GATA gene transcriptions

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

EpoR is thought to contribute to differentiation via multiple signaling pathways including the STAT5 pathway. Credit: Monkeyontheloose.

Although "the P3, P6 substitutions alter the conserved 'GATAAG' I box motif, a 'GATA' motif is present in the introduced EcoRV site. This introduced GATA sequence clearly does not serve as a functional I box [...]."[1]

"The I-box motif, 5'-GGATGAGATAAGA-3', or its shorter version 5'-GATAAG-3', has been found in the promoters of a large number of RBCS genes (Giuliano et al., 1988; Manzara and Gruissem, 1988). A related motif (the GATA box) is present in the promoters of the light-regulated chlorophyll a/b binding protein (CAB) genes of different species (Gidoni et al., 1989), and has been shown to be involved in the activation of an Arabidopsis CAB gene by light and by the circadian clock (Anderson and Kay, 1995). I-box and GATA binding factors have been identified in nuclear extracts from tobacco and tomato leaves and cotyledons (Borello et al., 1993; Giuliano et al., 1988; Manzara et al., 1991; Schindler and Cashmore, 1990). The I-box has therefore been suggested to be involved in light-regulated and/or leaf-specific gene expression of photosynthetic genes (Manzara et al., 1991), but to date no I-box binding protein has been cloned from plants."[2]

SRF is important during the development of the embryo, as it has been linked to the formation of mesoderm.[3][4]

The Serum response factor (SRF) has been shown to interact with GATA4.[5][6]

Cell specific developmental expression is tightly controlled, but, once expressed, require no additional activation -- GATA transcription factor (GATA), hepatocyte nuclear factors (HNF), PIT-1, MyoD, Myf5, Hox, winged-helix transcription factors.

The class of diverse Cys4 zinc fingers includes the family of GATA-factors.

In the diagram on the right, STAT5 may be involved with an erythropoiesis receptor, or Epo Receptor. Murine, members of the subfamily Murinae, Epo Receptor truncations and known functions are included. Erythroid differentiation depends on transcriptional regulator GATA1, zinc finger DNA binding domain binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements. In erythropoiesis, EpoR is best known for inducing survival of progenitors.

Some "putative wound-response elements including AGC box-like sequences28, TCA motif-like sequences28, carrot extensin gene wound-response elements (AT-rich motif, TTTTTTT, TGACGT)29, constitutive PAL footprint and elicitor-inducible PAL footprint31, and proteinase inhibitor II footprint31 have been found in cabch29 promoter. Some cis-elements related to organ and tissue-specific expression such as GATA motif-like sequence, ASF-1 binding site-like elements also existed in 5′ upstream region. Meanwhile, some basic transcriptional regulatory cis-elements including G box-like and GC box-like elements are located in this region."[7]

"A computer search for transcription promoter elements [...] showed the presence of a prominent TATA box 22 nucleotides upstream of the transcription start site and an Sp1 site at position -42 to -33. The 5'-flanking sequence also contains three E boxes with CANNTG consensus sequences at positions -464 to -459, -90 to -85, and -52 to -47 that have been marked as E box, E1 box, and E2 box, respectively [...]. In addition, the 5'-flanking region contains one or more GRE, XRE, GATA-1, GCN-4, PEA-3, AP1, and AP2 consensus motifs and also three imperfect CArG sites [...]."[8]

Single transcription factor transdifferentiation

Brief expression of a single transcription factor, the ELT-7 GATA factor, can convert the identity of fully differentiated, specialized non-endodermal cells of the pharynx into fully differentiated intestinal cells in intact larvae and adult roundworm Caenorhabditis elegans with no requirement for a dedifferentiated intermediate.[9]

"ELT-7, a GATA transcription factor that regulates terminal intestinal differentiation (Maduro and Rothman, 2002; Sommermann et al., 2010), activates an intestinal marker (elt-2::lacZ::GFP) in non-intestinal cells when briefly ectopically expressed via a heat-shock promoter at any embryonic, larval, or adult stage [...]."[9]

