Floxing
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In genetic engineering, floxing refers to the
insertion Insertion may refer to: *Insertion (anatomy), the point of a tendon or ligament onto the skeleton or other part of the body *Insertion (genetics), the addition of DNA into a genetic sequence *Insertion, several meanings in medicine, see ICD-10-PCS ...
of a
DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
sequence (which is then said to be floxed) between two ''
LoxP Cre-Lox recombination is a site-specific recombinase technology, used to carry out deletions, insertions, translocations and inversions at specific sites in the DNA of cells. It allows the DNA modification to be targeted to a specific cell type ...
'' sequences, creating an artificial
gene cassette In biology, a gene cassette is a type of mobile genetic element that contains a gene and a recombination site. Each cassette usually contains a single gene and tends to be very small; on the order of 500–1,000 base pairs. They may exist incorpor ...
which can then be conditionally deleted (knocked out), translocated, or inverted in a process called
Cre-Lox recombination Cre-Lox recombination is a site-specific recombinase technology, used to carry out deletions, insertions, translocations and inversions at specific sites in the DNA of cells. It allows the DNA modification to be targeted to a specific cell typ ...
. Recombination between LoxP sites is catalysed by
Cre recombinase Cre recombinase is a tyrosine recombinase enzyme derived from the P1 bacteriophage. The enzyme uses a topoisomerase I-like mechanism to carry out site specific recombination events. The enzyme (38 kDa) is a member of the integrase family of si ...
. The term "floxing" is a portmanteau constructed from the phrase "flanking/flanked by LoxP". The floxing method is essential in the development of scientific model systems as it allows researchers to have spatial and temporal alteration of gene expression. The Cre-Lox system is widely used to manipulate gene expression in model organisms such as mice in order to study human diseases and drug development. For example, using the Cre-Lox system, researchers are able to study
oncogene An oncogene is a gene that has the potential to cause cancer. In tumor cells, these genes are often mutated, or expressed at high levels.
s and
tumor suppressor A tumor suppressor gene (TSG), or anti-oncogene, is a gene that regulates a cell (biology), cell during cell division and replication. If the cell grows uncontrollably, it will result in cancer. When a tumor suppressor gene is mutated, it results ...
genes and their role in the development and progression of
cancer Cancer is a group of diseases involving Cell growth#Disorders, abnormal cell growth with the potential to Invasion (cancer), invade or Metastasis, spread to other parts of the body. These contrast with benign tumors, which do not spread. Po ...
in mouse models.


Uses in research

Floxing a gene allows it to be deleted (knocked out), translocated or inserted (through various mechanisms in Cre-Lox recombination). The floxing of genes is essential in the development of scientific model systems as it allows spatial and temporal alteration of gene expression. In layman's terms, the gene can be knocked-out (inactivated) in a specific tissue ''
in vivo Studies that are ''in vivo'' (Latin for "within the living"; often not italicized in English) are those in which the effects of various biological entities are tested on whole, living organisms or cells, usually animals, including humans, an ...
'', at a specific time chosen by the scientist. The scientist can then evaluate the effects of the knocked-out gene and identify the gene's normal function. This is different from having the gene absent starting from conception, whereby inactivation or loss of genes that are essential for the development of the organism may interfere with the normal function of cells and prevent the production of viable offspring.


Mechanism of deletion

Deletion events are useful for performing
gene editing Gene editing may refer to: *Genetic engineering of any organism by genome editing. Gene editing is the emerging molecular biology technique which makes very specific targeted changes by insertion, deletion or substitution of genetic material in an ...
experiments through precisely removing segments of or even whole genes. Deletion requires floxing of the segment of interest with loxP sites which face the same direction. The Cre recombinase will detect the unidirectional loxP sites and excise the floxed segment of DNA. The successfully edited clones can be selected using a selection marker which can be removed using the same Cre-LoxP system. The same mechanism can be used to create conditional alleles by introducing an FRT/Flp site which accomplishes the same mechanism but with a different enzyme.


