Interferon regulatory factor gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

Interferon regulatory factors (IRF) are proteins which regulate transcription of interferons (see regulation of gene expression).[1] They are used in the JAK-STAT signaling pathway.[2] Interferon regulatory factors contain a conserved N-terminal region of about 120 amino acids, which folds into a structure that binds specifically to the interferon consensus sequence (ICS), which is located upstream of the interferon genes.[3] The remaining parts of the interferon regulatory factor sequence vary depending on the precise function of the protein.[3] The Kaposi sarcoma herpesvirus, KSHV[4], is a cancer virus that encodes four different IRF-like genes[5]; including vIRF1[6], which is a transforming oncoprotein that inhibits type 1 interferon activity.[7] In addition, the expression of IRF genes is under epigenetic regulation by promoter DNA methylation. [8]

Gene expressions

There "are totally 11 members (from IRF-1 to IRF-11) identified from vertebrates [10]. All the IRF members share a well-conserved N-terminal helix-turn-helix IRF superfamily domain (also called DNA-binding domain, DBD) with five conserved tryptophan (Trp) residues, which could recognize DNA sequences containing 5’-GAAA-3’ tetranucleotide, such as the IFN-stimulated response element (ISREs, GAAANNGAAA) [11, 12]. Moreover, it was reported that the IRS consensus (-78/-66, AANNGAAA), which existed in the promoter region of IFN-β, could be bound by the IRF family members [13[9]]. As for the C-terminus, most of the IRFs share an IRF-3 superfamily domain, which was also named as IRF associated domain 1 (IAD1). IRF-1 and IRF-2 do not possess conserved IAD1 domain, but they contain non-conserved activation domain (the last 100 amino acids of IRF-1 were rich in tyrosine) or repression domain (the final 25 amino acids of IRF-2 were rich in histidine, arginine and lysine) in their C-terminus, respectively."[10]

IRF1

Interferon regulatory factor 1 is a protein that in humans is encoded by the IRF1 gene.[11][12]

Interferon regulatory factor 1 was the first member of the interferon regulatory transcription factor (IRF) family identified. Initially described as a transcription factor able to activate expression of the cytokine Interferon beta,[13] IRF-1 was subsequently shown to function as a transcriptional activator or repressor of a variety of target genes.

"IRF1 regulates expression of ISGs in response to IFN-I and IFN-II by directly binding the ISRE or IRF-responsive element."[14]

The IRF-1 protein binds to the ISRE via an N-terminal helix-turn-helix DNA binding domain,[15] which is highly conserved among all IRF proteins.

Beyond its function as a transcription factor, IRF-1 has also been shown to trans-activate the tumour suppressor protein p53 through the recruitment of its co-factor p300.[16]

IRF-1 has been shown to play roles in the immune response, regulating apoptosis, DNA damage and tumor suppression.[17]

It has been shown that the extreme C-terminus of IRF-1 regulates its ability to activate transcription, nanobodies targeting this domain (MF1) are able to increase IRF-1 activity.[18]

IRF2

Interferon regulatory factor 2 is a protein that in humans is encoded by the IRF2 gene.[19]

IRF2 encodes interferon regulatory factor 2, a member of the interferon regulatory transcription factor (IRF) family. IRF2 competitively inhibits the IRF1-mediated transcriptional activation of interferons alpha and beta, and presumably other genes that employ IRF1 for transcription activation. However, IRF2 also functions as a transcriptional activator of histone H4.[20]

IRF3

Interferon regulatory factor 3 (IRF3) is an interferon regulatory factor.[21]

IRF3 is a member of the interferon regulatory transcription factor (IRF) family.[21] IRF3 was originally discovered as a homolog of IRF1 and IRF2. IRF3 has been further characterized and shown to contain several functional domains including a nuclear export signal, a DNA-binding domain, a C-terminal IRF association domain and several regulatory phosphorylation sites.[22] IRF3 is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP.[23] This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes.[24]

IRF3 plays an important role in the innate immune system's response to viral infection.[25] Aggregated MAVS have been found to activate IRF3 dimerization.[26] A 2015 study shows phosphorylation of innate immune adaptor proteins MAVS, STING and TRIF at a conserved pLxIS motif recruits and specifies IRF3 phosphorylation and activation by the Serine/threonine-protein kinase TBK1, thereby activating the production of type-I interferons.[27] Another study has shown that IRF3-/- knockouts protect from myocardial infarction.[28] The same study identified IRF3 and the type I IFN response as a potential therapeutic target for post-myocardial infarction cardioprotection.[28]

