Langbahn Team – Weltmeisterschaft

E-box

An E-box (enhancer box) is a DNA response element found in some eukaryotes that acts as a protein-binding site and has been found to regulate gene expression in neurons, muscles, and other tissues.[1] Its specific DNA sequence, CANNTG (where N can be any nucleotide), with a palindromic canonical sequence of CACGTG,[2] is recognized and bound by transcription factors to initiate gene transcription. Once the transcription factors bind to the promoters through the E-box, other enzymes can bind to the promoter and facilitate transcription from DNA to mRNA.

Discovery

The E-box was discovered in a collaboration between Susumu Tonegawa's and Walter Gilbert's laboratories in 1985 as a control element in immunoglobulin heavy-chain enhancer.[3][4] They found that a region of 140 base pairs in the tissue-specific transcriptional enhancer element was sufficient for different levels of transcription enhancement in different tissues and sequences. They suggested that proteins made by specific tissues acted on these enhancers to activate sets of genes during cell differentiation.

In 1989, David Baltimore's lab discovered the first two E-box binding proteins, E12 and E47.[5] These immunoglobulin enhancers could bind as heterodimers to proteins through bHLH domains. In 1990, another E-protein, ITF-2A (later renamed E2-2Alt) was discovered that can bind to immunoglobulin light chain enhancers.[6] Two years later, the third E-box binding protein, HEB, was discovered by screening a cDNA library from HeLa cells.[7] A splice-variant of the E2-2 was discovered in 1997 and was found to inhibit the promoter of a muscle-specific gene.[8]

Since then, researchers have established that the E-box affects gene transcription in several eukaryotes and found E-box binding factors that identify E-box consensus sequences.[9] In particular, several experiments have shown that the E-box is an integral part of the transcription-translation feedback loop that comprises the circadian clock.

Binding

E-box binding proteins play a major role in regulating transcriptional activity. These proteins usually contain the basic helix-loop-helix protein structural motif, which allows them to bind as dimers.[10] This motif consists of two amphipathic α-helices, separated by a small sequence of amino acids, that form one or more β-turns. The hydrophobic interactions between these α-helices stabilize dimerization. Besides, each bHLH monomer has a basic region, which helps mediate recognition between the bHLH monomer and the E-box (the basic region interacts with the major groove of the DNA). Depending on the DNA motif ("CAGCTG" versus "CACGTG") the bHLH protein has a different set of basic residues.

Relative Position of CTRR and E-Box

The E-box binding is modulated by Zn2+ in mice. The CT-Rich Regions (CTRR) located about 23 nucleotides upstream of the E-box is important in E-box binding, transactivation (increased rate of genetic expression), and transcription of circadian genes BMAL1/NPAS2 and BMAL1/CLOCK complexes.[11]

The binding specificity of different E-boxes is found to be essential in their function. E-boxes with different functions have a different number and type of binding factor.[12]

The consensus sequence of the E-box is usually CANNTG; however, there exist other E-boxes of similar sequences called noncanonical E-boxes. These include, but are not limited to:

Role in the circadian clock

The link between E-box-regulated genes and the circadian clock was discovered in 1997, when Hao, Allen, and Hardin (Department of Biology at Texas A&M University) analyzed rhythmicity in the period (per) gene in Drosophila melanogaster.[16] They found a circadian transcriptional enhancer upstream of the per gene within a 69 bp DNA fragment. Depending upon PER protein levels, the enhancer drove high levels of mRNA transcription in both LD (light-dark) and DD (constant darkness) conditions. The enhancer was found to be necessary for high-level gene expression but not for circadian rhythmicity. It also works independently as a target of the BMAL1/CLOCK complex.

The E-box plays an important role in circadian genes; so far, nine E/E'BOX controlled circadian genes have been identified: PER1, PER2, BHLHB2, BHLHB3, CRY1, DBP, Nr1d1, Nr1d2, and RORC.[17] As the E-box is connected to several circadian genes, it is possible that the genes and proteins associated with it are "crucial and vulnerable points in the (circadian) system."[18]

The E-box is one of the top five transcription factor families associated with the circadian phase and is found in most tissues.[19] A total of 320 E-box-controlled genes are found in the SCN (suprachiasmatic nucleus), liver, aorta, adrenal, WAT (white adipose tissue), brain, atria, ventricle, prefrontal cortex, skeletal muscle, BAT (brown adipose tissue), and calvarial bone.

