ID4

ID4 is a protein coding gene. In humans, it encodes for the protein known as DNA-binding protein inhibitor ID-4.[5][6] This protein is known to be involved in the regulation of many cellular processes during both prenatal development and tumorigenesis. This is inclusive of embryonic cellular growth, senescence, cellular differentiation, apoptosis, and as an oncogene in angiogenesis.[7]

For the film which uses "ID4" as a marketing initialism, see Independence Day (1996 film).

ID4
Identifiers
Aliases	ID4, IDB4, bHLHb27, inhibitor of DNA binding 4, HLH protein
External IDs	OMIM: 600581 MGI: 99414 HomoloGene: 1186 GeneCards: ID4
Gene location (Human) Chr. Chromosome 6 (human)[1] Band 6p22.3 Start 19,837,370 bp[1] End 19,842,197 bp[1]
Gene location (Mouse) Chr. Chromosome 13 (mouse)[2] Band 13 A5|13 24.71 cM Start 48,261,228 bp[2] End 48,266,026 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • protein dimerization activity • GO:0001106 transcription corepressor activity • RNA polymerase II transcription factor binding • GO:0001948 protein binding • GO:0001200, GO:0001133, GO:0001201 DNA-binding transcription factor activity, RNA polymerase II-specific • GO:0001131, GO:0001151, GO:0001130, GO:0001204 DNA-binding transcription factor activity • transcription factor binding Cellular component • cytoplasm • cell nucleus Biological process • prostate gland stromal morphogenesis • negative regulation of fat cell differentiation • negative regulation of astrocyte differentiation • regulation of transcription, DNA-templated • negative regulation of neuron differentiation • central nervous system myelination • regulation of transcription from RNA polymerase II promoter • negative regulation of transcription from RNA polymerase II promoter • transcription, DNA-templated • seminal vesicle morphogenesis • cellular protein localization • brain development • positive regulation of gene expression • positive regulation of osteoblast differentiation • prostate gland epithelium morphogenesis • negative regulation of oligodendrocyte differentiation • circadian rhythm • positive regulation of cell proliferation • prostate gland morphogenesis • neuroblast proliferation • cerebral cortex neuron differentiation • cellular proliferation • negative regulation of transcription, DNA-templated • hippocampus development • fat cell differentiation • positive regulation of transcription from RNA polymerase II promoter • G1/S transition of mitotic cell cycle • neuron differentiation • negative regulation of DNA binding • regulation of cell cycle • osteoblast differentiation Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	3400	15904
Ensembl	ENSG00000172201	ENSMUSG00000021379
UniProt	P47928	P41139
RefSeq (mRNA)	NM_001546	NM_031166
RefSeq (protein)	NP_001537	NP_112443
Location (UCSC)	Chr 6: 19.84 – 19.84 Mb	Chr 13: 48.26 – 48.27 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

Structure

The gene spans 3.3kb on the plus strand. It is composed of 3 exons and during transcription its mRNA is 2343 bp. The encoded protein consists of 161 amino acids, is 16.6 KDa and contains a poly-Ala segment from amino acid 39 to 48, a helix-loop-helix motif from amino acid 65 to 105 and a poly-Pro region from amino acid 118 to 124. This protein is expressed in various tissues.[7]

Function

The ID4 gene is part of the ID gene family. This family is also known as inhibitors of DNA binding protein family and are composed of transcription inhibitory proteins which modulate a number of processes. They are transcriptional regulators that work by negatively regulating their basic helix-loop-helix (bHLH) transcription factors by forming heterodimers. The heterodimer is what inhibits their DNA binding and transcriptional activity.

Transcription factors containing a basic helix-loop-helix (bHLH) motif regulate expression of tissue-specific genes in a number of mammalian and insect systems. DNA-binding activity of the bHLH proteins is dependent on formation of homo- and/or heterodimers. Dominant-negative (antimorph) HLH proteins encoded by Id-related genes, such as ID4, also contain the HLH-dimerization domain but lack the DNA-binding basic domain. Consequently, ID proteins inhibit binding to DNA and transcriptional transactivation by heterodimerization with bHLH proteins.[6]

Regulation during embryogenesis

The ID4 gene plays a pivotal role in development and is a key player in many pathways of embryogenesis and foetal development. ID4 expression is upregulated in embryogenesis during days 9.5 and 13.5 of gestation [8] and restricted to specific cells of the central and peripheral nervous system.[9] ID4 transcription control has both negative and positive regulatory elements inclusive of novel inhibitory functions.[10]

