3d Genome Organization
3d Genome Organization - Related Videos
13:55
Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
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Cited by 36 •
2013
Here we describe a protocol for simultaneous detection of histone modifications by immunofluorescence and DNA sequences by DNA FISH followed by 3D microscopy and analyses (3D immuno-DNA FISH).
11:09
Revealing the Cytoskeletal Organization of Invasive Cancer Cells in 3D
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Cited by 31 •
2013
This article presents a method to fluorescently label collagen that can be further used for both fix and live imaging of 3D cell cultures. We also provide an optimized protocol to visualize endogenous cytoskeletal proteins of cells cultured in 3D environments.
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.
09:51
Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms
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Cited by 45 •
2018
Utilizing a preassembled Cas9 ribonucleoprotein complex (RNP) is a powerful method for precise, efficient genome editing. Here, we highlight its utility across a broad range of cells and organisms, including primary human cells and both classic and emerging model organisms.
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
Loop formation can bring an enhancer and promoter into physical proximity even when they are separated along the linear DNA sequence. This arrangement creates a spatial opportunity for regulatory communication and helps connect genome architecture with transcription. Mapping such contacts therefore reveals how distant regulatory elements may coordinate gene activity within the nucleus.
Topologically associating domains organize nearby genomic regions into interaction neighborhoods, whereas compartments help separate broadly active and inactive chromatin. These structures provide different levels of spatial organization: domains constrain local contacts, while compartments distinguish larger functional environments. Examining both can clarify how genome folding relates to coordinated transcription and cellular identity.
Chromatin compaction changes how genomic regions are arranged within the nucleus and can influence their functional accessibility. Because genome architecture is linked with transcription, replication, and DNA repair, altered folding may affect more than gene expression alone. Studying compaction alongside loops, domains, and compartments gives genetics researchers a broader view of genome regulation.
Imaging approaches reveal the spatial positioning of genomic regions within the nucleus, while chromosome-conformation methods map physical interaction patterns between regions. Together, these strategies connect visible nuclear arrangement with contact-based measurements. Using both perspectives can help researchers interpret how loops, domains, compartments, and regulatory-element contacts contribute to genome function.
A study first selects an imaging or chromosome-conformation approach suited to the spatial question, then examines relationships among genomic regions and organizing features such as loops, domains, and compartments. Researchers interpret these patterns alongside transcription, replication, or repair questions. The resulting maps help connect nuclear structure with genetic regulation and cellular behavior.
This framework is useful when researchers need to understand how cells establish distinct identities or how regulatory architecture changes in disease. Mapping genome structure can expose altered relationships among chromatin regions and regulatory elements during development or in cancer. Such findings help relate disrupted chromatin structure to changes in genome function rather than viewing DNA sequence alone.