Transcriptional regulation by CHIP/LDB complexes

PLoS Genetics

Volumn 6, Issue 8, 2010, Pages

  Bronstein, Revital ^a   Levkovitz, Liron ^a   Yosef, Nir ^a   Yanku, Michaela ^a   Ruppin, Eytan ^a   Sharan, Roded ^a   Westphal, Heiner ^b   Oliver, Brian ^c   Segal, Daniel ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTOR PROTEIN; APTEROUS PROTEIN; DROSOPHILA PROTEIN; GS ALPHA PROTEIN; PANNIER PROTEIN; PROTEASOME; PROTEIN CHIP; PROTEIN LDB; SINGLE STRANDED DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; X BOX BINDING PROTEIN 1; AP PROTEIN, DROSOPHILA; CHI PROTEIN, DROSOPHILA; HOMEODOMAIN PROTEIN; NUCLEAR PROTEIN; PNR PROTEIN, DROSOPHILA; SSDP PROTEIN, DROSOPHILA;

ARTICLE; BINDING SITE; CONTROLLED STUDY; DROSOPHILA; ENZYMATIC DEGRADATION; FEMALE; FORELIMB; GENE FUNCTION; GENE INTERACTION; GENE MUTATION; GENE SILENCING; GENE TARGETING; INSECT DEVELOPMENT; MALE; NONHUMAN; PROTEIN FUNCTION; PROTEIN INTERACTION; RNA INTERFERENCE; THORAX; TRANSCRIPTION REGULATION; ANIMAL; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PROTEIN BINDING;

ANIMALS; DROSOPHILA; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; NUCLEAR PROTEINS; PROTEIN BINDING; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 77957376759     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001063     Document Type: Article

References (72)

