Jove
Visualize
Contact Us

Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

You might also read

Related Articles

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

Sort by
Same author

PanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets.

bioRxiv : the preprint server for biology·2026
Same author

Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.

HGG advances·2026
Same author

RFX6 expression is central to the development and function of the neuroendocrine compartments of the pancreas and intestine and strongly affects diabetes risk.

Diabetology international·2026
Same author

Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors.

bioRxiv : the preprint server for biology·2026
Same author

Genome writing and Targeted Delivery of the <i>NKX6-3/ANK1</i> gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs.

bioRxiv : the preprint server for biology·2026
Same author

Efferocytosis-induced metabolic shift in bone macrophages drives lactate production and modulates inflammation and osteoclastogenesis.

Frontiers in immunology·2025
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 Experiment Video

Updated: May 30, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

A computational method to search for DNA structural motifs in functional genomic elements.

Stephen C J Parker1, Aaron Harlap, Thomas D Tullius

  • 1Bioinformatics Program, Boston University, Boston, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 25, 2011
PubMed
Summary

Computational methods now help discover DNA motifs by analyzing sequence and structure. This study introduces a new approach to find DNA structural motifs, identifying one linked to the RLM1 transcription factor in yeast.

More Related Videos

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Related Experiment Videos

Last Updated: May 30, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
12:24

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • High-throughput DNA sequencing generates vast genomic data, necessitating advanced computational tools for motif discovery.
  • Traditional motif discovery algorithms focus on nucleotide sequence, overlooking DNA's structural recognition by proteins.
  • Proteins can bind DNA based on its three-dimensional shape, not just its linear sequence.

Purpose of the Study:

  • To develop a computational method for predicting local DNA structural profiles.
  • To identify common DNA structural motifs within genomic sequences.
  • To find a DNA structural motif associated with the transcription factor RLM1 in yeast.

Main Methods:

  • Developed a computational method to predict local structural profiles of DNA sequences.
  • Searched these profiles for common DNA structural motifs.
  • Applied the method to the Saccharomyces cerevisiae genome.

Main Results:

  • Successfully predicted local structural profiles for DNA sequences.
  • Identified a novel DNA structural motif within the yeast genome.
  • This motif is associated with the binding of the transcription factor RLM1.

Conclusions:

  • The developed method effectively identifies DNA structural motifs.
  • DNA structure plays a role in transcription factor binding, exemplified by RLM1.
  • This approach enhances motif discovery by incorporating structural information.