223:. The upper helix of the known IREs shows stronger conservation of structure compared to the lower helix. The bases composing the helixes are variable. The mid-stem bulged C is a highly characteristic feature (though this has been seen to be a G in the ferritin IRE for lobster). The apical loop of the known IREs all consist of either the AGA or AGU triplet. This is pinched by a paired G-C and there is additionally a bulged U, C or A in the upper helix. The crystal structure and NMR data show a bulged U in the lower stem of the ferritin IRE. This is consistent with the predicted secondary structure. IREs in many other mRNAs do not have any support for this bulged U. Consequently, two RFAM models have been created for the IRE—one with a bulged U and one without.
26:
117:
274:
In humans, 12 genes have been shown to be transcribed with the canonical IRE structure, but several mRNA structures, that are non-canonical, have been shown to interact with IRPs and be influenced by iron concentration. Software and algorithms have been developed to locate more genes that are also
212:
The two leading theories describe how iron probably interacts to impact posttranslational control of transcription. The classical theory suggests that IRPs, in the absence of iron, bind avidly to the mRNA IRE. When iron is present, it interacts with the protein to cause it to release the mRNA. For
216:
In the second theory two proteins compete for the IRE binding site—both IRP and eukaryotic
Initiation Factor 4F (eIF4F). In the absence of iron IRP binds about 10 times more avidly than the initiation factor. However, when Iron interacts at the IRE, it causes the mRNA to change its shape, thus
213:
example, In high iron conditions in humans, IRP1 binds with an iron-sulphur complex and adopts an aconitase conformation unsuitable for IRE binding. In contrast, IRP2 is degraded in high iron conditions. There is variation in affinity between different IREs and different IRPs.
126:
1224:
1020:
940:
132:
130:
127:
1520:"Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy"
131:
448:
446:
129:
1452:
723:(January 1999). "An atypical iron-responsive element (IRE) within crayfish ferritin mRNA and an iron regulatory protein 1 (IRP1)-like protein from crayfish hepatopancreas".
217:
favoring the binding of the eIF4F. Several studies have identified non-canonical IREs. It has also been shown that IRP binds to some IREs better than others.
192:. When iron concentration is low, IRPs bind the IRE in the ferritin mRNA and cause reduced translation rates. In contrast, binding to multiple IREs in the
779:(November 1997). "Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins".
128:
1578:
1284:"Molecular cloning of mouse glycolate oxidase. High evolutionary conservation and presence of an iron-responsive element-like sequence in the mRNA"
334:
169:
2066:
653:"Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions"
2098:
1691:
1937:
1524:
1342:
1288:
1162:
535:
Ma, Jia; Haldar, Suranjana; Khan, Mateen A.; Sharma, Sohani Das; Merrick, William C.; Theil, Elizabeth C.; Goss, Dixie J. (2012-05-29).
537:"Fe2+ binds iron responsive element-RNA, selectively changing protein-binding affinities and regulating mRNA repression and activation"
1158:"Succinate dehydrogenase b mRNA of Drosophila melanogaster has a functional iron-responsive element in its 5'-untranslated region"
725:
193:
1879:
1757:
1875:"Myotonic dystrophy kinase-related Cdc42-binding kinase acts as a Cdc42 effector in promoting cytoskeletal reorganization"
413:(2008). "Systemic iron homeostasis and the iron-responsive element/iron-regulatory protein (IRE/IRP) regulatory network".
293:. Others show a less obvious connection. ACO2 encodes an isomerase catalysing the reversible isomerisation of citrate and
1096:"Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA"
357:& Karl Volz (December 2006). "Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA".
781:
1402:(November 2003). "The role of the iron responsive element in the control of ferroportin1/IREG1/MTP1 gene expression".
1016:"A cytosolic protein binds to structural elements within the iron regulatory region of the transferrin receptor mRNA"
2079:
415:
1997:(April 2002). "Deregulated human Cdc14A phosphatase disrupts centrosome separation and chromosome segregation".
1569:
1511:
1220:"Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements"
402:
1576:(May 2007). "Iron-regulatory proteins limit hypoxia-inducible factor-2alpha expression in iron deficiency".
1399:
461:
80:
1404:
1379:
35:
1792:
1503:
888:"Identification of the iron-responsive element for the translational regulation of human ferritin mRNA"
871:
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Genomic
Interval files with IRE predictions made using the RFAM models on the hg18 human genome
1933:"Regulation of the anaphase-promoting complex by the dual specificity phosphatase human Cdc14a"
1866:
1687:"The family of iron responsive RNA structures regulated by changes in cellular iron and oxygen"
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Khan, M. A.; Ma, J.; Walden, W. E.; Merrick, W. C.; Theil, E. C.; Goss, D. J. (2014-06-02).
