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Research Newsletter - June 2007

Spotlight

In an article paper published in Development, HSCI Principal Faculty Member, Andy McMahon, a professor in Harvard's Faculty of Arts and Sciences, and his team report on the genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.

Chipping Away at Hedgehog-Mediated Neural Patterning

The Hedgehog signaling pathway represents one of approximately six major families of signaling pathways that dictate development in most bilateria. An especially interesting property of Hedgehog signaling is that it acts as a morphogen in the vertebrate neural tube, specifying the fate of several ventral neuronal sub-types in a dose-dependent fashion. Over the past decade, the cellular response to this process has been studied extensively, resulting in detailed models of how a concentration gradient of hedgehog protein is converted from an "analogue" signal to discrete thresholds that specify unique, mutually exclusive cell identities. The "digitization" of this signal ultimately occurs at the transcriptional level, where all Hedgehog signaling is mediated by the Gli proteins (Gli1-3). Identifying Gli targets in a systematic fashion is therefore central to understanding the action of Hedgehog on its target field.

Recently, a technique known as ChIP-on-chip has been used to biochemically identify transcription factor binding sites in a variety of biological systems. In this method, the transcription factor is cross-linked to DNA and the sample is then sonicated into small DNA::protein fragments and immunoprecipitated with an antibody against the transcription factor of interest. The immunoprecipitated DNA, representing the associated transcription factor binding sites, is then detected by hybridization using DNA microarrays containing oligonucleotides (tiling arrays) representing the candidate genomic regions.

We sought to identify Gli targets in ventral neuronal progenitors using ES cells differentiated to a neural progenitor cell type. An epitope-tagged Gli1 protein was used to directly isolate cis-regulatory sequences by ChIP. ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog target genes predicted from previous transcriptional profiling studies. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in several of these genes established them as direct Hh-targets. These approaches provide significant new insights into both tissue specific and general transcriptional targets in a critical Hh-mediated patterning patterning event.

Because Hedgehog signaling in the neural tube is a relatively well characterized system, this model provides a particularly good opportunity for validating candidate targets. The core of the strategy, a genetically inducible system for epitope-tagging transcription factors, should be broadly applicable to the study of other transcription factors in a multitude of experimental systems.

Vokes SA, Ji H, McCuine S, Tenzen T, Giles S, Zhong S, Longabaugh WJ, Davidson EH, Wong WH, McMahon AP. Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning. Development. 2007 May;134(10):1977-89. Read Abstract.

Scientific Papers

Review and Commentary

  • Chien KR, Nakamura T. Latent TGF-beta-binding protein 2 binds to DANCE/fibulin-5 and regulates elastic fiber assembly. EMBO J. 2007 Jun 21. Read Abstract.
  • Goessling W, North TE, Zon LI. New waves of discovery: modeling cancer in zebrafish. J Clin Oncol. 2007 Jun 10;25(17):2473-9. Read Abstract.
  • Kim CB. MAPK-ing out the pathways in lung stem cell regulation. Cell Stem Cell. 2007 Jun 7;1(1):11-3. Read Abstract.
  • Li Y, Xu L, Olsen BR. Lessons from genetic forms of osteoarthritis for the pathogenesis of the disease. Osteoarthritis Cartilage. 2007 Jun 13. Read Abstract.
  • Stubbs MC, Armstrong SA. FLT3 as a therapeutic target in childhood acute leukemia. Curr Drug Targets. 2007 Jun;8(6):703-14. Read Abstract.
  • Stubbs MC, Armstrong SA. Therapeutic implications of leukemia stem cell development. Clin Cancer Res. 2007 Jun 15;13(12):3439-42. Read Abstract.

