An intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of noncoding DNA. Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function. It is one of the DNA sequences sometimes referred to as junk DNA, though it is only one phenomenon labeled such and in scientific studies today, the term is less used. Recently transcribed RNA from the DNA fragments in intergenic regions were known as "dark matter" or "dark matter transcripts".
According to the ENCODE project's study of the human genome, due to "both the expansion of genic regions by the discovery of new isoforms and the identification of novel intergenic transcripts, there has been a marked increase in the number of intergenic regions (from 32,481 to 60,250) due to their fragmentation and a decrease in their lengths (from 14,170 bp to 3,949 bp median length)"
Scientists have now artificially synthesized proteins from intergenic regions.
Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function. However, it has been known for a long time that these regions do contain functionally important elements such as promoters and enhancers. In particular, intergenic regions often contain enhancer DNA sequences, which can activate expression of discrete sets of genes over distances of several thousand base pairs. Changes in the proteins bound on enhancers reprogram gene expression and affect the cell phenotype.   Also intergenic regions may contain as yet unidentified genes such as noncoding RNAs. Though little is known about them, they are thought to have regulatory functions. In recent years the ENCODE project has been studying intergenic regions in humans in more detail. Statistical methods have been specifically developed to detect trait- or disease-associated regions located in intergenic region using whole genome sequencing data, including the sliding window procedure and dynamic window procedure.
Intergenic regions in organisms
- Promoter (biology)
- Noncoding DNA
- Repetitive DNA
- Regulator gene
- Whole genome sequencing
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