E-box like CLOCK-related elements (EL-box; GGCACGAGGC) are also important in maintaining circadian rhythmicity in clock-controlled genes. Similarly to the E-box, the E-box like CLOCK related element can also induce transcription of BMAL1/CLOCK, which can then lead to expression in other EL-box containing genes (Ank, DBP, Nr1d1).[20] However, there are differences between the EL-box and the regular E-box. Suppressing DEC1 and DEC2 has a stronger effect on E-box than on EL-box. Furthermore, HES1, which can bind to a different consensus sequence (CACNAG, known as the N-box), shows suppression effect in EL-box, but not in E-box.

Both non-canonical E-boxes and E-box-like sequences are crucial for circadian oscillation. Recent research on this forms an hypothesis that either a canonical or non-canonical E-box followed by an E-box like sequence with 6 base pair interval in between is a necessary combination for circadian transcription.[21] In silico analysis also suggests that such an interval existed in other known clock-controlled genes.


Role of proteins which bind to E-boxes

There are several proteins that bind to the E-box and affect gene transcription.

CLOCK-ARNTL complex

The CLOCK-ARNTL (BMAL1) complex is an integral part of the mammalian circadian cycle and vital in maintaining circadian rhythmicity.

Knowing that binding activates transcription of the per gene in the promoter region, researchers discovered in 2002 that DEC1 and DEC2 (bHLH transcription factors) repressed the CLOCK-BMAL1 complex through direct interaction with BMAL1 and/or competition for E-box elements. They concluded that DEC1 and DEC2 were regulators of the mammalian molecular clock.[22]

In 2006, Ripperger and Schibler discovered that the binding of this complex to the E-box drove circadian DBP transcription and chromatin transitions (a change from chromatin to facultative heterochromatin).[23] It was concluded that CLOCK regulates DBP expression by binding to E-box motifs in enhancer regions located in the first and second introns.

MYC (c-Myc, an oncogene)

MYC (c-Myc), a gene that codes for a transcription factor Myc, is important in regulating mammalian cell proliferation and apoptosis.

In 1991, researchers tested whether c-Myc could bind to DNA by dimerizing it to E12. Dimers of E6, the chimeric protein, were able to bind to an E-box element (GGCCACGTGACC) which was recognized by other HLH proteins.[24] Expression of E6 suppressed the function of c-Myc, which showed a link between the two.

In 1996, it was found that Myc heterodimerizes with MAX and that this heterodimeric complex could bind to the CAC(G/A)TG E-box sequence and activate transcription.[25]

In 1998, it was concluded that the function of c-Myc depends upon activating transcription of particular genes through E-box elements.[26]

MYOD1 (MyoD)

MyoD comes from the Mrf bHLH family and its main role is myogenesis, the formation of muscular tissue.[9] Other members in this family include myogenin, Myf5, Myf6, Mist1, and Nex-1.

When MyoD binds to the E-box motif CANNTG, muscle differentiation and expression of muscle-specific proteins is initiated.[27] The researchers ablated various parts of the recombinant MyoD sequence and concluded that MyoD used encompassing elements to bind the E-box and the tetralplex structure of the promoter sequence of the muscle specific gene α7 integrin and sarcomeric sMtCK.

MyoD regulates HB-EGF (Heparin-binding EGF-like growth factor), a member of the EGF (Epidermal growth factor) family that stimulates cell growth and proliferation.[9] It plays a role in the development of hepatocellular carcinoma, prostate cancer, breast cancer, esophageal cancer, and gastric cancer.

MyoD can also bind to noncanonical E boxes of MyoG and regulate its expression.[28]

MyoG (Myogenin)

MyoG belongs to the MyoD transcription factor family. MyoG-E-Box binding is necessary for neuromuscular synapse formation as an HDAC-Dach2-myogenin signaling pathway in skeletal muscle gene expression has been identified.[29] Decreased MyoG expression has been shown in patients with muscle wasting symptom.[30]

MyoG and MyoD have also been shown to involve in myoblast differentiation.[31] They act by transactivating cathepsin B promotor activity and inducing its mRNA expression.

