed genes, with 4369 exhibiting alternative splicing.
  • Observed light-upregulation of genes in the plastid-localized methyl-erythritol-phosphate (MEP) pathway compared to cytosolic mevalonate (MVA) pathway genes.
  • Intron retention was the most common light-induced splicing event, and 1709 novel lncRNA transcripts were discovered.

Conclusions:

  • Light significantly influences gene expression and alternative splicing in rice.
  • The MEP pathway is crucial for light-induced chloroplast biogenesis and photomorphogenesis.
  • This research provides valuable insights into light-regulated transcriptomics and splicing in rice.