ID4 expression has been shown to be discrete in the early stages, with transcription transiently expressed in subsets of migrating neural crest cells, the dorsal myocardium, the segmental plate mesoderm, and the tail bud. Later stages show ID4 expression in the telencephalic vesicles and corneal epithelium.[11] ID4 expression is only detected in neuronal tissues and the ventral portion of the epithelium in the developing stomach during embryogenesis.[12]

ID4 is expressed in the central nervous system and is required for G1-S transition and to enhance proliferation in early cortical progenitors. It is complexly involved in regulating neural stem cell proliferation and differentiation by inhibiting proliferation of differentiating neurons through enhancement of RB1-mediated pathways. This is either by direct interaction or through interaction with other molecules of the cell cycle machinery.[13] ID4 also regulates the lateral expansion of the proliferative zone in the developing cortex and hippocampus. This is integral to normal brain size formation. ID4 regulates neural progenitor proliferation and differentiation.[13] Its expression is seen in the neural tube much later than other ID genes.[11]

ID4 was also shown to be involved in the regulation of cardiac mesoderm function in frog embryos and human embryonic stem cells. Ablation of the ID gene family mouse embryos showed failure of anterior cardiac progenitor specification and the development of heartless embryos. This study also demonstrated that ID4 protein is involved in the regulating cardiac cell fate by a pathway which represses two inhibitors of cardiogenic mesoderm formation (TCF3 and FOXA2) whilst activating inducers (EVX1, GRRP1, and MESP1).[14]

Clinical significance

Role in endometriosis

ID4 has been linked to the molecular pathogenicity of endometriosis. These pathways are still poorly understood. It is thought that ID4 plays a role in the transcription of HOXA9 and CDKN1A which are known to be associated with endometriosis.

A genome wide association study revealed over 100 candidate genes associated with endometriosis. Of these, six were shown to have a highly reliable association, of which the ID4 gene was identified. This is thought to be due to an independent single nucleotide polymorphism at loci rs7739264 near ID4 on chromosome 6p22.3. ID4 is implicated in the molecular pathogenicity of endometriosis as being differentially expressed between the proliferative, early and mid-secretory phases.[15]

Tumorigenesis association

ID4 is not expressed in normal ovary and fallopian tubes. It has been shown to be overexpressed in most primary ovarian cancers. The ID4 gene is also seen to be overexpressed in most ovarian, endometrial and breast cancer cell lines.[16] The mechanism behind this is believed to be that ID4 regulates HOXA9 and CDKN1A genes, which are mediators of cell proliferation and differentiation. HOXA genes are known to play a role in the differentiation of fallopian tubes, uterus, cervix and vagina.[17]

In B-Cell (B lymphocyte) acute lymphoblastic leukaemia (B-ALL), ID4 is overexpressed due to being located in close proximity to the IgH enhancer region.[18][19]

In Non Hodgkin lymphoma, the ID4 promoter region is implicated in follicular lymphomas, diffuse B Cell lymphomas and lymphoid cell lines due to hypermethylation.[20]

In brain tumours, more specifically oligodendroglial tumours and glioblastomas, the ID4 gene has been shown to be expressed in the neoplastic astrocytes but not expressed in the neoplastic oligodendrocytes.[21]

The ID4 promoter region has been found to be hypermethylated and its mRNA suppressed in breast cancer cell lines including that of primary breast cancers. Patients with invasive carcinomas have shown ID4 expression in their breast cancer specimens. This has been identified as a significant risk factor in nodal metastasis.[22] ID4 is constitutively expressed in normal human mammary epithelium but found to be suppressed in ER positive breast carcinomas and preneoplastic lesions. ER negative carcinomas also show ID4 expression.[23] There is a hypothesis that ID4 acts as a tumour suppressor factory in human breast tissue where oestrogen is responsible for regulation of ID4 expression in the mammary ductal epithelium.[23]

It is unclear whether the ID4 gene plays a role in bladder cancer. ID4 is found on the 6p22.3 amplicon which is frequently associated with advance stage bladder cancer. ID4 has also been shown to be overexpressed in bladder cancer cell lines. This overexpression is equally seen in both normal urothelium which lines the urinary tract inclusive of the renal pelvis, ureters, bladder and parts of the urethra, but also seen in fresh cancer tissues.[24]

ID4 is closely associated with gastric cancer. The ID4 promoter region is hypermethylated and infrequently expressed in gastric adenocarcinomas and frequently expressed in gastric cancer cell lines. In contrast, ID4 is highly expressed in normal gastric mucosa. There is an undefined but significant association seen in ID4 promoter hypermethylation (which results in its down regulation) and microsatellite instability.[25]

