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.
Intergenic regions in organisms
- Tropp, Burton E. (2008). Molecular Biology: Genes to Proteins. Jones & Bartlett Learning. ISBN 9780763709167.
- van Bakel, H; Nislow, C; Blencowe, BJ; Hughes, TR (May 18, 2010). "Most "dark matter" transcripts are associated with known genes". PLOS Biology. 8 (5): e1000371. doi:10.1371/journal.pbio.1000371. PMC 2872640. PMID 20502517.
- Djebali S; Davis CA; Merkel A; et al. (September 2012). "Landscape of transcription in human cells". Nature. 489 (7414): 101–8. Bibcode:2012Natur.489..101D. doi:10.1038/nature11233. PMC 3684276. PMID 22955620.
- Dhar, P. K.; Thwin, C.; Tun, K.; Tsumoto, Y.; Maurer-Stroh, S.; Eisenhaber, F.; Surana, U. (2009). "Synthesizing non-natural parts from natural genomic template". Journal of Biological Engineering. 3: 2. doi:10.1186/1754-1611-3-2. PMC 2642765. PMID 19187561.
- Schmidt, SF (September 2015). "Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers". Genome Res. 25 (9): 1281–1294. doi:10.1101/gr.188300.114. PMC 4561488. PMID 26113076.
- Vlahopoulos, SA (August 2017). "Aberrant control of NF-κB in cancer permits transcriptional and phenotypic plasticity, to curtail dependence on host tissue: molecular mode". Cancer Biology & Medicine. 14 (3): 254–270. doi:10.20892/j.issn.2095-3941.2017.0029. PMC 5570602. PMID 28884042.
- Birney E; Stamatoyannopoulos JA; Dutta A; et al. (June 2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346.
- Dunham I; Kundaje A; Aldred SF; et al. (September 2012). "An integrated encyclopedia of DNA elements in the human genome". Nature. 489 (7414): 57–74. Bibcode:2012Natur.489...57T. doi:10.1038/nature11247. PMC 3439153. PMID 22955616.
- Francis, Warren (June 13, 2017). "Similar Ratios of Introns to Intergenic Sequence across Animal Genomes". Genome Biology and Evolution. 9 (6): 1582–1598. doi:10.1093/gbe/evx103. PMC 5534336. PMID 28633296.
- Gardner, Malcolm; Hall, N; Fung, E; White, O; Berriman, M; Hyman, RW; Carlton, JM; Pain, A; et al. (3 October 2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498–511. Bibcode:2002Natur.419..498G. doi:10.1038/nature01097. PMC 3836256. PMID 12368864.