TCF3 (E47)

E47 is produced by alternative spliced E2A in E47 specific bHLH-encoding exons. Its role is to regulate tissue specific gene expression and differentiation. Many kinases have been associated with E47 including 3pk and MK2. These 2 proteins form a complex with E47 and reduce its transcription activity.[32] CKII and PKA are also shown to phosphorylate E47 in vitro.[33][34][35]

Similar to other E-box binding proteins, E47 also binds to the CANNTG sequence in the E-box. In homozygous E2A knock-out mice, B cells development stops before the DJ arrangement stage and the B cells fail to mature.[36] E47 has been shown to bind either as heterodimer(with E12)[37] or as homodimer(but weaker).[38]

Recent research

Although the structural basis for how BMAL1/CLOCK interact with the E-box is unknown, recent research has shown that the bHLH protein domains of BMAL1/CLOCK are highly similar to other bHLH containing proteins, e.g. Myc/Max, which have been crystallized with E-boxes.[39] It is surmised that specific bases are necessary to support this high affinity binding. Furthermore, the sequence constraints on the region around the circadian E-box are not fully understood: it is believed to be necessary but not sufficient for E-boxes to be randomly spaced from each other in the genetic sequence in order for circadian transcription to occur. Recent research involving the E-box has been aimed at trying to find more binding proteins as well as discovering more mechanisms for inhibiting binding.

Researchers at the Medical School of Nanjing University found that the amplitude of FBXL3 (F-box/Leucine rich-repeat protein) is expressed via an E-box.[40] They studied mice with FBXL3 deficiency and found that it regulates feedback loops in circadian rhythms by affecting circadian period length.

A study published April 4, 2013 by researchers at Harvard Medical School found that the nucleotides on either side of an E-box influences which transcription factors can bind to the E-box itself.[41] These nucleotides determine the 3-D spatial arrangement of the DNA strand and restrict the size of binding transcription factors. The study also found differences in binding patterns between in vivo and in vitro strands.

