Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

Evolutionary Relationships through Genome Comparisons

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...

You might also read

Related Articles

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

Sort by

Same author

The dark genome in cardiovascular medicine.

European heart journal·2026

Same author

Widespread DNA off-targeting confounds RNA chromatin occupancy studies.

Nature biotechnology·2026

Same author

A microRNA generated via lysosomal processing of ribosomal RNA suppresses proinflammatory responses.

Life science alliance·2026

Same author

Direct roles of long non-coding RNAs in transcription activation.

Nature structural & molecular biology·2026

Same author

<i>EPB41L4A-AS1</i> long noncoding RNA acts in both <i>cis</i>- and <i>trans</i>-acting transcriptional regulation and controls nucleolar biology.

eLife·2026

Same author

The syntenic long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene.

PLoS genetics·2025

Search research articles

Related Experiment Video

Updated: Nov 21, 2025

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences.

Caroline Jane Ross¹, Aviv Rom¹, Amit Spinrad¹

¹Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel.

|January 12, 2021

Summary

LncLOOM identifies conserved functional elements in long noncoding RNA (lncRNA) genes across species. This computational framework aids in discovering important RNA motifs within the noncoding genome.

Keywords:

3′UTR CHASERR CHD2 Homology Integer linear programming Long noncoding RNA MicroRNA Molecular evolution OIP5-AS1

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Related Experiment Videos

Last Updated: Nov 21, 2025

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Animal genomes encode thousands of long noncoding RNA (lncRNA) genes, with a subset possessing crucial functions.
lncRNA functionality is often linked to short sequence elements acting as binding sites for regulatory molecules.
Evolutionary sequence divergence in lncRNAs hinders identification of conserved functional elements and prioritization for experimental study.

Purpose of the Study:

To introduce LncLOOM, a novel algorithmic framework for discovering and evaluating conserved short motifs in syntenic regions.
To address the challenge of identifying functional elements in lncRNAs across distantly related species.

Main Methods:

LncLOOM employs a graph-based representation of input sequences.
Utilizes integer linear programming for efficient comparison of large sequences and motif significance evaluation.
Applied to identify conserved motifs in lncRNAs and 3'UTRs across vertebrate species.

Main Results:

LncLOOM successfully identifies specific, biologically relevant motifs conserved across vertebrates and beyond.
Discovered novel functional RNA elements within the CHASERR lncRNA, essential for regulating CHD2 expression.
Demonstrated capability in finding conserved elements in both lncRNAs and 3'UTRs.

Conclusions:

LncLOOM is a powerful tool for discovering functionally relevant elements in the noncoding genome.
The framework is expected to be widely adopted for noncoding element discovery.
Facilitates identification of conserved regulatory elements in lncRNAs and other noncoding RNAs.