Physical Genome Mapping
Physical Genome Mapping - Related Videos
08:48
High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization
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Cited by 5 •
2012
Genome assemblies based on massively parallel DNA sequencing technologies are usually highly fragmented. The development of physical chromosome maps can potentially improve genome assemblies. Here, we demonstrate innovative approaches to chromosome preparation, fluorescent in situ hybridization, and imaging that significantly increase throughput of the physical map development.
09:31
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Cited by 56 •
2016
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
10:43
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae
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Cited by 11 •
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.
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.
10:05
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).
FAQs
Landmarks convert chromosome structure into trackable positions. Restriction sites, sequence-tagged sites, and cloned DNA fragments provide reference points that can be compared across overlapping regions. By determining how these landmarks align, researchers order DNA segments and relate sequence data to chromosome structure, making the map useful for anchoring genomic information rather than treating each fragment as an isolated piece.
Overlapping fragments provide the evidence needed to reconstruct the larger arrangement of DNA. Shared regions connect individual cloned fragments, allowing researchers to place them in an ordered series and preserve their relationships along a chromosome. This organization supports genome assembly because sequence information can be interpreted within a larger structural framework instead of as disconnected fragment data.
Distances expressed in base pairs add quantitative information to the order of landmarks and fragments. The map can therefore show not only which regions occur next to one another, but also their estimated spacing along a chromosome. This positional detail helps anchor sequence data, locate genes within chromosome structure, and compare the arrangement of corresponding regions across organisms.
Construction begins by identifying usable landmarks or cloned DNA fragments, such as restriction sites, sequence-tagged sites, and overlapping clones. Researchers then compare the fragments, determine their overlaps, order them along the chromosome, and estimate the distances between mapped positions in base pairs. The resulting arrangement provides a structural reference for interpreting sequence information and chromosome organization.
A physical map gives sequencing projects an organized framework for placing sequence data along chromosomes. Ordered fragments and landmarks help anchor separate sequence pieces to defined chromosome positions, which is especially valuable when repetitive or poorly assembled regions make direct reconstruction difficult. The map therefore links sequence information with larger-scale chromosome structure during genome analysis.
In biology, researchers use physical maps to support gene-location studies, disease gene investigations, and analysis of structural variation. The maps also enable comparisons of chromosome structure across organisms by providing positional relationships among DNA regions. These applications make the approach useful not only for genome assembly, but also for studying how chromosome organization relates to genes and genomic differences.