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Related Experiment Video

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Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Published on: August 5, 2020

Plant simple sequence repeats: distribution, variation, and effects on gene expression.

Natalya Sharopova¹

¹250 Biological Sciences Building, 1445 Gortner Avenue, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA. sharo002@umn.edu

|March 22, 2008

Summary

Simple sequence repeats (SSRs) in Arabidopsis and rice genes influence gene expression at multiple levels. These DNA elements may also play a role in protein evolution through variation control.

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Published on: June 24, 2021

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Simple sequence repeats (SSRs) are repetitive DNA sequences with potential regulatory roles.
Understanding SSR functions is crucial for deciphering gene regulation and evolution.

Purpose of the Study:

To investigate the genome-wide impact of SSRs on gene expression in Arabidopsis and rice.
To explore the potential mechanisms by which SSRs affect gene regulation.
To examine the role of SSR variation in protein evolution.

Main Methods:

Genome-wide analysis of SSRs in conjunction with gene functional annotations.
Integration of public gene expression data from Arabidopsis and rice.
Analysis of DNA methylation, histone acetylation, and transcript turnover data.
Comparative analysis of SSR distribution in Arabidopsis, maize, and rice genes.

Main Results:

Over 15,000 Arabidopsis and 16,000 rice SSRs were analyzed, suggesting SSRs affect hundreds of genes.
SSRs may influence gene expression at both transcriptional and posttranscriptional levels.
Certain functional gene groups are enriched with SSRs, sometimes containing similar non-homologous repeats.
SSR variation distribution indicates a potential two-level control mechanism contributing to protein evolution.

Conclusions:

SSRs are significant regulators of gene expression in plants.
SSRs contribute to gene regulation through epigenetic modifications and transcript dynamics.
SSR variation provides a mechanism for evolutionary adaptation and protein diversification.