1. Alvarez M, Rhodes SJ, Bidwell JP (2003) Context-dependent transcription: all politics is local. Gene 313: 43-57.
2. Rosenfeld MG, Lunyak VV, Glass CK (2006) Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. Genes & Development 20: 1405-1428.
3. Ma J (2005) Crossing the line between activation and repression. Trends Genet 21: 54-59.
4. Matthews JM, Visvader JE (2003) LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins. EMBO Rep 4: 1132-1137.
5. Cohen B, McGuffin ME, Pfeifle C, Segal D, Cohen SM (1992) apterous, a gene required for imaginal disc development in Drosophila encodes a member of the LIM family of developmental regulatory proteins. Genes & Development 6: 715-729.
6. Rincon-Limas DE, Lu C-H, Canal I, Calleja M, Rodriguez-Esteban CN, et al. (1999) Conservation of the expression and function of apterous orthologs in Drosophila and mammals. Proceedings of the National Academy of Sciences of the United States of America 96: 2165-2170.
7. van Meyel DJ, O'Keefe DD, Jurata LW, Thor S, Gill GN, et al. (1999) Chip and Apterous Physically Interact to Form a Functional Complex during Drosophila Development. Molecular Cell 4: 259-265.
8. Milan M, Cohen SM (1999) Regulation of LIM homeodomain activity in vivo: a tetramer of dLDB and apterous confers activity and capacity for regulation by dLMO. Mol Cell 4: 267-273.
9. Milan M, Diaz-Benjumea FJ, Cohen SM (1998) Beadex encodes an LMO protein that regulates Apterous LIM-homeodomain activity in Drosophila wing development: a model for LMO oncogene function. Genes Dev 12: 2912-2920.
10. van Meyel DJ, Thomas JB, Agulnick AD (2003) Ssdp proteins bind to LIMinteracting co-factors and regulate the activity of LIM-homeodomain protein complexes in vivo. Development 130: 1915-1925.
11. Herranz H, Milan M (2006) Notch and affinity boundaries in Drosophila. Bioessays 28: 113-116.
12. Shoresh M, Orgad S, Shmueli O, Werczberger R, Gelbaum D, et al. (1998) Overexpression Beadex mutations and loss-of-function heldup-a mutations in Drosophila affect the 39 regulatory and coding components, respectively, of the Dlmo gene. Genetics 150: 283-299.
13. Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, et al. (2002) Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development. Proc Natl Acad Sci U S A 99: 14320-14325.
14. Weihe U, Milan M, Cohen SM (2001) Regulation of Apterous activity in Drosophila wing development. Development 128: 4615-4622.
15. Milan M, Cohen SM (2000) Temporal regulation of apterous activity during development of the Drosophila wing. Development 127: 3069-3078.
16. Ramain P, Khechumian R, Khechumian K, Arbogast N, Ackermann C, et al. (2000) Interactions between chip and the achaete/scute-daughterless heterodimers are required for pannier-driven proneural patterning. Mol Cell 6: 781-790.
17. Romani S, Campuzano S, Macagno ER, Modolell J (1989) Expression of achaete and scute genes in Drosophila imaginal discs and their function in sensory organ development. Genes Dev 3: 997-1007.
18. Zenvirt S, Nevo-Caspi Y, Rencus-Lazar S, Segal D (2008) Drosophila LIM-only is a positive regulator of transcription during thoracic bristle development. Genetics 179: 1989-1999.
19. Asmar J, Biryukova I, Heitzler P (2008) Drosophila dLMO-PA isoform acts as an early activator of achaete/scute proneural expression. Dev Biol 316: 487-497.
20. Agulnick AD, Taira M, Breen JJ, Tanaka T, Dawid IB, et al. (1996) Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins. Nature 384: 270-272.
21. Nishioka N, Nagano S, Nakayama R, Kiyonari H, Ijiri T, et al. (2005) Ssdp1 regulates head morphogenesis of mouse embryos by activating the Lim1-Ldb1 complex. Development 132: 2535-2546.
22. Gungor C, Taniguchi-Ishigaki N, Ma H, Drung A, Tursun B, et al. (2007) Proteasomal selection of multiprotein complexes recruited by LIM homeodomain transcription factors. Proc Natl Acad Sci U S A 104: 15000-15005.
23. Osada H, Grutz G, Axelson H, Forster A, Rabbitts TH (1995) Association of erythroid transcription factors: complexes involving the LIM protein RBTN2 and the zinc-finger protein GATA1. Proc Natl Acad Sci U S A 92: 9585-9589.
24. Wadman IA, Osada H, Grutz GG, Agulnick AD, Westphal H, et al. (1997) The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNAbinding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. Embo J 16: 3145-3157.
25. Xu Z, Huang S, Chang LS, Agulnick AD, Brandt SJ (2003) Identification of a TAL1 target gene reveals a positive role for the LIM domain-binding protein Ldb1 in erythroid gene expression and differentiation. Mol Cell Biol 23: 7585-7599.
26. Cai Y, Xu Z, Nagarajan L, Brandt SJ (2008) Single-stranded DNA-binding proteins regulate the abundance and function of the LIM-homeodomain transcription factor LHX2 in pituitary cells. Biochem Biophys Res Commun 373: 303-308.
27. Xu Z, Meng X, Cai Y, Liang H, Nagarajan L, et al. (2007) Single-stranded DNA-binding proteins regulate the abundance of LIM domain and LIM domain-binding proteins. Genes Dev 21: 942-955.
28. Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, et al. (2003) Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299: 697-700.
29. Bayarsaihan D, Soto RJ, Lukens LN (1998) Cloning and characterization of a novel sequence-specific single-stranded-DNA-binding protein. Biochem J 331 (Pt2): 447-452.
30. Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 13: 773-780.
31. Wingender E, Chen X, Hehl R, Karas H, Liebich I, et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28: 316-319.
32. Haenlin M, Cubadda Y, Blondeau F, Heitzler P, Lutz Y, et al. (1997) Transcriptional activity of Pannier is regulated negatively by heterodimerization of the GATA DNA-binding domain with a cofactor encoded by the u-shaped gene of Drosophila. Genes & Development 11: 3096-3108.
33. Ghazi A, Paul L, VijayRaghavan K (2003) Prepattern genes and signaling molecules regulate stripe expression to specify Drosophila flight muscle attachment sites. Mechanisms of Development 120: 519-528.