The "END-1 GATA transcription factor, which specifies the endoderm progenitor (Zhu et al., 1997), does not activate widespread intestinal gene expression after the MCT [...]."[9]

Cardiomyocytes

Cell-based in vivo therapies may provide a transformative approach to augment vascular and muscle growth and to prevent non-contractile scar formation by delivering transcription factors[10] or microRNAs[11] to the heart.[12] Cardiac fibroblasts, which represent 50% of the cells in the mammalian heart, can be reprogrammed into cardiomyocyte-like cells in vivo by local delivery of cardiac core transcription factors (GATA4, MEF2C, TBX5 and for improved reprogramming plus ESRRG, MESP1, Myocardin and ZFPM2) after coronary ligation.[10][13] These results implicated therapies that can directly remuscularize the heart without cell transplantation. However, the efficiency of such reprogramming turned out to be very low and the phenotype of received cardiomyocyte-like cells does not resemble those of a mature normal cardiomyocyte. Furthermore, transplantation of cardiac transcription factors into injured murine hearts resulted in poor cell survival and minimal expression of cardiac genes.[14]

Blood stem cells

Definitive hematopoiesis emerges during embryogenesis via an endothelial-to-hematopoietic transition. Combination of four transcription factors, GATA2, GFI1B, c-Fos, and ETV6, is sufficient to induce in vitro development leading to the formation of endothelial-like precursor cells, with the subsequent appearance of hematopoietic cells.[15] Transient expression of six transcription factors (RUNX1T1, HLF, LMO2, Prdm5, PBX1, ZFP36) and also N-Myc with MEIS1, to improve reprogramming efficacy, is sufficient to activate the gene networks governing hematopoietic stem cells functional identity in committed blood cells. This finding marks a significant step toward one of the most sought-after goals of regenerative medicine: the ability to produce hematopoietic stem cells suitable for transplantation, using more mature or differentiated blood cells to make up the shortfall of bone marrow transplants[16] It should be noted, however, that the transcription factors used in this study belong to a group of proto-oncogenes and therefore these cells could be dangerous to humans. Still to be answered are the precise contribution of each of the eight factors to the reprogramming process and whether approaches that do not rely on viruses and transcription factors can have similar success. It also is not yet known whether the same results can be achieved using human cells or whether other, non-blood cells can be reprogrammed to iHSCs.[17]

Human genes

Gene ID: 2623 is GATA1 GATA binding protein 1. "This gene encodes a protein which belongs to the GATA family of transcription factors. The protein plays an important role in erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin. Mutations in this gene have been associated with X-linked dyserythropoietic anemia and thrombocytopenia."[18]

  1. NP_002040.1 erythroid transcription factor, smart00401 Location:202 → 247, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:203 → 247, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[18]
  2. XP_011542199.1 erythroid transcription factor isoform X1, smart00401 Location:202 → 247, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:203 → 247, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[18]
  3. XP_011542200.1 erythroid transcription factor isoform X2, smart00401 Location:119 → 164, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:120 → 164, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[18]
  4. XP_024308131.1 erythroid transcription factor isoform X3, cd00202 Location:120 → 164, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[18]

Gene ID: 2624 is GATA2 GATA binding protein 2. "This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded protein plays an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages. Alternative splicing results in multiple transcript variants."[19]

  1. NP_001139133.1 endothelial transcription factor GATA-2 isoform 1. Transcript Variant: This variant (1) represents the longest transcript. Both variants 1 and 2 encode the same isoform (1). cd00202 Location:349 → 398, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[19]
  2. NP_001139134.1 endothelial transcription factor GATA-2 isoform 2. Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate splice site in the CDS but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1. cd00202 Location:294 → 336, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[19]
  3. NP_116027.2 endothelial transcription factor GATA-2 isoform 1. Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1). cd00202 Location:349 → 398, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[19]

Gene ID: 2625 is GATA3 GATA binding protein 3. "This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia."[20]

