Hypersensitive site
Encyclopedia
A hypersensitive site is a short region of chromatin
and is detected by its super sensitivity to cleavage by DNase I and other various nuclease
s (DNase II and micrococcal nuclease
s). In a hypersensitive site, the nucleosomal structure is not organized in the usual fashion, which results in a 100 fold increase in sensitivity to enzyme attack than in bulk chromatin
.
In DNA being transcribed, 5' hypersensitive sites appear before transcription begins, and the DNA sequences within the hypersensitive sites are required for gene expression
. Note: hypersensitive sites precede active promoters.
Hypersensitive sites are generated as a result of the binding of transcription factor
s that displace histone octamer
s.
They can also be located by indirect end labelling. A fragment of DNA is cut once at the hypersensitive site with DNase
and at another site with a restriction enzyme
. The distance from the known restriction site to the DNase cut is then measured to give the location.
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
and is detected by its super sensitivity to cleavage by DNase I and other various nuclease
Nuclease
A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase"....
s (DNase II and micrococcal nuclease
Micrococcal nuclease
Micrococcal Nuclease is an endo-exonuclease that preferentially digests single-stranded nucleic acids.The rate of cleavage is 30 times greater at the 5' side of A or T than at G or C and results in the production of mononucleotides and oligonucleotides with terminal 3'-phosphates...
s). In a hypersensitive site, the nucleosomal structure is not organized in the usual fashion, which results in a 100 fold increase in sensitivity to enzyme attack than in bulk chromatin
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
.
Location
Hypersensitive sites are found on every active gene, and many of these genes often have more than one hypersensitive site. Most often, hypersensitive sites are found only in chromatin of cells in which the associated gene is being expressed, and do not occur when the gene is inactive.In DNA being transcribed, 5' hypersensitive sites appear before transcription begins, and the DNA sequences within the hypersensitive sites are required for gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
. Note: hypersensitive sites precede active promoters.
Hypersensitive sites are generated as a result of the binding of transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s that displace histone octamer
Histone octamer
A histone octamer is an octamer of the histones found at the center of a nucleosome core particle. It consists of 2 copies of each of the four core histone proteins . The octamer assembles when a tetramer, containing two copies of both H3 and H4, complexes with two H2A/H2B dimers...
s.
They can also be located by indirect end labelling. A fragment of DNA is cut once at the hypersensitive site with DNase
Deoxyribonuclease
A deoxyribonuclease is any enzyme that catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone. Thus, deoxyribonucleases are one type of nuclease...
and at another site with a restriction enzyme
Restriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
. The distance from the known restriction site to the DNase cut is then measured to give the location.