Blood

  • Bihl F, Mosam A, Henry LN, Chisholm JV 3rd, Dollard S, Gumbi P, Cassol E, Page T, Mueller N, Kiepiela P, Martin JN, Coovadia HM, Scadden DT, Brander C. Kaposi's sarcoma-associated herpesvirus-specific immune reconstitution and antiviral effect of combined HAART/chemotherapy in HIV clade C-infected individuals with Kaposi's sarcoma. AIDS. 2007 Jun;21(10):1245-1252. Read Abstract.
  • Glodek AM, Le Y, Dykxhoorn DM, Park SY, Mostoslavsky G, Mulligan R, Lieberman J, Beggs HE, Honczarenko M, Silberstein LE. Focal adhesion kinase is required for CXCL12-induced chemotactic and pro-adhesive responses in hematopoietic precursor cells. Leukemia. 2007 Jun 14. Read Abstract.
  • North TE, Goessling W, Walkley CR, Lengerke C, Kopani KR, Lord AM, Weber GJ, Bowman TV, Jang IH, Grosser T, Fitzgerald GA, Daley GQ, Orkin SH, Zon LI. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature. 2007 Jun 21;447(7147):1007-11. Read Abstract.
  • Pardanani A, Lasho TL, Finke C, Mesa RA, Hogan WJ, Ketterling RP, Gilliland DG, Tefferi A. Extending JAK2V617F and MPLW515 Mutation Analysis to Single Hematopoietic Colonies and B- and T-lymphocytes. Stem Cells. 2007 Jun 1. Read Abstract.
  • Tatetsu H, Ueno S, Hata H, Yamada Y, Takeya M, Mitsuya H, Tenen DG, Okuno Y. Down-regulation of PU.1 by methylation of distal regulatory elements and the promoter is required for myeloma cell growth. Cancer Res. 2007 Jun 1;67(11):5328-36. Read Abstract.
  • Walkley CR, Olsen GH, Dworkin S, Fabb SA, Swann J, McArthur GA, Westmoreland SV, Chambon P, Scadden DT, Purton LE. A Microenvironment-Induced Myeloproliferative Syndrome Caused by Retinoic Acid Receptor gamma Deficiency. Cell. 2007 Jun 15;129(6):1097-1110. Read Abstract.
  • Walkley CR, Shea JM, Sims NA, Purton LE, Orkin SH. Rb Regulates Interactions between Hematopoietic Stem Cells and Their Bone Marrow Microenvironment. Cell. 2007 Jun 15;129(6):1081-95. Read Abstract.
  • Yang J, Chai L, Liu F, Fink LM, Lin P, Silberstein LE, Amin HM, Ward DC, Ma Y. Bmi-1 is a target gene for SALL4 in hematopoietic and leukemic cells. Proc Natl Acad Sci USA. 2007 Jun 19;104(25):10494-9. Read Abstract.

Cancer

  • Paffett-Lugassy N, Hsia N, Fraenkel PG, Paw B, Leschinsky I, Barut B, Bahary N, Caro J, Handin R, Zon LI. Functional conservation of erythropoietin signaling in zebrafish. Blood. 2007 Jun 19. Read Abstract.
  • Yamamoto G, Nannya Y, Kato M, Sanada M, Levine RL, Kawamata N, Hangaishi A, Kurokawa M, Chiba S, Gilliland DG, Koeffler HP, Ogawa S. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays. Am J Hum Genet. 2007 Jul;81(1):114-26. Read Abstract.

Developmental Biology

  • Chen B, Cepko CL. Requirement of histone deacetylase activity for the expression of critical photoreceptor genes. BMC Dev Biol. 2007 Jun 29;7(1):78. Read Abstract.
  • Egli D, Rosains J, Birkhoff G, Eggan K. Developmental reprogramming after chromosome transfer into mitotic mouse zygotes. Nature. 2007 Jun 7;447(7145):679-85. Read Abstract.
  • Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedlinger K. Directly Reprogrammed Fibroblasts Show Global Epigenetic Remodeling and Widespread Tissue Contribution. Cell Stem Cell. 2007 Jun 7;1(1):55-70. Read Abstract.
  • Pfaff KL, Straub CT, Chiang K, Bear DM, Zhou Y, Zon LI. The zebrafish cassiopeia mutant reveals that SIL is required for mitotic spindle organization. Mol Cell Biol. 2007 Jun 18. Read Abstract.
  • Trimarchi JM, Stadler MB, Roska B, Billings N, Sun B, Bartch B, Cepko CL. Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling. J Comp Neurol. 2007 Jun 20;502(6):1047-65. Read Abstract.
  • Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007 Jun 6. Read Abstract.

