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02:02Cis-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...
02:02Cis-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...
03:36Genome 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.
01:28Global Regulatory Systems
Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
02:54Evolutionary 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...
02:04Covalently Linked Protein Regulators
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
These groups modify specific amino acids in a protein.
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Related Experiment Video
Updated: Jul 10, 2026
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
Published on: May 31, 2011
A universal framework for regulatory element discovery across all genomes and data types.
Olivier Elemento1, Noam Slonim, Saeed Tavazoie
1Lewis-Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
Molecular Cell
|October 30, 2007
Summary
This study introduces a novel framework for identifying regulatory DNA and RNA motifs by analyzing gene expression data. The method offers high sensitivity and accuracy for discovering gene regulatory elements across diverse genomes.
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Published on: February 11, 2019
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Deciphering the noncoding regulatory genome is challenging.
- Existing methods for characterizing regulatory elements are limited.
- Gene expression data is abundant but lacks comprehensive regulatory element analysis.
Purpose of the Study:
- To develop a general framework for detecting regulatory DNA and RNA motifs.
- To provide a broadly applicable method for characterizing regulatory elements.
- To uncover the dynamics shaped by regulatory elements in gene expression.
Main Methods:
- Assessing mutual information between sequence and gene expression measurements.
- A general framework for motif discovery with minimal assumptions.
- Application across diverse data types and genomes.
Main Results:
- Exceptional sensitivity and near-zero false-positive rates in motif discovery.
- Identification of putative and established transcription-factor binding sites.
- Discovery of microRNA (miRNA) target sites.
- Revealed spatial configurations, co-occurrences, and context-dependent selection of motifs.
- Demonstrated the impact of posttranscriptional processes on eukaryotic transcriptomes.
Conclusions:
- The developed framework is a versatile tool for regulatory motif discovery.
- The approach enhances understanding of gene regulation across species.
- Highlights the complex interplay of DNA, RNA, and posttranscriptional regulation.