References

  1. ^ Massari, M. E.; Murre, C. (2000). "Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms". Molecular and Cellular Biology. 20 (2): 429–440. CiteSeerX 10.1.1.321.6077. doi:10.1128/mcb.20.2.429-440.2000. PMC 85097. PMID 10611221.
  2. ^ Chaudhary, J; Skinner, M K. (May 1999). "Basic helix-loop-helix proteins can act at the E-box within the serum response element of the c-fos promoter to influence hormone-induced promoter activation in Sertoli cells". Mol Endocrinol. 13 (5): 774–786. doi:10.1210/mend.13.5.0271. PMID 10319327.
  3. ^ Ephrussi, A; Church, GM; Tonegawa, S; Gilbert, W (1985). "B lineage-specific interactions of an immunoglobulin enhancer with cellular factors in vivo". Science. 227 (4683): 134–140. Bibcode:1985Sci...227..134E. doi:10.1126/science.3917574. PMID 3917574.
  4. ^ Church, GM; Ephrussi, A; Gilbert, W; Tonegawa, S (1985). "Cell-type-specific contacts to immunoglobulin enhancers in nuclei". Nature. 313 (6005): 798–801. Bibcode:1985Natur.313..798C. doi:10.1038/313798a0. PMID 3919308. S2CID 1878459.
  5. ^ Murre, C; Mc Caw, P S; Vaessin, H; et al. (Aug 1989). "Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence". Cell. 58 (3): 537–544. doi:10.1016/0092-8674(89)90434-0. PMID 2503252. S2CID 29339773.
  6. ^ Henthorn, P; Kiledjian, M; Kadesch, T (1990). "Two distinct transcription factors that bind the immunoglobulin enhancer microE5/kappa 2 motif". Science. 247 (4941): 467–470. Bibcode:1990Sci...247..467H. doi:10.1126/science.2105528. PMID 2105528.
  7. ^ Hu S-J, Olson E N; Kingston, R E. (1992). "HEB". Mol Cell Biol. 12 (3): 1031–1042. doi:10.1128/MCB.12.3.1031. PMC 369535. PMID 1312219.
  8. ^ Chen, B; Lim, R W. (Jan 1997). "Physical and functional interactions between the transcriptional inhibitors Id3 and ITF-2b. Evidence toward a novel mechanism regulating muscle-specific gene expression". J Biol Chem. 272 (4): 2459–2463. doi:10.1074/jbc.272.4.2459. PMID 8999959.
  9. ^ a b c Mädge B.: E-Box. In: Schwab M. (Ed.) Encyclopedia of Cancer. Springer-Verlag Berlin Heidelberg, 2009.
  10. ^ Ellenberger, T; Fass, D; Arnaud, M; Harrison, S C. (Apr 1994). "Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer". Genes Dev. 8 (8): 970–980. doi:10.1101/gad.8.8.970. PMID 7926781.
  11. ^ Muñoz, Estela; Michelle Brewer; Ruben Baler (2006). "Modulation of BMAL/CLOCK/E-Box complex activity by a CT-rich cis-acting element". Molecular and Cellular Endocrinology. 252 (1–2): 74–81. doi:10.1016/j.mce.2006.03.007. PMID 16650525. S2CID 38180029.
  12. ^ Bose, Sudeep; Boockfor, Fredric R. (2010). "Episodes of prolactin gene expression in GH3 cells are dependent on selective promoter binding of multiple circadian elements". Endocrinology. 151 (5): 2287–2296. doi:10.1210/en.2009-1252. PMC 2869263. PMID 20215567.
  13. ^ Yoo, S.H.; Ko, C.H.; Lowrey, P.L.; et al. (2005). "A noncanonical E-box enhancer drives mouse Period2 circadian oscillations in vivo". Proc. Natl. Acad. Sci. USA. 102 (7): 2608–2613. Bibcode:2005PNAS..102.2608Y. doi:10.1073/pnas.0409763102. PMC 548324. PMID 15699353.
  14. ^ Zhang, X.; Patel, S. P.; McCarthy, J. J.; Rabchevsky, A. G.; Goldhamer, D. J.; Esser, K. A. (2012). "A non-canonical E-box within the MyoD core enhancer is necessary for circadian expression in skeletal muscle". Nucleic Acids Res. 40 (8): 3419–3430. doi:10.1093/nar/gkr1297. PMC 3333858. PMID 22210883.
  15. ^ Salero, Enrique; Giménez, Cecilio; Zafra, Francisco (15 March 2003). "Identification of a non-canonical E-box motif as a regulatory element in the proximal promoter region of the apolipoprotein E gene". The Biochemical Journal. 370 (3): 979–986. doi:10.1042/BJ20021142. PMC 1223214. PMID 12444925.