Gene ID: 3661 is IRF3 interferon regulatory factor 3 on 19q13.33: "This gene encodes a member of the interferon regulatory transcription factor (IRF) family. The encoded protein is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP. This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes. The protein plays an important role in the innate immune response against DNA and RNA viruses. Mutations in this gene are associated with Encephalopathy, acute, infection-induced, herpes-specific, 7."[29]

IRF4

Interferon regulatory factor 4 also known as MUM1 is a protein that in humans is encoded by the IRF4 gene,[30][31][32] located at 6p25-p23.

In melanocytic cells the IRF4 gene may be regulated by MITF.[33] IRF4 is a transcription factor that has been implicated in acute leukemia.[34] This gene is strongly associated with pigmentation: sensitivity of skin to sun exposure, freckles, blue eyes, and brown hair color.[35] A variant has been implicated in greying of hair.[36]

IRF5

Interferon regulatory factor 5 is a protein that in humans is encoded by the IRF5 gene.[37]

IRF5 is a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Alternative splice variants encoding different isoforms exist.[37]

An adaptor protein named TASL plays an important regulatory role in IRF5 activation by being phosphorylated at the pLxIS motif,[38] drawing a similar analogy to the IRF3 activation pathway through the adaptor proteins MAVS, STING and TRIF.[39]

IRF6

Interferon regulatory factor 6 (IRF6) is a protein that in humans is encoded by the IRF6 gene.[40]

This gene encodes a member of the interferon regulatory transcription factor (IRF) family. Family members share a highly conserved N-terminal helix-turn-helix DNA-binding domain and a less conserved C-terminal protein-binding domain.[41] The function of IRF6 is related to the formation of connective tissue, for example that of the palate.[42] This gene encodes a member of the interferon regulatory transcription factor (IRF) family. In addition, it has been observed that IRF6 gene is under epigenetic regulation by promoter methylation.[8]

IRF7

Interferon regulatory factor 7 (IRF7) is a member of the interferon regulatory factor family of transcription factors.

IRF7 encodes interferon regulatory factor 7, a member of the interferon regulatory transcription factor (IRF) family. IRF7 has been shown to play a role in the transcriptional activation of virus-inducible cellular genes, including the type I interferon genes. In particular, IRF7 regulates many interferon-alpha genes.[43] Constitutive expression of IRF7 is largely restricted to lymphoid tissue, largely plasmacytoid dendritic cells, whereas IRF7 is inducible in many tissues. Multiple IRF7 transcript variants have been identified, although the functional consequences of these have not yet been established.[44]

The IRF7 pathway was shown to be silenced in some metastatic breast cancer cell lines, which may help the cells avoid the host immune response.[45] Restoring IRF7 to these cell lines reduced metastases and increased host survival time in animal models.

The IRF7 gene and product were shown to be defective in a patient with severe susceptibility to H1N1 influenza, while susceptibility to other viral diseases such as CMV, RSV, and parainfluenza was unaffected.[46]

IRF8

Interferon regulatory factor 8 (IRF8) also known as the interferon consensus sequence-binding protein (ICSBP), is a protein that in humans is encoded by the IRF8 gene.[47][3][48] IRF8 is a transcription factor that plays critical roles in the regulation of lineage commitment and in myeloid cell maturation including the decision for a common myeloid progenitor (CMP) to differentiate into a monocyte precursor cell.

Interferon Consensus Sequence-binding protein (ICSBP) is a transcription factor of the interferon regulatory factor (IRF) family. Proteins of this family are composed of a conserved DNA-binding domain in the N-terminal region and a divergent C-terminal region that serves as the regulatory domain. The IRF family proteins bind to the IFN-stimulated response element (ISRE) and regulate expression of genes stimulated by type I IFNs, namely IFN-α and IFN-β. IRF family proteins also control expression of IFN-α and IFN-β-regulated genes that are induced by viral infection.[47]

Many "GAS-containing STAT1-target genes have been identified (40), including guanylate-binding protein (GBP), SOCS1, IRF1, and IRF8."[14]

