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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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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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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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Translational Regulation01:29

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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,...
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Riboswitches01:56

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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A Reference-Free Algorithm Discovers Regulation in the Plant Transcriptome.

Elisabeth Meyer1,2, Evan V Saldivar3,4, Marek Kokot5

  • 1Department of Biochemistry Stanford University Stanford California USA.

Plant Direct
|April 13, 2026
PubMed
Summary
This summary is machine-generated.

We developed SPLASH, a novel algorithm for analyzing gene regulation without a reference genome. This method uncovered new insights into plant gene expression, including allelic variation and cryptic splicing in maize and Arabidopsis.

Keywords:
genomicsreference‐freetranscriptomics

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Most plant genomes and their regulatory mechanisms are not fully understood.
  • Analyzing gene expression and regulation typically requires a reference genome.

Purpose of the Study:

  • To introduce SPLASH, a new algorithm for detecting sequence variation.
  • To analyze transcriptional and post-transcriptional regulation using RNA-seq data without a reference genome.
  • To discover novel regulatory mechanisms in plants.

Main Methods:

  • Utilized SPLASH, a reference genome-free sequence variation detection algorithm.
  • Analyzed RNA-sequencing data to study gene regulation.
  • Applied the algorithm to maize and Arabidopsis datasets.

Main Results:

  • Discovered allelic variation in gene expression during maize pollen development.
  • Identified imbibition-dependent cryptic splicing in Arabidopsis seeds.
  • Demonstrated SPLASH's capability to reveal differential regulation of genes from parental haplotypes in hybrids.

Conclusions:

  • SPLASH enables the discovery of novel plant regulatory mechanisms.
  • The algorithm provides a powerful tool for studying gene regulation in species lacking reference genomes.
  • This approach advances our understanding of plant genomics and transcriptomics.