Regulatory Motif Identification
Regulatory Motif Identification - Related Videos
07:55
Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
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Cited by 3 •
2011
A straight-forward and robust method to identify potential regulatory motifs in co-regulated genes is presented. SCOPE does not require any user parameters and returns motifs that represent excellent candidates for regulatory signals. The identification of such regulatory signals helps to understand the underlying biology.
14:28
Peptide-based Identification of Functional Motifs and their Binding Partners
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Cited by 2 •
2013
Techniques to dissect the mechanisms underlying the secretion of HIV-1 Nef in exosomes are described. Specific short peptides derived from Nef and protein transfection were exploited to determine the structure, function, and binding partners of Nef’s Secretion Modification Region. These procedures have general relevance in many mechanistic studies.
02:02
Cis-regulatory Sequences
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2020
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...
08:19
Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster
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Cited by 15 •
2011
Phenotypic variation for traits can result from mutations in cis-regulatory element (CRE) sequences that control gene expression patterns. Methods derived for use in Drosophila melanogaster can quantitatively compare the levels of spatial and temporal patterns of gene expression mediated by modified or naturally occurring CRE variants.
12:24
DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
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Cited by 10 •
2014
This video article describes an in vitro microarray based method to determine the gene targets and binding sites for two component system response regulators.
FAQs
Finding a motif in a sequence does not by itself show that a regulatory protein binds there or changes transcription. The pattern serves as a candidate site because its sequence matches a recurring motif model, but computational search alone cannot establish activity. Experimental assays can test protein binding and whether that interaction alters transcription.
Confidence improves when motif predictions agree with several independent signals. Conservation across genomic regions can support functional importance, while chromatin data can provide information about regulatory sequence context and expression data can connect the region to gene activity. Combining these evidence types produces a stronger regulatory model than relying on sequence matching alone.
The sequence being analyzed may be DNA or RNA, and the relevant binding molecule may be a transcription factor or another regulatory protein. This distinction matters because a recurring pattern is interpreted in relation to the type of sequence and the protein expected to recognize it. The resulting candidates can be examined within promoters, enhancers, or other regulatory elements.
A typical workflow begins by analyzing selected DNA or RNA sequences with a computational motif-search method. Researchers then compare candidate patterns across genomic regions to identify recurring or conserved regulatory signals. The resulting candidates can be evaluated alongside conservation, chromatin, and expression information, followed by experimental assays that test binding and effects on transcription.
Researchers can apply this approach when they need to connect noncoding sequences with gene regulation. It supports investigations of gene expression, development, disease-associated variants, and genome organization. By identifying candidate motifs within promoters, enhancers, and other regulatory regions, the method helps generate regulatory models that can be examined with additional biological and experimental evidence.
Experimental assays can determine whether an associated regulatory protein binds a predicted sequence and whether that interaction alters transcription. These results provide functional evidence that sequence analysis alone cannot supply. In combination with motif comparisons and genomic context, assay findings help distinguish plausible regulatory candidates from patterns that merely resemble known recurring sequences.