IRF9

Interferon regulatory factor 9 is a protein that in humans is encoded by the IRF9 gene, previously known as ISGF3G.[49][50][51]

Gene ID: 10379 is IRF9 interferon regulatory factor 9 on 14q12: "This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Mutations in this gene result in Immunodeficiency 65."[52]

"Interferon-I binding to [interferon α receptor] IFNAR results in receptor dimerization and increased [Janus kinase 1] JAK1 and [tyrosine kinase 2] TYK2 kinase activity via juxtapositioning and transphosphorylation (13). Subsequently, JAK1 and TYK2 phosphorylate IFNAR1 and IFNAR2 on target tyrosine residues that become docking sites for [signal transducer and activator of transcription 1] STAT1 and STAT2 (14). Receptor-bound STAT1 and STAT2 are thus phosphorylated on a critical tyrosine residue (pTyr) driving SH2-pTyr mediated dimer formation, nuclear translocation, and transcriptional activation. In the canonical pathway of IFN-I-mediated signaling, Tyr701 phosphorylation of STAT1 and Tyr690 of STAT2 leads to heterodimerization, interaction with [interferon regulatory factor 9] IRF9 and formation of [interferon-stimulated gene factor 3] ISGF3 [...]. After translocation to the nucleus, this complex binds the [interferon-stimulated response element] ISRE (consensus sequence AGTTTCN2TTTCN) of over 300 [interferon-stimulated genes] ISGs, such as ISG15, [2'-5'-oligoadenylate synthetase 1-3] OAS1-3, [interferon-induced protein with tetratricopeptide repeats 1-3] IFIT1-3, or MX1 and 2 that are instrumental in antiviral activity (13–15) [...]."[14]

"Most of the knowledge about the DNA responsive elements involved in IFN-I and IFN-II signaling dates from early experiments that focused on individual genes and their role in the antiviral response (83). Accordingly, the ISRE was shown to exist in proximal ISG promoters as a single element or in multiple copies, in either orientation with (minor) consensus sequence variations (AGTTTCN2TTTCN; [...]). Functional analysis of a selection of IFN-I-inducible genes (84, 85), [...] has revealed that ISRE is essential for IFN induction."[14]

Interactions

IRF1 has been shown to interact with:

IRF2 has been shown to interact with BRD7,[65] EP300[66] and PCAF.[66][60]

IRF3 has been shown to interact with IRF7.[67]

IRF4 has been shown to interact with:

IRF7 has been shown to interact with IRF3.[67] Also, IRF7 has been shown to interact with Aryl Hydrocarbon Receptor Interacting Protein (AIP), which is a negative regulator for the antiviral pathway.[72]

IRF8 has been shown to interact with IRF1[56][57] and COPS2.[73]

IRF9 has been shown to interact with STAT2[74][75] and STAT1.[74]

Consensus sequences

Consensus sequence for IRF-3 is GCTTTCC.[76]

IRF-3 samplings

Copying a responsive elements consensus sequence GCTTTCC and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GCTTTCC (starting with SuccessablesIRF3.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GCTTTCC, 0.
  2. negative strand, positive direction, looking for GCTTTCC, 1, GCTTTCC at 1097.
  3. positive strand, negative direction, looking for GCTTTCC, 0.
  4. positive strand, positive direction, looking for GCTTTCC, 0.
  5. complement, negative strand, negative direction, looking for CGAAAGG, 0.
  6. complement, negative strand, positive direction, looking for CGAAAGG, 0.
  7. complement, positive strand, negative direction, looking for CGAAAGG, 0.
  8. complement, positive strand, positive direction, looking for CGAAAGG, 1, CGAAAGG at 1097.
  9. inverse complement, negative strand, negative direction, looking for GGAAAGC, 0.
  10. inverse complement, negative strand, positive direction, looking for GGAAAGC, 0.
  11. inverse complement, positive strand, negative direction, looking for GGAAAGC, 1, GGAAAGC at 1678.
  12. inverse complement, positive strand, positive direction, looking for GGAAAGC, 0.
  13. inverse negative strand, negative direction, looking for CCTTTCG, 1, CCTTTCG at 1678.
  14. inverse negative strand, positive direction, looking for CCTTTCG, 0.
  15. inverse positive strand, negative direction, looking for CCTTTCG, 0.
  16. inverse positive strand, positive direction, looking for CCTTTCG, 0.