623:
607:
566:
548:
507:
424:
368:
353:
William E. Walden; Anna I. Selezneva; Jerome Dupuy; Anne
Volbeda; Juan C. Fontecilla-Camps;
87:
1928:
2083:
936:"Iron regulates ferritin mRNA translation through a segment of its 5' untranslated region"
428:
181:
1713:
1686:
1831:
1809:
1804:
1755:(January 1997). "The aconitase family: three structural variations on a common theme".
1655:
1622:
1621:
Campillos, Monica; Cases, Ildefonso; Hentze, Matthias W.; Sanchez, Mayka (2010-07-01).
1113:
685:
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281:. The IRE is found over a diverse taxonomic range—mainly eukaryotes but not in plants.
201:
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136:
Crystal structure of iron regulatory protein 1 in complex with ferritin H IRE-RNA,
1822:
1450:(March 2006). "A novel iron responsive element in the 3'UTR of human MRCKalpha".
822:
1465:
1225:
Proceedings of the
National Academy of Sciences of the United States of America
1021:
Proceedings of the
National Academy of Sciences of the United States of America
941:
Proceedings of the
National Academy of Sciences of the United States of America
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329:
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185:
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252:
1591:
1338:"Regulation of the 75-kDa subunit of mitochondrial complex I by iron"
306:
264:
887:
2012:
594:
Campillos, M.; Cases, I.; Hentze, M. W.; Sanchez, M. (2010-07-01).
268:
244:
124:
494:"Iron-dependent regulation of the divalent metal ion transporter"
62:
2061:
2050:
301:
involved in complex oxygen sensing pathways by the induction of
240:
232:
177:
57:
1805:"Hypoxia-inducible factors and the response to hypoxic stress"
313:. CDC14A encodes a dual-specificity phosphatase implicated in
74:
289:
Many genes regulated by IREs have clear and direct roles in
172:(IRPs, also named IRE-BP or IRBP). The IRE is found in
25:
818:"Two covariance models for iron-responsive elements"
1453:
110:
98:
86:
73:
68:
56:
48:
43:
18:
816:Stevens SG, Gardner PP, Brown C (September 2011).
200:(involved in iron acquisition) leads to increased
188:(an iron storage protein) contains one IRE in its
317:and also interacts with interphase centrosomes.
305:under low oxygen conditions. CDC42BPA encodes a
1623:"SIREs: searching for iron-responsive elements"
596:"SIREs: searching for iron-responsive elements"
541:Proceedings of the National Academy of Sciences
8:
2077:Iron Responsive Elements Prediction Server
2067:Transterm page for Iron Responsive Element
24:
2058:Page for Iron response element - Model II
1950:
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1579:Nature Structural & Molecular Biology
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726:Insect Biochemistry and Molecular Biology
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511:
2047:Page for Iron response element - Model I
345:
15:
429:10.1146/annurev.nutr.28.061807.155521
7:
1692:Cellular and Molecular Life Sciences
231:Genes known to contain IREs include
1938:The Journal of Biological Chemistry
1525:The Journal of Biological Chemistry
1343:The Journal of Biological Chemistry
1289:The Journal of Biological Chemistry
1163:The Journal of Biological Chemistry
1114:10.1002/j.1460-2075.1991.tb07716.x
275:responsive to iron concentration.
176:(untranslated regions) of various
14:
1633:(Web Server issue): W360–W367.
180:whose products are involved in
1880:Molecular and Cellular Biology
1758:Trends in Biochemical Sciences
1:
1771:10.1016/S0968-0004(96)10069-4
1418:10.1016/S0168-8278(03)00408-2
739:10.1016/S0965-1748(98)00097-6
513:10.1016/s0014-5793(01)03189-1
1823:10.1016/j.molcel.2010.09.022
782:Journal of Molecular Biology
2099:Cis-regulatory RNA elements
311:cytoskeletal reorganisation
285:Processes regulated by IREs
259:(encoding the ferroportin)
184:. For example, the mRNA of
2115:
1466:10.1016/j.bbrc.2005.12.155
416:Annual Review of Nutrition
1705:10.1007/s00018-007-7198-4
606:(Web Server): W360–W367.
