Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

10.7K
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...
10.7K
Leaky Scanning02:28

Leaky Scanning

5.3K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.3K
Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

10.1K
Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
10.1K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

1.1K
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...
1.1K
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

11.0K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
11.0K
Initiation of Translation02:33

Initiation of Translation

35.2K
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
35.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the <i>Picornavirales</i>.

Virus evolution·2026
Same author

Mechanism of nucleolytic degradation of human ribosomes.

bioRxiv : the preprint server for biology·2026
Same author

The dynamics and strategy of RNA replication in astroviruses.

NAR molecular medicine·2026
Same author

The LARP1 RRM functions as a ribosome responsive regulator of TOP mRNAs.

bioRxiv : the preprint server for biology·2026
Same author

Mouse skeletal muscle satellite cells co-opt the tenogenic gene <i>Scleraxis</i> to instruct regeneration.

eLife·2026
Same author

Flexibility and modulation of translation initiation in enterovirus genomes.

PLoS pathogens·2026

Related Experiment Video

Updated: Oct 2, 2025

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

12.7K

Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency.

Ivaylo P Ivanov1, James A Saba2,3, Chen-Ming Fan4

  • 1Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892.

Proceedings of the National Academy of Sciences of the United States of America
|February 26, 2022
PubMed
Summary

This study reveals that upstream open reading frames (uORFs) in Hox mRNA leaders inhibit gene expression by affecting translation start site selection. Modulating eukaryotic translation initiation factors (eIFs) or ribosome homeostasis alters this stringency, impacting gene-specific expression.

Keywords:
Hox geneseIF1eIF5start codon selection stringencyuORF

More Related Videos

Xenopus laevis as a Model to Identify Translation Impairment
10:24

Xenopus laevis as a Model to Identify Translation Impairment

Published on: September 27, 2015

10.8K
An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides
09:58

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

Published on: November 29, 2016

16.0K

Related Experiment Videos

Last Updated: Oct 2, 2025

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
10:37

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs

Published on: May 10, 2018

12.7K
Xenopus laevis as a Model to Identify Translation Impairment
10:24

Xenopus laevis as a Model to Identify Translation Impairment

Published on: September 27, 2015

10.8K
An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides
09:58

An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides

Published on: November 29, 2016

16.0K

Area of Science:

  • Molecular Biology
  • Genetics
  • Gene Regulation

Background:

  • Translation start site selection in eukaryotes is governed by sequence context and translation initiation factors (eIFs).
  • Homeobox (Hox) genes play crucial roles in development, and their precise regulation is essential.

Purpose of the Study:

  • To investigate the role of upstream open reading frames (uORFs) and translation initiation factors in regulating Hox gene expression.
  • To analyze the 5' leaders of Hox mRNAs for conserved uORFs and their functional impact.

Main Methods:

  • Bioinformatic analysis of mammalian genes and cap analysis of gene expression (CAGE-seq) data.
  • Reporter assays to assess Hox gene expression modulated by uORFs and eIFs.
  • Manipulation of ribosome homeostasis via protein depletion or puromycin treatment.

Main Results:

  • Identified conserved uORFs in the 5' leaders of 13 Hox genes, often in suboptimal sequence contexts.
  • Demonstrated that these conserved uORFs inhibit Hox reporter gene expression.
  • Showed that altering levels of eIF1 or eIF5, or modifying ribosome homeostasis, modulates Hox reporter expression by affecting start codon selection stringency.

Conclusions:

  • Conserved uORFs in Hox mRNA 5' leaders act as regulatory elements that inhibit translation initiation.
  • Start codon selection stringency, influenced by eIFs and ribosome homeostasis, provides a mechanism for gene-specific regulation of Hox genes.
  • Global translation changes can lead to specific effects on gene expression through altered translation initiation.