IRF3 distal promoters

Positive strand, negative direction: GGAAAGC at 1678

Negative strand, positive direction: GCTTTCC at 1097

Interferon-stimulated response element samplings

Copying a responsive elements consensus sequence AGTTTCNNTTTCN and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGTTTCNNTTTCN (starting with SuccessablesISRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for AGTTTCNNTTTCN, 0.
  2. positive strand, negative direction, looking for AGTTTCNNTTTCN, 0.
  3. positive strand, positive direction, looking for AGTTTCNNTTTCN, 0.
  4. negative strand, positive direction, looking for AGTTTCNNTTTCN, 0.
  5. complement, negative strand, negative direction, looking for TCAAAGNNAAAGN, 0.
  6. complement, positive strand, negative direction, looking for TCAAAGNNAAAGN, 0.
  7. complement, positive strand, positive direction, looking for TCAAAGNNAAAGN, 0.
  8. complement, negative strand, positive direction, looking for TCAAAGNNAAAGN, 0.
  9. inverse complement, negative strand, negative direction, looking for NGAAANNGAAACT, 0.
  10. inverse complement, positive strand, negative direction, looking for NGAAANNGAAACT, 0.
  11. inverse complement, positive strand, positive direction, looking for NGAAANNGAAACT, 0.
  12. inverse complement, negative strand, positive direction, looking for NGAAANNGAAACT, 0.
  13. inverse negative strand, negative direction, looking for NCTTTNNCTTTGA, 0.
  14. inverse positive strand, negative direction, looking for NCTTTNNCTTTGA, 0.
  15. inverse positive strand, positive direction, looking for NCTTTNNCTTTGA, 0.
  16. inverse negative strand, positive direction, looking for NCTTTNNCTTTGA, 0.

IFN-stimulated response element samplings

Copying a responsive elements consensus sequence GAAANNGAAA and putting the sequence in "⌘F" finds 15 GAAA but none with GAAANNGAAA between ZNF497 and A1BG or 17 GAAA but none with GAAANNGAAA between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GAAANNGAAA (starting with SuccessablesIFN.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for GAAANNGAAA, 0.
  2. positive strand, negative direction, looking for GAAANNGAAA, 0.
  3. positive strand, positive direction, looking for GAAANNGAAA, 0.
  4. negative strand, positive direction, looking for GAAANNGAAA, 1, GAAATAGAAA at 2629.
  5. complement, negative strand, negative direction, looking for CTTTNNCTTT, 0.
  6. complement, positive strand, negative direction, looking for CTTTNNCTTT, 0.
  7. complement, positive strand, positive direction, looking for CTTTNNCTTT, 1, CTTTATCTTT at 2629.
  8. complement, negative strand, positive direction, looking for CTTTNNCTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTCNNTTTC, 1, TTTCGTTTTC at 2477.
  10. inverse complement, positive strand, negative direction, looking for TTTCNNTTTC, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTCNNTTTC, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTCNNTTTC, 0.
  13. inverse negative strand, negative direction, looking for AAAGNNAAAG, 0.
  14. inverse positive strand, negative direction, looking for AAAGNNAAAG, 1, AAAGCAAAAG at 2477.
  15. inverse positive strand, positive direction, looking for AAAGNNAAAG, 0.
  16. inverse negative strand, positive direction, looking for AAAGNNAAAG, 0.

IFN distal promoters

Negative strand, negative direction: TTTCGTTTTC at 2477.

Negative strand, positive direction: GAAATAGAAA at 2629.