255:(encoding DMT1), NDUFS1,
23:
1177:10.1074/jbc.270.51.30781
1570:Martina U. Muckenthaler
1512:Martina U. Muckenthaler
1239:10.1073/pnas.93.10.4925
1035:10.1073/pnas.86.10.3574
955:10.1073/pnas.84.23.8478
906:10.1126/science.3685996
554:10.1073/pnas.1120045109
403:Martina U. Muckenthaler
373:10.1126/science.1133116
164:) is a short conserved
158:iron-responsive element
1952:10.1074/jbc.M108126200
1627:Nucleic Acids Research
1539:10.1074/jbc.M603876200
1357:10.1074/jbc.M100941200
1303:10.1074/jbc.274.4.2401
795:10.1006/jmbi.1997.1377
657:Nucleic Acids Research
600:Nucleic Acids Research
303:oxygen regulated genes
170:iron response proteins
145:
1405:Journal of Hepatology
1400:Antonello Pietrangelo
837:10.4161/rna.8.5.16037
462:M. Polycarpou-Schwarz
154:iron response element
135:
36:sequence conservation
19:Iron response element
1893:10.1128/mcb.18.1.130
299:transcription factor
198:transferrin receptor
2000:Nature Cell Biology
1945:(51): 48237–48242.
1532:(32): 22865–22874.
1350:(29): 27685–27692.
1170:(51): 30781–30786.
900:(4833): 1570–1573.
367:(5807): 1903–1908.
208:Mechanism of action
32:secondary structure
2082:2012-04-25 at the
1639:10.1093/nar/gkq371
1574:Matthias W. Hentze
1516:Matthias W. Hentze
1380:Athina Lymboussaki
669:10.1093/nar/gku248
612:10.1093/nar/gkq371
411:Matthias W. Hentze
355:Elizabeth C. Theil
315:cell cycle control
297:. EPAS1 encodes a
221:Structural details
168:which is bound by
146:
1931:(December 2001).
1793:Amar J. Majmundar
1699:(22): 2945–2955.
1685:(November 2007).
1504:Yevhen Vainshtein
1232:(10): 4925–4930.
1156:(December 1995).
1028:(10): 3574–3578.
948:(23): 8478–8482.
934:(December 1987).
886:(December 1987).
872:J. G. Barriocanal
663:(10): 6567–6577.
547:(22): 8417–8422.
492:(December 2001).
150:molecular biology
138:Protein Data Bank
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1987:Peter K. Jackson
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1873:(January 1998).
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1803:(October 2010).
1801:M. Celeste Simon
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1388:Giuliana Montosi
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1296:(4): 2401–2407.
1282:(January 1999).
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1108:(7): 1903–1909.
1101:The EMBO Journal
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2084:Wayback Machine
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2039:External links
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2013:10.1038/ncb777
2007:(4): 317–322.
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1810:Molecular Cell
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1107:
1103:
1102:
1097:
1094:(July 1991).
1093:
1089:
1085:
1081:
1077:
1073:
1069:
1063:
1060:
1055:
1051:
1046:
1041:
1036:
1031:
1027:
1023:
1022:
1017:
1013:
1012:J. B. Harford
1009:
1005:
1001:
997:
993:
989:
988:D. M. Koeller
983:
980:
975:
971:
966:
961:
956:
951:
947:
943:
942:
937:
933:
929:
923:
920:
915:
911:
907:
903:
899:
895:
894:
889:
885:
881:
880:J. B. Harford
877:
873:
869:
868:T. A. Rouault
865:
861:
855:
852:
847:
843:
838:
833:
829:
825:
824:
819:
812:
809:
804:
800:
796:
792:
788:
784:
783:
778:
774:
773:T. A. Rouault
770:
766:
762:
756:
753:
748:
744:
740:
736:
732:
728:
727:
722:
718:
714:
710:
704:
701:
696:
692:
687:
682:
678:
674:
670:
666:
662:
658:
654:
647:
644:
639:
635:
630:
625:
621:
617:
613:
609:
605:
601:
597:
590:
587:
582:
578:
573:
568:
564:
560:
555:
550:
546:
542:
538:
531:
528:
523:
519:
514:
509:
505:
501:
500:
495:
491:
490:M. A. Hediger
487:
486:N. C. Andrews
483:
482:T. A. Rouault
479:
475:
471:
467:
463:
459:
455:
449:
447:
443:
438:
434:
430:
426:
422:
418:
417:
412:
408:
404:
398:
395:
390:
386:
382:
378:
374:
370:
366:
362:
361:
356:
349:
346:
340:
336:
333:
331:
328:
327:
323:
321:
318:
316:
312:
308:
304:
300:
296:
292:
284:
282:
280:
276:
272:
270:
266:
262:
258:
254:
250:
246:
242:
238:
234:
226:
224:
222:
218:
214:
207:
205:
203:
199:
195:
191:
187:
183:
179:
175:
171:
167:
163:
159:
155:
151:
143:
139:
119:
116:
113:
109:
106:
103:
101:
97:
94:
91:
89:
85:
82:
79:
76:
72:
67:
64:
61:
59:
55:
51:
47:
42:
37:
33:
27:
22:
17:
2004:
1998:
1969:
1942:
1936:
1919:
1884:
1878:
1849:
1814:
1808:
1787:
1762:
1756:
1739:
1696:
1690:
1673:
1630:
1626:
1616:
1583:
1577:
1556:
1529:
1523:
1482:
1457:
1451:
1440:Radek Cmejla
1434:
1409:
1403:
1374:
1347:
1341:
1334:G. A. Freyer
1320:
1293:
1287:
1272:S. A. Kohler
1266:
1229:
1223:
1218:(May 1996).
