A minigene is a minimal gene fragment that includes an exon and the control regions necessary for the gene to express itself in the same way as a wild type gene fragment. This is a minigene in its most basic sense. More complex minigenes can be constructed containing multiple exons and intron(s). Minigenes provide a valuable tool for researchers evaluating splicing patterns both in vivo and in vitro biochemically assessed experiments. Specifically, minigenes are used as splice reporter vectors  and act as a probe to determine which factors are important in splicing outcomes. They can be constructed to test the way both cis-regulatory elements (RNA effects) and trans-regulatory elements (associated proteins/splicing factors) affect gene expression.

TYPES

In order to provide a good minigene model, the gene fragment should have all of the necessary elements to ensure it exhibits the same alternative splicing (AS) patterns as the wild type gene, i.e., the length of the fragment must include all upstream and downstream sequences which can affect its splicing. Therefore, most minigene designs begin with a thorough in silico analysis of the requirements of the experiment before any "wet" lab work is conducted.With the advent of Bioinformatics and widespread use of computers, several good programs now exist for the identification of cis-acting control regions that affect the splicing outcomes of a gene and advanced programs can even consider splicing outcomes in various tissue types. Differences in minigenes are usually reflected in the final size of the fragment, which is in turn a reflection of the complexity of the minigene itself. The number of foreign DNA elements (exon and introns) inserted into the constitutive exons and introns of a given fragment varies with the type of experiment and the information being sought

USES

RNA splicing errors have been estimated to occur in a third of genetic diseases. To understand pathogenesis and identify potential targets of therapeutic intervention in these diseases, explicating the splicing elements involved is essential. Determining the complete set of components involved in splicing presents many challenges due to the abundance of alternative splicing, which occurs in most human genes, and the specificity in which splicing is carried out in vivo.Splicing is distinctly conducted from cell type to cell type and across different stages of cellular development.

Endocrine diseases

RNA splicing errors can have drastic effects on how proteins function, including the hormones secreted by the endocrine system. These effects on hormones have been identified as the cause of many endocrine disorders including thyroid-related pathological conditions, rickets, hyperinsulinemic hypoglycemia and congenital adrenal hyperplasia.

Neurodegenerative diseases

Accumulation of tau protein is associated with neurodegenerative diseases including Alzheimer's and Parkinson's diseases as well as other tauopathies. Tau protein isoforms are created by alternative splicing of exons 2, 3 and 10. The regulation of tau splicing is specific to stage of development, physiology and location. Errors in tau splicing can occur in both exons and introns and, depending on the error, result in changes to protein structure or loss of function. Aggregation of these abnormal tau proteins correlates directly with pathogenesis and disease progression. Minigenes have been used by several researchers to help understand the regulatory components responsible for mRNA splicing of the TAU gene.

Cancer

Cancer is a complex, heterogeneous disease that can be hereditary or the result of environmental stimuli. Minigenes are used to help oncologists understand the roles pre-mRNA splicing plays in different cancer types. Of particular interest are cancer specific genetic mutations that disrupt normal splicing events, including those affecting spliceosome components and RNA-binding proteins such as heterogeneous nuclear ribonucleoparticules (hnRNP), serine/arginine-rich (SR) proteins and small ribonucleoproteins (snRNP).