34. Ghazi A, Anant S, VijayRaghavan K (2000) Apterous mediates development of direct flight muscles autonomously and indirect flight muscles through epidermal cues. Development 127: 5309-5318.
35. Heitzler P, Haenlin M, Ramain P, Calleja M, Simpson P (1996) A genetic analysis of pannier, a gene necessary for viability of dorsal tissues and bristle positioning in Drosophila. Genetics 143: 1271-1286.
36. Morcillo P, Rosen C, Baylies MK, Dorsett D (1997) Chip, a widely expressed chromosomal protein required for segmentation and activity of a remote wing margin enhancer in Drosophila. Genes Dev 11: 2729-2740.
37. Fernandez-Funez P, Lu CH, Rincon-Limas DE, Garcia-Bellido A, Botas J (1998) The relative expression amounts of apterous and its co-factor dLdb/Chip are critical for dorso-ventral compartmentalization in the Drosophila wing. Embo J 17: 6846-6853.
38. Irvine KD, Wieschaus E. (1994) fringe, a Boundary-specific signaling molecule, mediates interactions between dorsal and ventral cells during Drosophila wing development. Cell 79: 595-606.
39. Blair SS, Brower DL, Thomas JB, Zavortink M (1994) The role of apterous in the control of dorsoventral compartmentalization and PS integrin gene expression in the developing wing of Drosophila. Development 120: 1805-1815.
40. Brand AH, Perrimon N (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118: 401-415.
41. O'Keefe DD, Thor S, Thomas JB (1998) Function and specificity of LIM domains in Drosophila nervous system and wing development. Development 125: 3915-3923.
42. Wu L (2006) Structure and functional characterization of single-strand DNA binding protein SSDP1: carboxyl-terminal of SSDP1 has transcription activity. Biochem Biophys Res Commun 339: 977-984.
43. Bejarano F, Luque CM, Herranz H, Sorrosal G, Rafel N, et al. (2008) A gain-off unction suppressor screen for genes involved in dorsal-ventral boundary formation in the Drosophila wing. Genetics 178: 307-323.
44. Ostendorff HP, Peirano RI, Peters MA, Schluter A, Bossenz M, et al. (2002) Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors. Nature 416: 99-103.
45. Dejardin J, Cavalli G (2004) Chromatin inheritance upon Zeste-mediated Brahma recruitment at a minimal cellular memory module. Embo J 23: 857-868.
46. Kal AJ, Mahmoudi T, Zak NB, Verrijzer CP (2000) The Drosophila Brahma complex is an essential coactivator for the trithorax group protein Zeste. Genes & Development 14: 1058-1071.
47. Heitzler P, Vanolst L, Biryukova I, Ramain P (2003) Enhancer-promoter communication mediated by Chip during Pannier-driven proneural patterning is regulated by Osa. Genes & Development 17: 591-596.
48. Mukherjee T, Schafer U, Zeidler MP (2006) Identification of Drosophila genes modulating janus kinase/signal transducer and activator of transcription signal transduction. Genetics 172: 1683-1697.
49. Ramana CV, Grammatikakis N, Chernov M, Nguyen H, Goh KC, et al. (2000) Regulation of c-myc expression by IFN-gamma through Stat1-dependent and -independent pathways. Embo J 19: 263-272.
50. Liang H, Samanta S, Nagarajan L (2005) SSBP2, a candidate tumor suppressor gene, induces growth arrest and differentiation of myeloid leukemia cells. Oncogene 24: 2625-2634.
51. Liu J-W, Nagpal JK, Sun W, Lee J, Kim MS, et al. (2008) ssDNA-Binding Protein 2 Is Frequently Hypermethylated and Suppresses Cell Growth in Human Prostate Cancer. Clin Cancer Res 14: 3754-3760.
52. Otsu M, Sitia R (2007) Diseases Originating from Altered Protein Quality Control in the Endoplasmic Reticulum. Current Medicinal Chemistry 14: 1639-1652.
53. Ryoo HD, Steller H (2007) Unfolded protein response in Drosophila: why another model can make it fly. Cell Cycle 6: 830-835.
54. Furman DP, Bukharina TA (2008) How Drosophila melanogaster Forms its Mechanoreceptors. Curr Genomics 9: 312-323.
55. Lee A-H, Scapa EF, Cohen DE, Glimcher LH (2008) Regulation of Hepatic Lipogenesis by the Transcription Factor XBP1. Science 320: 1492-1496.
56. Acosta-Alvear D, Zhou Y, Blais A, Tsikitis M, Lents NH, et al. (2007) XBP1 Controls Diverse Cell Type- and Condition-Specific Transcriptional Regulatory Networks. Molecular Cell 27: 53-66.
57. Bourne HR, Sanders DA, McCormick F (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature 349: 117-127.
58. Kimura K-I, Kodama A, Hayasaka Y, Ohta T (2004) Activation of the cAMP/ PKA signaling pathway is required for post-ecdysial cell death in wing epidermal cells of Drosophila melanogaster. Development 131: 1597-1606.
59. Kiger Jr. JA, Natzle JE, Kimbrell DA, Paddy MR, Kleinhesselink K, et al. (2007) Tissue remodeling during maturation of the Drosophila wing. Developmental Biology 301: 178-191.
60. Fabre CCG, Casal J, Lawrence PA (2008) The abdomen of Drosophila: does planar cell polarity orient the neurons of mechanosensory bristles? Neural Dev 3: 12.
61. Dietzl G, Chen D, Schnorrer F, Su KC, Barinova Y, et al. (2007) A genomewide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448: 151-156.
62. Ryder E, Ashburner M, Bautista-Llacer R, Drummond J, Webster J, et al. (2007) The DrosDel Deletion Collection: A Drosophila Genomewide Chromosomal Deficiency Resource. Genetics 177: 615-629.
63. Litchfield JT, Jr., Wilcoxon F (1948) A simplified method of evaluating dose effect experiments. Fed Proc 7: 240.
64. Benjamini Y, Hochberg Y. (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.
65. Gupta V, Parisi M, Sturgill D, Nuttall R, Doctolero M, et al. (2006) Global analysis of X-chromosome dosage compensation. J Biol 5: 3.
66. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
67. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31: 265-273.
68. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
69. Reiner A, Yekutieli D, Benjamini Y (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19: 368-375.
70. Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucl Acids Res 36: D773-D79.
71. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
72. Dennis G, Jr., Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.