1216:M. W. Hentze
1194:
1167:
1161:
1146:S. A. Kohler
1140:
1105:
1099:
1092:M. W. Hentze
1084:A. Constable
1072:R. Stripecke
1062:
1025:
1019:
1014:(May 1989).
996:M. W. Hentze
982:
945:
939:
922:
897:
891:
860:M. W. Hentze
854:
827:
821:
811:
789:(1): 72–83.
786:
780:
761:K. J. Addess
755:
730:
724:
721:K. Soderhall
703:
660:
656:
646:
603:
599:
589:
544:
540:
530:
503:
499:FEBS Letters
497:
478:M. W. Hentze
470:J. T. Rogers
420:
414:
397:
364:
358:
348:
319:
314:
310:
302:
290:
288:
278:
277:
273:
230:
220:
219:
215:
211:
161:
157:
153:
147:
1991:Jiri Bartek
1925:J. Bembenek
1753:J. R. Guest
1745:M. J. Gruer
1683:E. C. Theil
1508:Jens Stolte
1444:Jiri Petrak
1208:T. Dandekar
1068:T. Dandekar
992:J. L. Casey
932:H. N. Munro
823:RNA Biology
713:O. Melefors
709:T. S. Huang
423:: 197–213.
44:Identifiers
1995:Jiri Lukas
1859:X. Q. Chen
1765:(1): 3–6.
1566:Bruno Galy
1492:Bruno Galy
1280:L. C. Kuhn
1276:E. Menotti
1200:N. K. Gray
1154:L. C. Kuhn
1080:B. Goossen
1076:N. K. Gray
1004:L. N. Chan
733:(1): 1–9.
717:M. I. Lind
454:H. Gunshin
407:Bruno Galy
341:References
295:isocitrate
114:structures
105:SO:0000233
69:Other data
30:Predicted
1867:E. Manser
1647:0305-1048
876:A. Dancis
677:0305-1048
620:0305-1048
563:0027-8424
247:, Sdhb,
166:stem-loop
93:Eukaryota
88:Domain(s)
2093:Category
2080:Archived
2029:28955777
2021:11901424
1961:11598127
1855:T. Leung
1841:20965423
1731:30770865
1723:17849083
1714:11136088
1665:20460462
1608:37819604
1600:17417656
1548:16760464
1474:16412980
1426:14568251
1366:11313346
846:21881407
777:A. Pardi
747:10070739
695:24728987
638:20460462
581:22586079
522:11741608
474:F. Kishi
466:A. Rofts
437:18489257
389:26572367
381:17185597
324:See also
261:CDC42BPA
251:, Hao1,
186:ferritin
1911:9418861
1832:3143508
1779:9020582
1656:2896125
1312:9891009
1258:8643505
1186:8530520
1132:2050126
1054:2498873
974:3479802
928:N. Aziz
914:3685996
893:Science
803:9398517
686:4041422
629:2896125
572:3365203
360:Science
257:SLC40A1
253:SLC11A2
196:of the
81:Cis-reg
63:RF00037
2027:
2019:
1993:&
1959:
1927:&
1909:
1902:121465
1899:
1871:L. Lim
1869:&
1863:I. Tan
1839:
1829:
1799:&
1777:
1751:&
1729:
1721:
1711:
1681:&
1663:
1653:
1645:
1606:
1598:
1572:&
1546:
1514:&
1472:
1446:&
1424:
1398:&
1364:
1332:&
1326:E. Lin
1310:
1278:&
1256:
1246:
1214:&
1184:
1152:&
1130:
1123:452865
1120:
1090:&
1052:
1045:287180
1042:
1010:&
972:
965:299567
962:
930:&
912:
882:&
844:
801:
775:&
745:
719:&
693:
683:
675:
636:
626:
618:
579:
569:
561:
520:
488:&
435:
409:&
387:
379:
307:kinase
265:CDC14A
194:3' UTR
190:5' UTR
152:, the
140:entry
49:Symbol
38:of IRE
2025:S2CID
1929:H. Yu
1727:S2CID
1604:S2CID
1249:39381
385:S2CID