ID4 is not found in normal epitheliums nor adenomas of colorectal cancer. Hypermethylation of ID4 causes silencing of the gene. This has been identified as a significant independent risk factor for poor prognosis of colorectal cancer. It is also frequently observed in liver metastases of colorectal cancer specimens.[26]

Developmental disorders

Rett syndrome is an X linked neurodevelopment disorder. It is often identified after six to eight months of age in females. In human brain tissue specimens of Rett syndrome patients, the family of ID genes are seen to be significantly increased in expression.[27]

Society and culture

Commonly used names

The ID4 gene is also known as DNA-binding protein inhibitor ID-4, Id-4, IDb4, IDB4, Inhibitor of DNA binding 4, Inhibitor of differentiation 4, helix protein 271, Inhibitor of DNA binding 4 HLH Protein, Inhibitor of Differentiation 4, Inhibitor of DNA Binding 4 Dominant Negative Helix-Loop-Helix Protein, Class B Basic Helix-Loop-Helix Protein 27, and BHLHb272.

See also

• Inhibitor of DNA-binding protein

References

1. GRCh38: Ensembl release 89: ENSG00000172201 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000021379 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. Pagliuca A, Bartoli PC, Saccone S, Della Valle G, Lania L (Oct 1995). "Molecular cloning of ID4, a novel dominant negative helix-loop-helix human gene on chromosome 6p21.3-p22". Genomics. 27 (1): 200–3. doi:10.1006/geno.1995.1026. PMID 7665172.
6. "Entrez Gene: ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein".
7. "Atlas of Genetics and Cytogenetics in Oncology and Haematology".
8. Riechmann V, van Crüchten I, Sablitzky F (1994). "The expression pattern of Id4, a novel dominant negative helix-loop-helix protein, is distinct from Id1, Id2 and Id3". Nucleic Acids Research. 22 (5): 749–755. doi:10.1093/nar/22.5.749. PMC 307878. PMID 8139914.
9. Riechmann V, Sablitzky F (July 1995). "Mutually exclusive expression of two dominant-negative helix-loop-helix (dnHLH) genes, Id4 and Id3, in the developing brain of the mouse suggests distinct regulatory roles of these dnHLH proteins during cellular proliferation and differentiation of the nervous system". Cell Growth & Differentiation. 6: 837–843.
10. Pagliuca A, Cannada-Bartoli P, Lania L (March 1998). "A role for Sp and helix-loop-helix transcription factors in the regulation of the human Id4 gene promoter activity". Journal of Biological Chemistry. 273 (13): 7668–7674. doi:10.1074/jbc.273.13.7668. PMID 9516472.
11. Kee Y, Bronner-Fraser M (December 2001). "ID4 expression and its relationship to other ID genes during avian embryonic development". Mechanisms of Development. 109 (2): 341–345. doi:10.1016/S0925-4773(01)00576-7.
12. Jen Y, Manova K, Benezra R (November 1996). "Expression patterns of Id1, Id2, and Id3 are highly related but distinct from that of Id4 during mouse embryogenesis". Developmental Dynamics. 207 (3): 235–252. doi:10.1002/(SICI)1097-0177(199611)207:3<235::AID-AJA1>3.0.CO;2-I. PMID 8922523.
13. Yun K, Mantani A, Garel S, Rubenstein J, Israel MA (November 2004). "Id4 regulates neural progenitor proliferation and differentiation in vivo". Development. 131 (21): 5441–5448. doi:10.1242/dev.01430. PMID 15469968.
14. Cunningham TJ, Yu MS, McKeithan WL, et al. (2017). "Id genes are essential for early heart formation". Genes & Development. 31 (13): 1325–1338. doi:10.1101/gad.300400.117. PMC 5580654. PMID 28794185.