  1. NP_001002295.1 trans-acting T-cell-specific transcription factor GATA-3 isoform 1. Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). smart00401 Location:313 → 362, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:317 → 367, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[20]
  2. NP_002042.1 trans-acting T-cell-specific transcription factor GATA-3 isoform 2. Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1. smart00401 Location:312 → 361, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:316 → 366, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[20]
  3. XP_005252500.1 trans-acting T-cell-specific transcription factor GATA-3 isoform X1. smart00401 Location:313 → 362, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:317 → 367, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[20]
  4. XP_005252499.1 trans-acting T-cell-specific transcription factor GATA-3 isoform X1. smart00401 Location:313 → 362, ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG], cd00202 Location:317 → 367, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[20]

Gene ID: 2626 is GATA4 GATA binding protein 4. "This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants."[21]

  1. NP_001295022.1 transcription factor GATA-4 isoform 1. cd00202 Location:271 → 322, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]
  2. NP_001295023.1 transcription factor GATA-4 isoform 3. cd00202 Location:64 → 115, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C.[21]
  3. NP_001361202.1 transcription factor GATA-4 isoform 3.[21]
  4. NP_001361203.1 transcription factor GATA-4 isoform 4.[21]
  5. NP_002043.2 transcription factor GATA-4 isoform 2. cd00202 Location:270 → 321, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]
  6. XP_011542119.1 transcription factor GATA-4 isoform X1. cd00202 Location:271 → 322, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]
  7. XP_011542120.1 transcription factor GATA-4 isoform X1. cd00202 Location:271 → 322, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]
  8. XP_016868801.1 transcription factor GATA-4 isoform X1. cd00202 Location:271 → 322, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]
  9. XP_005272442.1 transcription factor GATA-4 isoform X1. cd00202 Location:271 → 322, ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C. pfam05349 Location:1 → 205, GATA-N; GATA-type transcription activator, N-terminal.[21]