Mechanism of inversion

Inversion events are useful for inactivating a gene or DNA sequence without actually removing it, and thereby maintaining a consistent amount of genetic material. The inverted genes are not often associated with abnormal
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...
s, meaning the inverted genes are generally viable. Cre-LoxP recombination that results in inversion requires loxP sites flanking the gene of interest, with the loxP sites oriented towards each other as
inverted repeats An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero ...
. By undergoing Cre recombination, the region flanked by the loxP sites will become inverted, i.e. re-inserted in the same position but in reverse orientation; this process is not permanent and can be reversed.  


Mechanism of translocation

Translocation events occur when the loxP sites flank genes on two different DNA molecules in a unidirectional orientation. Cre recombinase is then used to generate a translocation between the two DNA molecules, exchanging the genetic material from one DNA molecule to the other, forming a simultaneous translocation of both floxed genes.


Common applications in research

Cardiomyocytes Cardiac muscle (also called heart muscle or myocardium) is one of three types of vertebrate muscle tissues, the others being skeletal muscle and smooth muscle. It is an involuntary, striated muscle that constitutes the main tissue of the wall of ...
(heart muscle tissue) have been shown to express a type of Cre recombinase that is highly specific to cardiomyocytes and can be used by researchers to perform highly efficient recombinations. This is achieved by using a type of Cre whose expression is driven by the \alpha-myosin heavy chain promoter (\alpha-MyHC). These recombinations are capable of disrupting genes in a manner that is specific to heart tissue ''in vivo'' and allows for the creation of conditional knockouts of the heart, mostly for use as controls. For example, using the
Cre recombinase Cre recombinase is a tyrosine recombinase enzyme derived from the P1 bacteriophage. The enzyme uses a topoisomerase I-like mechanism to carry out site specific recombination events. The enzyme (38 kDa) is a member of the integrase family of si ...
with the \alpha-MyHC promoter causes the floxed gene to be inactivated in the heart alone. Further, these knockouts can be made inducible. In several mouse studies,
tamoxifen Tamoxifen, sold under the brand name Nolvadex among others, is a selective estrogen receptor modulator used to prevent breast cancer in women and men. It is also being studied for other types of cancer. It has been used for Albright syndrome ...
is used to induce the expression of
Cre recombinase Cre recombinase is a tyrosine recombinase enzyme derived from the P1 bacteriophage. The enzyme uses a topoisomerase I-like mechanism to carry out site specific recombination events. The enzyme (38 kDa) is a member of the integrase family of si ...
. In this case,
Cre recombinase Cre recombinase is a tyrosine recombinase enzyme derived from the P1 bacteriophage. The enzyme uses a topoisomerase I-like mechanism to carry out site specific recombination events. The enzyme (38 kDa) is a member of the integrase family of si ...
is fused to a portion of the mouse
estrogen receptor Estrogen receptors (ERs) are proteins found in cell (biology), cells that function as receptor (biochemistry), receptors for the hormone estrogen (17β-estradiol). There are two main classes of ERs. The first includes the intracellular estrogen ...
(ER) which contains a mutation within its ligand binding domain (LBD). The mutation renders the receptor inactive, which leads to incorrect localization through its interactions with chaperone proteins such as heat shock protein 70 and 90 (
Hsp70 The 70 kilodalton heat shock proteins (Hsp70s or DnaK) are a family of conserved ubiquitously expressed heat shock proteins. Proteins with similar structure exist in virtually all living organisms and play crucial roles in the development of can ...
and
Hsp90 Hsp90 (heat shock protein 90) is a chaperone (protein), chaperone protein that assists other proteins to protein folding, fold properly, stabilizes proteins against heat stress, and aids in protein degradation. It also stabilizes a number of ...
). Tamoxifen binds to Cre-ER and disrupts its interactions with the chaperones, which allows the Cre-ER fusion protein to enter the nucleus and perform recombination on the floxed gene. Additionally,
Cre recombinase Cre recombinase is a tyrosine recombinase enzyme derived from the P1 bacteriophage. The enzyme uses a topoisomerase I-like mechanism to carry out site specific recombination events. The enzyme (38 kDa) is a member of the integrase family of si ...
can be induced by heat when under the control of specific heat shock elements (HSEs).


References

{{reflist DNA Genetics techniques