15. Painter JN, Anderson CA, Nyholt DR, Macgregor S, Lin J, Lee SH, Zondervan KT, et al. (2011). "Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis". Nature Genetics. 43 (1): 51–54. doi:10.1038/ng.731. PMC 3019124. PMID 21151130.
16. Ren Y, Cheung HW, von Maltzhan G, et al. (August 2012). "Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4". Science Translational Medicine. 4 (147): 147ra112. doi:10.1126/scitranslmed.3003778. PMC 3633234. PMID 22896676.
17. Kobayashi A, Behringer RR (Dec 2003). "Developmental genetics of the female reproductive tract in mammals". Nature Reviews. Genetics. 4 (12): 969–980. doi:10.1038/nrg1225. PMID 14631357.
18. Bellido M, Aventín A, Lasa A, Estivill C, Carnicer MJ, Pons C, Matías-Guiu X, Bordes R, Baiget M, Sierra J, Nomdedéu JF (September 2003). "Id4 is deregulated by a t(6;14)(p22;q32) chromosomal translocation in a B-cell lineage acute lymphoblastic leukemia". Haematologica. 88 (9): 994–1001. PMID 12969807.
19. Russell LJ, Akasaka T, Majid A, Sugimoto KJ, Loraine Karran E, Nagel I, Harder L, Claviez A, Gesk S, Moorman AV, Ross F, Mazzullo H, Strefford JC, Siebert R, Dyer MJ, Harrison CJ (Jan 2008). "t(6;14)(p22;q32): a new recurrent IGH@ translocation involving ID4 in B-cell precursor acute lymphoblastic leukemia (BCP-ALL)". Blood. 111 (1): 387–391. doi:10.1182/blood-2007-07-092015. PMID 17940204.
20. Yoshihara H, Arai F, Hosokawa K, Hagiwara T, Takubo K, Nakamura Y, Gomei Y, Iwasaki H, Matsuoka S, Miyamoto K, Miyazaki H, Takahashi T, Suda T (December 2007). "Thrombopoietin/MPL signaling regulates hematopoietic stem cell quiescence and interaction with the osteoblastic niche". Cell Stem Cell. 1 (6): 685–697. doi:10.1016/j.stem.2007.10.020. PMID 18371409.
21. Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, Nicholas MK, Lamborn KR, Berger MS, Botstein D, Brown PO, Israel MA (April 2005). "TGene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme". Proceedings of the National Academy of Sciences of the United States of America. 102 (16): 5814–5819. doi:10.1073/pnas.0402870102. PMC 556127. PMID 15827123.
22. Umetani N, Giuliano AE, Hiramatsu SH, Amersi F, Nakagawa T, Martino S, Hoon DS (September 2006). "Prediction of breast tumor progression by integrity of free circulating DNA in serum". Journal of Clinical Oncology. 24 (26): 4270–4276. doi:10.1200/JCO.2006.05.9493. PMID 16963729.
23. Umetani N, de Maat MG, Sunami E, Hiramatsu S, Martinez S, Hoon DB (May 2006). "Methylation of p16 and Ras Association Domain Family Protein 1a during Colorectal Malignant Transformation". Molecular Cancer Research. 4 (5): 303–309. doi:10.1158/1541-7786.MCR-05-0199. PMID 16687485.
24. Wu Q, Hoffmann MJ, Hartmann FH, Schulz WA (2005). "Amplification and overexpression of the ID4 gene at 6p22.3 in bladder cancer". Molecular Cancer. 4 (16): 16. doi:10.1186/1476-4598-4-16. PMC 1131921. PMID 15876350.
25. Chan AS, Tsui WY, Chen X, Chu KM, Chan TL, Chan AS, Li R, So S, Yuen ST, Leung SY (October 2003). "Downregulation of ID4 by promoter hypermethylation in gastric adenocarcinoma". Oncogene. 22 (44): 6946–6953. doi:10.1038/sj.onc.1206799. PMID 14534543.
26. Umetani N, Mori T, Koyanagi K, Shinozaki M, Kim J, Giuliano AE, Hoon DS (July 2005). "Aberrant hypermethylation of ID4 gene promoter region increases risk of lymph node metastasis in T1 breast cancer". Oncogene. 24 (29): 4721–4727. doi:10.1038/sj.onc.1208538. PMID 15897910.
27. Peddada S, Yasui DH, LaSalle JM (June 2006). "Inhibitors of differentiation (ID1, ID2, ID3, ID4) genes are neuronal targets of MeCP2 that are elevated in Rett syndrome". Human Molecular Genetics. 15 (12): 2003–2014. doi:10.1093/hmg/ddl124. PMC 1931415. PMID 16682435.

