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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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Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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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.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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Riboswitches01:56

Riboswitches

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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.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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What is Gene Expression?01:36

What is Gene Expression?

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Master Transcription Regulators02:23

Master Transcription Regulators

6.9K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Alternative RNA Splicing02:18

Alternative RNA Splicing

21.1K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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Related Experiment Video

Updated: Jun 24, 2025

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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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, CA, 94305, USA.

Biorxiv : the Preprint Server for Biology
|June 3, 2024
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Summary
This summary is machine-generated.

We developed SPLASH, a novel algorithm for analyzing plant gene regulation without a reference genome. This method revealed new insights into maize pollen development and seed biology, uncovering previously unknown regulatory mechanisms.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Understanding plant genome regulation is crucial but challenging due to incomplete genomic data.
  • Existing methods often rely on reference genomes, limiting analysis in many species.

Purpose of the Study:

  • To introduce SPLASH, a new algorithm for reference-genome-free sequence variation detection.
  • To apply SPLASH to RNA-seq data for analyzing transcriptional and post-transcriptional regulation in plants.

Main Methods:

  • Utilized SPLASH, a novel algorithm designed for reference-genome-free analysis of sequence variations.
  • Applied SPLASH to RNA-sequencing data from maize and Arabidopsis.

Main Results:

  • Discovered differential homolog expression during maize pollen development.
  • Identified imbibition-dependent cryptic splicing in Arabidopsis seeds.
  • Demonstrated SPLASH's capability to detect differential regulation of genes from hybrid parental haplotypes.

Conclusions:

  • SPLASH enables the discovery of novel plant regulatory mechanisms without a reference genome.
  • The algorithm facilitates a deeper understanding of gene expression and regulation in diverse plant systems.