Genomic Interactions
Genomic Interactions - Related Videos
10:05
Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
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Cited by 5 •
2016
Identifying the direct targets of genome-targeting molecules remains a major challenge. To understand how DNA-binding molecules engage the genome, we developed a method that relies on crosslinking of small molecules to isolate chromatin (COSMIC).
08:31
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Cited by 2 •
2013
Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.
10:43
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
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Cited by 10 •
2017
We describe chromatin endogenous cleavage coupled with high-throughput sequencing (ChEC-seq), a chromatin immunoprecipitation (ChIP)-orthogonal method for mapping protein binding sites genome-wide with micrococcal nuclease (MNase) fusion proteins.
11:41
Mapping Mammalian 3D Genome Interactions with Micro-C-XL
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2023
A protocol for mapping the three-dimensional genome organization with nucleosome resolution using the genome-wide chromosome conformation capture method Micro-C-XL is presented here.
08:31
Genome Editing
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2023
A well-established technique for modifying specific sequences in the genome is gene targeting by homologous recombination, but this method can be laborious and only works in certain organisms. Recent advances have led to the development of “genome editing”, which works by inducing double-strand breaks in DNA using engineered nuclease enzymes guided to target genomic sites by either proteins or RNAs that recognize specific sequences. When a cell attempts to repair this damage, mutations can be...
FAQs
Enhancer-promoter contacts can connect a regulatory element with the gene whose expression it influences, even when the regions are separated across the genome. This relationship helps explain how regulatory information reaches target genes and why DNA sequence alone may not reveal the full basis of gene control. Mapping these contacts links genome organization with functional gene regulation.
Transcription-factor binding provides a protein-mediated connection to particular DNA regions, while chromatin looping brings separated genomic segments into a shared three-dimensional arrangement. Together, these mechanisms help organize communication among regulatory elements and genes. Their importance lies in showing that gene activity depends not only on linear DNA sequence, but also on how the genome is spatially arranged.
A sequence change may affect gene regulation through an interaction with a distant regulatory region rather than through a nearby gene alone. Genomic interaction analysis can therefore connect regulatory elements with their potential target genes and reveal effects that are not obvious from sequence location by itself. This perspective is especially useful when studying mutations associated with altered biological programs or disease.
Chromosome-conformation and related interaction-mapping assays are used to detect relationships among genomic regions and organize those relationships into interaction maps. Researchers can examine whether regulatory elements communicate with candidate target genes and assess contacts across distant parts of the genome. The resulting maps provide experimental evidence for studying three-dimensional genome organization and its relationship to gene expression.
An interaction map can identify connections between regulatory elements and genes, helping researchers propose which genes may be influenced by a particular genomic region. It also shows how distant regions participate in broader regulatory networks rather than acting as isolated sequence segments. These results support interpretation of genome-wide regulatory patterns and provide context for understanding functional consequences of genomic changes.
In genetics, these studies help investigate developmental programs, disease-associated mutations, and genome-wide effects that may remain hidden when researchers examine DNA sequence alone. By relating three-dimensional organization to regulatory communication, interaction maps can clarify how genetic changes influence gene expression. They therefore extend genetic analysis from identifying sequence differences to examining the regulatory relationships those differences may disrupt.