Further reading

• Loveys DA, Streiff MB, Kato GJ (1996). "E2A basic helix-loop-helix transcription factors are negatively regulated by serum growth factors and by the Id3 protein". Nucleic Acids Res. 24 (14): 2813–20. doi:10.1093/nar/24.14.2813. PMC 145994. PMID 8759016.
• Stewart HJ, Zoidl G, Rossner M, Brennan A, Zoidl C, Nave KA, Mirsky R, Jessen KR (1998). "Helix-loop-helix proteins in Schwann cells: a study of regulation and subcellular localization of Ids, REB, and E12/47 during embryonic and postnatal development". J. Neurosci. Res. 50 (5): 684–701. doi:10.1002/(SICI)1097-4547(19971201)50:5<684::AID-JNR6>3.0.CO;2-D. PMID 9418957.
• Rigolet M, Rich T, Gross-Morand MS, Molina-Gomes D, Viegas-Pequignot E, Junien C (1999). "cDNA cloning, tissue distribution and chromosomal localization of the human ID4 gene". DNA Res. 5 (5): 309–13. doi:10.1093/dnares/5.5.309. PMID 9872455.
• Beger C, Pierce LN, Kruger M, Marcusson EG, Robbins JM, Welcsh P, Welch PJ, Welte K, King MC, Barber JR, Wong-Staal F (2001). "Identification of Id4 as a regulator of BRCA1 expression by using a ribozyme-library-based inverse genomics approach". Proc. Natl. Acad. Sci. U.S.A. 98 (1): 130–5. doi:10.1073/pnas.98.1.130. PMC 14556. PMID 11136250.
• Jögi A, Persson P, Grynfeld A, Påhlman S, Axelson H (2002). "Modulation of basic helix-loop-helix transcription complex formation by Id proteins during neuronal differentiation". J. Biol. Chem. 277 (11): 9118–26. doi:10.1074/jbc.M107713200. PMID 11756408.
• Bellido M, Aventín A, Lasa A, Estivill C, Carnicer MJ, Pons C, Matías-Guiu X, Bordes R, Baiget M, Sierra J, Nomdedéu JF (2004). "Id4 is deregulated by a t(6;14)(p22;q32) chromosomal translocation in a B-cell lineage acute lymphoblastic leukemia". Haematologica. 88 (9): 994–1001. PMID 12969807.
• Chan AS, Tsui WY, Chen X, Chu KM, Chan TL, Chan AS, Li R, So S, Yuen ST, Leung SY (2003). "Downregulation of ID4 by promoter hypermethylation in gastric adenocarcinoma". Oncogene. 22 (44): 6946–53. doi:10.1038/sj.onc.1206799. PMID 14534543.
• Shan L, Yu M, Qiu C, Snyderwine EG (2004). "Id4 regulates mammary epithelial cell growth and differentiation and is overexpressed in rat mammary gland carcinomas". Am. J. Pathol. 163 (6): 2495–502. doi:10.1016/S0002-9440(10)63604-8. PMC 1892385. PMID 14633621.
• Umetani N, Takeuchi H, Fujimoto A, Shinozaki M, Bilchik AJ, Hoon DS (2005). "Epigenetic inactivation of ID4 in colorectal carcinomas correlates with poor differentiation and unfavorable prognosis". Clin. Cancer Res. 10 (22): 7475–83. doi:10.1158/1078-0432.CCR-04-0689. PMID 15569977.
• Yu L, Liu C, Vandeusen J, Becknell B, Dai Z, Wu YZ, Raval A, Liu TH, Ding W, Mao C, Liu S, Smith LT, Lee S, Rassenti L, Marcucci G, Byrd J, Caligiuri MA, Plass C (2005). "Global assessment of promoter methylation in a mouse model of cancer identifies ID4 as a putative tumor-suppressor gene in human leukemia". Nat. Genet. 37 (3): 265–74. doi:10.1038/ng1521. PMID 15723065.
• Wu Q, Hoffmann MJ, Hartmann FH, Schulz WA (2006). "Amplification and overexpression of the ID4 gene at 6p22.3 in bladder cancer". Mol. Cancer. 4 (1): 16. doi:10.1186/1476-4598-4-16. PMC 1131921. PMID 15876350.
• Peddada S, Yasui DH, LaSalle JM (2006). "Inhibitors of differentiation (ID1, ID2, ID3 and ID4) genes are neuronal targets of MeCP2 that are elevated in Rett syndrome". Hum. Mol. Genet. 15 (12): 2003–14. doi:10.1093/hmg/ddl124. PMC 1931415. PMID 16682435.
• Hagiwara K, Nagai H, Li Y, Ohashi H, Hotta T, Saito H (2007). "Frequent DNA methylation but not mutation of the ID4 gene in malignant lymphoma". Journal of Clinical and Experimental Hematopathology. 47 (1): 15–8. doi:10.3960/jslrt.47.15. PMID 17510533.
• Noetzel E, Veeck J, Niederacher D, Galm O, Horn F, Hartmann A, Knüchel R, Dahl E (2008). "Promoter methylation-associated loss of ID4 expression is a marker of tumour recurrence in human breast cancer". BMC Cancer. 8: 154. doi:10.1186/1471-2407-8-154. PMC 2435120. PMID 18513385.

External links

• ID4+protein,+human at the US National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the United States National Library of Medicine, which is in the public domain.