IRS consensus samplings

Copying a responsive elements consensus sequence AANNGAAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AANNGAAA (starting with SuccessablesIRS.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for AANNGAAA, 1, AATAGAAA at 1733.
  2. positive strand, negative direction, looking for AANNGAAA, 13, AAAAGAAA at 4394, AAAAGAAA at 4389, AAAAGAAA at 4382, AATAGAAA at 4081, AAAAGAAA at 2838, AAAAGAAA at 2821, AAAAGAAA at 2800, AAAAGAAA at 2055, AAGGGAAA at 1660, AAAGGAAA at 1642, AAAAGAAA at 1630, AAATGAAA at 1582, AAAAGAAA at 226.
  3. positive strand, positive direction, looking for AANNGAAA, 2, AAAAGAAA at 2278, AACGGAAA at 134.
  4. negative strand, positive direction, looking for AANNGAAA, 2, AAAGGAAA at 2831, AATAGAAA at 2629.
  5. complement, negative strand, negative direction, looking for TTNNCTTT, 13, TTTTCTTT at 4394, TTTTCTTT at 4389, TTTTCTTT at 4382, TTATCTTT at 4081, TTTTCTTT at 2838, TTTTCTTT at 2821, TTTTCTTT at 2800, TTTTCTTT at 2055, TTCCCTTT at 1660, TTTCCTTT at 1642, TTTTCTTT at 1630, TTTACTTT at 1582, TTTTCTTT at 226.
  6. complement, positive strand, negative direction, looking for TTNNCTTT, 1, TTATCTTT at 1733.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 2, TTTCCTTT at 2831, TTATCTTT at 2629.
  8. complement, negative strand, positive direction, looking for TTNNCTTT, 2, TTTTCTTT at 2278, TTGCCTTT at 134.
  9. inverse complement, negative strand, negative direction, looking for TTTCNNTT, 13, TTTCTTTT at 4395, TTTCTTTT at 4390, TTTCTTTT at 4383, TTTCTTTT at 4086, TTTCTTTT at 2839, TTTCTCTT at 2827, TTTCTTTT at 2822, TTTCTCTT at 2810, TTTCTTTT at 2805, TTTCGTTT at 2481, TTTCGTTT at 2475, TTTCTTTT at 2056, TTTCCTTT at 1642.
  10. inverse complement, positive strand, negative direction, looking for TTTCNNTT, 1, TTTCTTTT at 26.
  11. inverse complement, positive strand, positive direction, looking for TTTCNNTT, 1, TTTCCTTT at 2831.
  12. inverse complement, negative strand, positive direction, looking for TTTCNNTT, 2, TTTCTCTT at 4387, TTTCTTTT at 2279.
  13. inverse negative strand, negative direction, looking for AAAGNNAA, 1, AAAGAAAA at 26.
  14. inverse positive strand, negative direction, looking for AAAGNNAA, 13, AAAGAAAA at 4395, AAAGAAAA at 4390, AAAGAAAA at 4383, AAAGAAAA at 4086, AAAGAAAA at 2839, AAAGAGAA at 2827, AAAGAAAA at 2822, AAAGAGAA at 2810, AAAGAAAA at 2805, AAAGCAAA at 2481, AAAGCAAA at 2475, AAAGAAAA at 2056, AAAGGAAA at 1642.
  15. inverse positive strand, positive direction, looking for AAAGNNAA, 2, AAAGAGAA at 4387, AAAGAAAA at 2279.
  16. inverse negative strand, positive direction, looking for AAAGNNAA, 1, AAAGGAAA at 2831.

IRS UTRs

Negative strand, negative direction: TTTCTTTT at 4395, TTTCTTTT at 4390, TTTCTTTT at 4383, TTTCTTTT at 4086.

Positive strand, negative direction: AAAAGAAA at 4394, AAAAGAAA at 4389, AAAAGAAA at 4382, AATAGAAA at 4081.

IRS core promoters

Negative strand, negative direction: TTTCTTTT at 2839, TTTCTCTT at 2827, TTTCTTTT at 2822.

Positive strand, negative direction: AAAAGAAA at 2838, AAAAGAAA at 2821.

Negative strand, positive direction: TTTCTCTT at 4387.

IRS proximal promoters

Negative strand, negative direction: TTTCTCTT at 2810, TTTCTTTT at 2805.

Positive strand, negative direction: AAAAGAAA at 2800.

IRS distal promoters

Negative strand, negative direction: TTTCGTTT at 2481, TTTCGTTT at 2475, TTTCTTTT at 2056, AATAGAAA at 1733, TTTCCTTT at 1642.

Positive strand, negative direction: AAAAGAAA at 2055, AAGGGAAA at 1660, AAAGGAAA at 1642, AAAAGAAA at 1630, AAATGAAA at 1582, AAAAGAAA at 226, TTTCTTTT at 26.

Negative strand, positive direction: AAAGGAAA at 2831, AATAGAAA at 2629, TTTCTTTT at 2279.

Positive strand, positive direction: TTTCCTTT at 2831, AAAAGAAA at 2278, AACGGAAA at 134.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikipedia.

See also

References

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