  16. ^ Hao, H; Allen, D L; Hardin, P E. (Jul 1997). "A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster". Mol Cell Biol. 17 (7): 3687–3693. doi:10.1128/MCB.17.7.3687. PMC 232220. PMID 9199302.
  17. ^ Panda, S; Antoch MP; Miller BH; Su AI; Schook AB; Straume M; Schultz PG; Kay SA; Takahashi JS; Hogenesch JB (May 2002). "Coordinated transcription of key pathways in the mouse by the circadian clock". Cell. 109 (3): 307–320. doi:10.1016/S0092-8674(02)00722-5. PMID 12015981.
  18. ^ Herzog, Erik (October 2007). "Neurons and networks in daily rhythms". Nature Reviews Neuroscience. 8 (10): 790–802. doi:10.1038/nrn2215. PMID 17882255. S2CID 33687097.
  19. ^ Yan, Jun; Haifang Wang; Yuting Liu; Chunxuan Shao (October 2008). "Analysis of Gene Regulatory Networks in the Mammalian Circadian Rhythm". PLOS Computational Biology. 4 (10): e1000193. Bibcode:2008PLSCB...4E0193Y. doi:10.1371/journal.pcbi.1000193. PMC 2543109. PMID 18846204.
  20. ^ Ueshima, T; Kawamoto T; Honda KK; Noshiro M; Fujimoto K; Nakao S; Ichinose N; Hashimoto S; Gotoh O; Kato Y (December 2012). "Identification of a new clock-related element EL-box involved in circadian regulation by BMAL1/CLOCK and HES1". Gene. 510 (2): 118–125. doi:10.1016/j.gene.2012.08.022. PMID 22960268.
  21. ^ Nakahata, Y; Yoshida M; Takano A; Soma H; Yamamoto T; Yasuda A; Nakatsu T; Takumi T (January 2008). "A direct repeat of E-box-like elements is required for cell-autonomous circadian rhythm of clock genes". BMC Mol Biol. 9 (1): 1. doi:10.1186/1471-2199-9-1. PMC 2254435. PMID 18177499.
  22. ^ Honma, S; Kawamoto, T; Takagi, Y; Fujimoto, K; Sato, F; Noshiro, M; Kato, Y; Honma, K. (2002). "Dec1 and Dec2 are regulators of the mammalian molecular clock". Nature. 419 (6909): 841–844. Bibcode:2002Natur.419..841H. doi:10.1038/nature01123. PMID 12397359. S2CID 4426418.
  23. ^ Ripperger, J A.; Schibler, U. (Mar 2006). "Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions" (PDF). Nat. Genet. 38 (3): 369–374. doi:10.1038/ng1738. PMID 16474407. S2CID 13433446.
  24. ^ Prendergast, G C; Ziff, E B. (Jan 1991). "Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region". Science. 251 (4990): 186–189. Bibcode:1991Sci...251..186P. doi:10.1126/science.1987636. PMID 1987636.
  25. ^ Desbarats, L; Gaubatz, S; Eilers, M. (Feb 1996). "Discrimination between different E-box-binding proteins at an endogenous target gene of c-myc". Genes Dev. 10 (4): 447–460. doi:10.1101/gad.10.4.447. PMID 8600028.
  26. ^ Xiao, Q; Claassen, G; Shi, J; Adachi, S; Seivy, J; Hann, S R. (Dec 1998). "Transactivation-defective c-MycS retains the ability to regulate proliferation and apoptosis". Genes Dev. 12 (24): 3803–3808. doi:10.1101/gad.12.24.3803. PMC 317265. PMID 9869633.
  27. ^ Shklover, J; Etzioni, S; Weisman-Shomer, P; Yafe, A; Bengal, E; Fry, M. (2007). "MyoD uses overlapping but distinct elements to bind E-box and tetraplex structures of regulatory sequences of muscle-specific genes". Nucleic Acids Res. 35 (21): 7087–7095. doi:10.1093/nar/gkm746. PMC 2175354. PMID 17942416.
  28. ^ Bergstrom, D. A.; Penn, B. H.; Strand, A.; Perry, R. L.; Rudnicki, M. A.; Tapscott, S. J. (2002). "Promoter-specific regulation of MyoD binding and signal transduction cooperate to pattern gene expression". Mol. Cell. 9 (3): 587–600. doi:10.1016/s1097-2765(02)00481-1. PMID 11931766.
  29. ^ Tang, H; Goldman, D (2006). "Activity-dependent gene regulation in skeletal muscle is mediated by a histone deacetylase (HDAC)-Dach2-myogenin signal transduction cascade". Proc Natl Acad Sci USA. 103 (45): 16977–16982. Bibcode:2006PNAS..10316977T. doi:10.1073/pnas.0601565103. PMC 1636564. PMID 17075071.
  30. ^ Ramamoorthy, S; Donohue, M; Buck, M. (2009). "Decreased Jun-D and myogenin expression in muscle wasting of human cachexia". Am J Physiol Endocrinol Metab. 297 (2): E392–401. doi:10.1152/ajpendo.90529.2008. PMC 2724118. PMID 19470832.
