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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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Inheritance of Chromatin Structures03:17

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Heterochromatin

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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Updated: Apr 23, 2026

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms.

Hongde Liu1, Jinchen Zhai, Kun Luo

  • 1State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. liuhongde@seu.edu.cn.

BMC Molecular Biology
|October 6, 2014
PubMed
Summary
This summary is machine-generated.

Chromatin organization varies around single nucleotide polymorphisms (SNPs) based on their genomic location. Newly occurring mutations are preferentially found near these SNPs, suggesting a link between mutation occurrence and chromatin structure.

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Previous research indicates nucleosomes are enriched with single nucleotide polymorphisms (SNPs) and mutations associate with CpG dinucleotides.
  • Understanding the relationship between chromatin organization and SNPs is crucial for deciphering mutation patterns.

Purpose of the Study:

  • To investigate if chromatin organization around SNPs is specific to the genomic locus.
  • To determine if newly occurring mutations are associated with SNPs and their surrounding chromatin structure.

Main Methods:

  • Classification of SNPs based on their genomic loci.
  • Investigation of chromatin organization in CD4+ T cells and lymphoblastoid cells.
  • Calculation of SNP frequency in proximity to somatic mutations.

Main Results:

  • Nucleosome occupancy differs around SNPs across various genomic loci.
  • Coding SNPs are enriched in nucleosomes with repressed histone modifications and DNA methylation.
  • Intron SNPs are found in nucleosome-depleted regions lacking histone modifications, while risk-associated non-coding SNPs show distinct epigenetic profiles.
  • A significantly low base-transversion allele frequency was observed in coding-synonymous SNPs.
  • SNP frequency was significantly higher at positions -1 and +1 relative to somatic mutation sites.

Conclusions:

  • Chromatin structure exhibits distinct patterns around coding versus non-coding SNPs.
  • New mutations show a tendency to occur immediately adjacent to SNPs at the -1 and +1 positions.