Acknowledgements

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

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

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

See also

References

  1. ↑ Robert G. K. Donald and Anthony R. Cashmore (1990). "Mutation of either G box or I box sequences profoundly affects expression from the Arabidopsis rbcS‐1A promoter". The EMBO Journal. 9 (6): 1717–1726. doi:10.1002/j.1460-2075.1990.tb08295.x. Retrieved 8 November 2018.
  2. ↑ Annkatrin Rose, Iris Meier and Udo Wienand (28 October 1999). "The tomato I-box binding factor LeMYBI is a member of a novel class of Myb-like proteins". The Plant Journal. 20 (6): 641–652. doi:10.1046/j.1365-313X.1999.00638.x. Retrieved 8 November 2018.
  3. ↑ Sepulveda JL, Vlahopoulos S, Iyer D, Belaguli N, Schwartz RJ (July 2002). "Combinatorial expression of GATA4, Nkx2-5, and serum response factor directs early cardiac gene activity". J. Biol. Chem. 277 (28): 25775–82. doi:10.1074/jbc.M203122200. PMID 11983708.
  4. ↑ Barron MR, Belaguli NS, Zhang SX, Trinh M, Iyer D, Merlo X, Lough JW, Parmacek MS, Bruneau BG, Schwartz RJ (March 2005). "Serum response factor, an enriched cardiac mesoderm obligatory factor, is a downstream gene target for Tbx genes". J. Biol. Chem. 280 (12): 11816–28. doi:10.1074/jbc.M412408200. PMID 15591049.
  5. ↑ Belaguli NS, Sepulveda JL, Nigam V, Charron F, Nemer M, Schwartz RJ (October 2000). "Cardiac tissue enriched factors serum response factor and GATA-4 are mutual coregulators". Mol. Cell. Biol. 20 (20): 7550–8. doi:10.1128/mcb.20.20.7550-7558.2000. PMC 86307. PMID 11003651.
  6. ↑ Morin S, Paradis P, Aries A, Nemer M (February 2001). "Serum response factor-GATA ternary complex required for nuclear signaling by a G-protein-coupled receptor". Mol. Cell. Biol. 21 (4): 1036–44. doi:10.1128/MCB.21.4.1036-1044.2001. PMC 99558. PMID 11158291.
  7. ↑ Guo Qing Tang, Yong Yan Bai & Shi Wei Loo (1 June 1996). "Functional properties of a cabbage chitinase promoter from cabbage (Brassica oleracea var. capitata)". Cell Research. 6 (9): 75–84. Retrieved 24 March 2019.
  8. ↑ Nibedita Lenka, Aruna Basu, Jayati Mullick, and Narayan G. Avadhani (22 November 1996). "The role of an E box binding basic helix loop helix protein in the cardiac muscle-specific expression of the rat cytochrome oxidase subunit VIII gene" (PDF). The Journal of Biological Chemistry. 271 (47): 30281–30289. doi:10.1074/jbc.271.47.30281. Retrieved 7 February 2019.
  9. ↑ 9.0 9.1 9.2 Misty R. Riddle, Abraham Weintraub, Ken C. Q. Nguyen, David H. Hall, and Joel H. Rothman (2013). "Transdifferentiation and remodeling of post-embryonic C. elegans cells by a single transcription factor". Development. 140 (24): 4844–9. doi:10.1242/dev.103010. Retrieved 29 December 2019.
  10. ↑ 10.0 10.1 Li Qian, Yu Huang, C. Ian Spencer, Amy Foley, Vasanth Vedantham, Lei Liu, Simon J. Conway, Ji-dong Fu & Deepak Srivastava (18 April 2012). "In vivo reprogramming of murine cardiac fibroblasts into induced cardiomyocytes". Nature. 485: 593–8. doi:10.1038/nature11044.
  11. ↑ Tilanthi M. Jayawardena, Bakytbek Egemnazarov, Elizabeth A. Finch, Lunan Zhang, J. Alan Payne, Kumar Pandya, Zhiping Zhang, Paul Rosenberg, Maria Mirotsou, and Victor J. Dzau. "MicroRNA-Mediated In Vitro and In Vivo Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes". Circulation Research.
  12. ↑ |doi=10.1016/j.molmed.2012.06.009 }}
  13. ↑ . doi:10.1016/j.stemcr.2013.07.005. Missing or empty |title= (help); Missing or empty |url= (help)
  14. ↑ . doi:10.1161/CIRCRESAHA.112.270264. Missing or empty |title= (help); Missing or empty |url= (help)
  15. ↑ Pereira, C. F., Chang, B., Qiu, J., Niu, X., Papatsenko, D., Hendry, C. E., ... & Moore, K. (2013). Induction of a hemogenic program in mouse fibroblasts. Cell stem cell, 13(2), 205-218. DOI: http://dx.doi.org/10.1016/j.stem.2013.05.024
  16. ↑ Jonah Riddell, Roi Gazit, Brian S. Garrison, et al., & Derrick J. Rossi (2014). Reprogramming Committed Murine Blood Cells to Induced Hematopoietic Stem Cells with Defined Factors. Cell, 157(30, 549–564, DOI: http://dx.doi.org/10.1016/j.cell.2014.04.006
  17. ↑ Boston Children's Hospital."Blood cells reprogrammed into blood stem cells in mice". ScienceDaily, 24 April 2014
  18. ↑ 18.0 18.1 18.2 18.3 18.4 RefSeq (July 2008). "GATA1 GATA binding protein 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 30 December 2019.
  19. ↑ 19.0 19.1 19.2 19.3 RefSeq (March 2009). "GATA2 GATA binding protein 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 30 December 2019.
  20. ↑ 20.0 20.1 20.2 20.3 20.4 RefSeq (November 2009). "GATA3 GATA binding protein 3 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 30 December 2019.
  21. ↑ 21.0 21.1 21.2 21.3 21.4 21.5 21.6 21.7 21.8 21.9 RefSeq (April 2015). "GATA4 GATA binding protein 4 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 30 December 2019.

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