  31. ^ Jane, D.T.; Morvay, L.C.; Koblinski, J.; et al. (2002). "Evidence that E-box promoter elements and MyoD transcription factors play a role in the induction of cathepsin B gene expression during human myoblast differentiation". Biol. Chem. 383 (12): 1833–1844. doi:10.1515/BC.2002.207. PMID 12553720. S2CID 26010667.
  32. ^ Neufeld, Bernd; Grosse-Wilde, Anne; Hoffmeyer, Angelika; Jordan, Bruce W. M.; Chen, Peifeng; Dinev, Dragomir; Ludwig, Stephan; Rapp, Ulf R. (7 July 2000). "Serine/Threonine kinases 3pK and MAPK-activated protein kinase 2 interact with the basic helix-loop-helix transcription factor E47 and repress its transcriptional activity". Journal of Biological Chemistry. 275 (27): 20239–20242. doi:10.1074/jbc.C901040199. PMID 10781029.
  33. ^ Johnson, Sally E.; Wang, Xueyan; Hardy, Serge; Taparowsky, Elizabeth J.; Konieczny, Stephen F. (April 1996). "Casein kinase II increases the transcriptional activities of MRF4 and MyoD independently of their direct phosphorylation". Molecular and Cellular Biology. 16 (4): 1604–1613. doi:10.1128/MCB.16.4.1604. PMC 231146. PMID 8657135.
  34. ^ Sloan, Steven R.; Shen, Chun-Pyn; McCarrick-Walmsley, Ruth; Kadesch, Tom (December 1996). "Phosphorylation of E47 as a potential determinant of B-cell-specific activity". Molecular and Cellular Biology. 16 (12): 6900–6908. doi:10.1128/MCB.16.12.6900. PMC 231693. PMID 8943345.
  35. ^ Shen, Chun-Pyn; Kadesch, Tom (August 1995). "B-cell-specific DNA binding by an E47 homodimer". Molecular and Cellular Biology. 15 (8): 4518–4524. doi:10.1128/MCB.15.8.4518. PMC 230691. PMID 7623842.
  36. ^ Bain, Gretchen; Maandag, Els C.; Izon, David J.; Amsen, Derk; Kruisbeek, Ada M.; Weintraub, Bennett C.; Krop, Ian; Schlissel, Mark S.; Feeney, Ann J.; van Roon, Marian; van der Valk, Martin; te Riele, Hein P.J.; Berns, Anton; Murre, Cornelius (2 December 1994). "E2A proteins are required for proper B cell development and initiation of immunoglobulin gene rearrangements". Cell. 79 (5): 885–92. doi:10.1016/0092-8674(94)90077-9. PMID 8001125. S2CID 34325904.
  37. ^ Lassar, Andrew B.; Davis, Robert L.; Wright, Woodring E.; Kadesch, Tom; Murre, Cornelius; Voronova, Anna; Baltimore, David; Weintraub, Harold (26 July 1991). "Functional activity of myogenic HLH proteins requires hetero-oligomerization with E12/E47-like proteins in vivo". Cell. 66 (2): 305–15. doi:10.1016/0092-8674(91)90620-E. PMID 1649701. S2CID 25957022.
  38. ^ Murre, Cornelius; McCaw, Patrick Schonleber; Vaessin, H.; Caudy, M.; Jan, L.Y.; Jan, Y.N.; Cabrera, Carlos V.; Buskin, Jean N.; Hauschka, Stephen D.; Lassar, Andrew B.; Weintraub, Harold; Baltimore, David (11 August 1989). "Interactions between heterologous helix-loop-helix proteins generate complexes that bind specifically to a common DNA sequence". Cell. 58 (3): 537–44. doi:10.1016/0092-8674(89)90434-0. PMID 2503252. S2CID 29339773.
  39. ^ Muñoz, E; Brewer, M; Baler, R. (Sep 2002). "Circadian Transcription: THINKING OUTSIDE THE E-BOX". J Biol Chem. 277 (39): 36009–36017. doi:10.1074/jbc.m203909200. PMID 12130638.
  40. ^ Shi, G; Xing, L; Liu, Z; et al. (2013). "Dual roles of FBXL3 in the mammalian circadian feedback loops are important for period determination and robustness of the clock". Proc Natl Acad Sci U S A. 110 (12): 4750–5. Bibcode:2013PNAS..110.4750S. doi:10.1073/pnas.1302560110. PMC 3606995. PMID 23471982.
  41. ^ Gordân, R; Shen, N; Dror, I; Zhou, T; Horton, J; Rohs, R; Bulyk, ML. (Apr 2013). "Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape". Cell Rep. 3 (4): 1093–104. doi:10.1016/j.celrep.2013.03.014. PMC 3640701. PMID 23562153.
Quelle: https://en.wikipedia.org/wiki/E-box