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

RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

9.1K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
9.1K
Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

6.9K
In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
6.9K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

862
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...
862
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

22.2K
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...
22.2K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

7.2K
Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.2K
Types of RNA01:20

Types of RNA

5.5K
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA Performs Diverse...
5.5K

You might also read

Related Articles

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

Sort by
Same author

Key challenges in communication across milestones of cancer care continuum: a systematic review.

BMC palliative care·2026
Same author

Patient-derived organoids reveal ductal dysfunction and CFTR-modulator responses in chronic pancreatitis.

Cell stem cell·2026
Same author

HDAC inhibition sensitizes pancreatic tumors to DNA damage by global redistribution of the transcriptional machinery.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Clinic-based Treatment of Type B Ulnar Polydactyly Saves Costs Compared With Treatment in the Operating Room.

Plastic and reconstructive surgery. Global open·2026
Same author

"Pinch Test" Facilitates Donor Sensory Nerve Selection Before Corneal Neurotization for Neurotrophic Keratopathy.

Cornea·2026
Same author

Structure of a dopamine-binding RNA aptamer reveals metal-mediated ligand recognition.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: May 21, 2025

Chromatin Isolation by RNA Purification ChIRP
11:09

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

86.0K

DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility.

Simone D Hall1, Khoa Tran1, Jonathan Zhu1

  • 1Department of Chemistry and Biochemistry, University of California San Diego, Urey Hall Room 6213, 9500 Gilman Drive MC 0314, La Jolla, CA, 92093, USA.

Functional & Integrative Genomics
|March 21, 2025
PubMed
Summary

The nuclear non-coding RNA DUBR regulates human colon cancer cell survival. It interacts with epigenetic proteins to control gene expression, impacting cancer progression and patient outcomes.

Keywords:
AP-1DUBRHCT116NuRD complexRAP-MS

More Related Videos

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture
10:34

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

Published on: July 22, 2016

23.5K
Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells
09:16

Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells

Published on: September 1, 2019

7.3K

Related Experiment Videos

Last Updated: May 21, 2025

Chromatin Isolation by RNA Purification ChIRP
11:09

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

86.0K
Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture
10:34

Detection of RNA-binding Proteins by In Vitro RNA Pull-down in Adipocyte Culture

Published on: July 22, 2016

23.5K
Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells
09:16

Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells

Published on: September 1, 2019

7.3K

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Cancer Research

Background:

  • Non-coding RNAs (ncRNAs) are crucial regulators of cellular processes, including cancer progression.
  • DUBR (Dppa2 upstream binding RNA), a nuclear ncRNA, is implicated in colon adenocarcinoma, with high expression linked to poor patient outcomes.
  • Its precise role in human colon cancer remains largely unelucidated.

Purpose of the Study:

  • To investigate the function of the nuclear ncRNA DUBR in human colon cancer cell line HCT116.
  • To identify DUBR's interacting partners and its regulatory mechanisms in cancer cells.
  • To determine DUBR's impact on cell survival, epigenome, and transcriptome.

Main Methods:

  • RNA immunoprecipitation and RNA-protein binding assays (RAP-MS) to identify interacting proteins.
  • ATAC-seq and RNA-seq to analyze epigenomic and transcriptomic changes.
  • Utilized the human colon cancer cell line HCT116 for experimental validation.

Main Results:

  • DUBR was identified to interact with epigenetic maintenance proteins, including NuRD complex members HDAC1 and CHD4.
  • DUBR regulates the accessibility of AP-1 transcription factor binding sites at enhancers.
  • These regulatory events influence genes involved in differentiation and morphogenesis, impacting HCT116 cell survival.

Conclusions:

  • DUBR functions as a critical regulator of human colon cancer cell survival.
  • DUBR exerts its function through interactions with epigenetic machinery, modulating enhancer activity and gene expression.
  • These findings highlight DUBR as a potential therapeutic target in colon adenocarcinoma.