330:5'UTR
269:EPAS1
245:ALAS2
178:mRNAs
2062:Rfam
2051:Rfam
2017:PMID
1957:PMID
1907:PMID
1837:PMID
1775:PMID
1719:PMID
1661:PMID
1643:ISSN
1596:PMID
1544:PMID
1470:PMID
1422:PMID
1362:PMID
1308:PMID
1254:PMID
1182:PMID
1128:PMID
1050:PMID
970:PMID
910:PMID
842:PMID
799:PMID
743:PMID
691:PMID
673:ISSN
634:PMID
616:ISSN
577:PMID
559:ISSN
518:PMID
433:PMID
377:PMID
249:ACO2
241:TFRC
233:FTH1
174:UTRs
142:2IPY
118:PDBe
77:type
58:Rfam
34:and
2060:at
2049:at
2009:doi
1947:doi
1943:276
1897:PMC
1889:doi
1827:PMC
1819:doi
1767:doi
1709:PMC
1701:doi
1651:PMC
1635:doi
1588:doi
1534:doi
1530:281
1462:doi
1458:341
1414:doi
1352:doi
1348:276
1298:doi
1294:274
1244:PMC
1234:doi
1172:doi
1168:270
1118:PMC
1110:doi
1040:PMC
1030:doi
960:PMC
950:doi
902:doi
898:238
832:doi
791:doi
787:274
735:doi
681:PMC
665:doi
624:PMC
608:doi
567:PMC
549:doi
545:109
508:doi
504:509
425:doi
369:doi
365:314
335:IRP
237:FTL
162:IRE
156:or
148:In
112:PDB
75:RNA
52:IRE
2095::
2023:.
2015:.
2003:.
1989:;
1985:;
1981:;
1977:;
1955:.
1941:.
1935:.
1905:.
1895:.
1885:18
1883:.
1877:.
1865:;
1861:;
1857:;
1835:.
1825:.
1815:40
1813:.
1807:.
1795:;
1773:.
1763:22
1761:.
1747:;
1725:.
1717:.
1707:.
1697:64
1695:.
1689:.
1659:.
1649:.
1641:.
1631:38
1629:.
1625:.
1602:.
1594:.
1584:14
1582:.
1568:;
1564:;
1542:.
1528:.
1522:.
1510:;
1506:;
1502:;
1498:;
1494:;
1490:;
1468:.
1456:.
1442:;
1420:.
1410:39
1408:.
1394:;
1390:;
1386:;
1382:;
1360:.
1346:.
1340:.
1328:;
1306:.
1292:.
1286:.
1274:;
1252:.
1242:.
1230:93
1228:.
1222:.
1210:;
1206:;
1202:;
1180:.
1166:.
1160:.
1148:;
1126:.
1116:.
1106:10
1104:.
1098:.
1086:;
1082:;
1078:;
1074:;
1070:;
1048:.
1038:.
1026:86
1024:.
1018:.
1006:;
1002:;
998:;
994:;
990:;
968:.
958:.
946:84
944:.
938:.
908:.
896:.
890:.
878:;
874:;
870:;
866:;
862:;
840:.
826:.
820:.
797:.
785:.
771:;
767:;
763:;
741:.
731:29
729:.
715:;
711:;
689:.
679:.
671:.
661:42
659:.
655:.
632:.
622:.
614:.
604:38
602:.
598:.
575:.
565:.
557:.
543:.
539:.
516:.
502:.
496:.
484:;
480:;
476:;
472:;
468:;
464:;
460:;
456:;
445:^
431:.
421:28
419:.
405:;
383:.
375:.
363:.
271:.
267:,
263:,
243:,
239:,
235:,
204:.
100:SO
2031:.
2011::
2005:4
1963:.
1949::
1913:.
1891::
1843:.
1821::
1781:.
1769::
1733:.
1703::
1667:.
1637::
1610:.
1590::
1550:.
1536::
1476:.
1464::
1428:.
1416::
1368:.
1354::
1314:.
1300::
1260:.
1236::
1188:.
1174::
1134:.
1112::
1056:.
1032::
976:.
952::
916:.
904::
848:.
834::
828:8
805:.
793::
749:.
737::
697:.
667::
640:.
610::
583:.
551::
524:.
510::
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427::
391:.
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160:(
144:.
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