Diabetes

  • King AJ, Fernandes JR, Hollister-Lock J, Nienaber CE, Bonner-Weir S, Weir GC. Normal relationship of beta and non-beta cells not needed for successful islet transplantation. Diabetes. 2007 Jun 11. Read Abstract.
  • Shibolet O, Podolsky DK. TLRs in the Gut.IV. Negative regulation of Toll-like receptors and intestinal homeostasis: addition by subtraction. Am J Physiol Gastrointest Liver Physiol. 2007 Jun;292(6):G1469-73. Read Abstract.
  • Xue B, Kim YB, Lee A, Toschi E, Bonner-Weir S, Kahn CR, Neel BG, Kahn BB. Protein tyrosine phosphatase 1B (PTB1B) deficiency reduces insulin resistance and the diabetic phenotype in mice with polygenic insulin resistance. J Biol Chem. 2007 Jun 1. Read Abstract.

Genetics and Genomics

  • Freeman JL, Adeniyi A, Banerjee R, Dallaire S, Maguire SF, Chi J, Ng BL, Zepeda C, Scott CE, Humphray S, Rogers J, Zhou Y, Zon LI, Carter NP, Yang F, Lee C. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. BMC Genomics. 2007 Jun 27;8(1):195 Read Abstract.
  • Hill AD, Chang BS, Hill RS, Garraway LA, Bodell A, Sellers WR, Walsh CA. A 2-Mb critical region implicated in the microcephaly associated with terminal 1q deletion syndrome. Am J Med Genet A. 2007 Jun 29. Read Abstract.

Immunology

  • Wong J, Obst R, Correia-Neves M, Losyev G, Mathis D, Benoist C. Adaptation of TCR repertoires to self-peptides in regulatory and nonregulatory CD4+ T cells. J Immunol. 2007 Jun 1;178(11):7032-41. Read Abstract.

Nervous System

  • Jin Z, Tietjen I, Bu L, Liu-Yesucevitz L, Gaur SK, Walsh CA, Piao X. Disease-associated Mutations Affect GPR56 Protein Trafficking and Cell Surface Expression. Hum Mol Genet. 2007 Jun 18. Read Abstract.
  • Molyneaux BJ, Arlotta P, Menezes JR, Macklis JD. Neuronal subtype specification in the cerebral cortex. Nat Rev Neurosci. 2007 Jun;8(6):427-37. Read Abstract.
  • Pruszak J, Sonntag KC, Aung MH, Sanchez-Pernaute R, Isacson O. Markers and Methods for Cell Sorting of Human Embryonic Stem Cell-derived Neural Cell Populations. Stem Cells. 2007 Jun 22. Read Abstract.
  • Tietjen I, Bodell A, Apse K, Mendonza AM, Chang BS, Shaw GM, Barkovich AJ, Lammer EJ, Walsh CA. Comprehensive EMX2 genotyping of a large schizencephaly case series. Am J Med Genet A. 2007 Jun 15;143(12):1313-6. Read Abstract.

Technology

  • Goessling W, North TE, Zon LI. Ultrasound biomicroscopy permits in vivo characterization of zebrafish liver tumors. Nat Methods. 2007 Jul;4(7):551-553. Read Abstract.
  • Liu F, Jenssen TK, Trimarchi J, Punzo C, Cepko CL., Ohno-Machado L, Hovig E, Patrick Kuo W. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates. BMC Genomics. 2007 Jun 7;8:153. Read Abstract.

Tissue Engineering

  • Borenstein JT, Weinberg EJ, Orrick BK, Sundback C, Kaazempur-Mofrad MR, Vacanti JP. Microfabrication of Three-Dimensional Engineered Scaffolds. Tissue Eng. 2007 Jun 24. Read Abstract.