Gene pie-1 BioInformatics Judith Holland April 28, 2008.

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Gene pie-1 BioInformatics Judith Holland April 28, 2008

Pharynx and Intestine in Excess pie-1 or pic-1 Y49E10.14 Gene Y49E /2 Transcripts (Ensembl) WBGene (WormBase)

Physical Characteristics Size: 335 Amino Acids Exons: bp Introns: bp Location: Chromosome III 12,426,742-12,429,055 12,426,742-12,429,055 (Ensembl)

Wormbase Exon Predictions

● Gene model confirmed by cDNA ● mRNA1096 bp ● derived from an annotated genomic sequence from Y49E10.14

How Discovered? ● Genetic Screen 1992 by Mello and Priess (5) ● Based on previous techniques of Priess 1987(10) and ● Kemphues 1988 (6) ● Work leads to Nobel Prize in Physiology 2006 for Mello and Fire for gene silencing by double stranded RNA interference

OSTR154H11, CK585182, yk637d9.3, ECO13237, CK582493, CK585183, ECO17587, yk712c8.3, ECO27143, yk613c12.5, yk613c12.3, U62896, OSTF154H11_2, yk276e3.3, yk637d9.5, yk712c8.5 cDNA/EST: 16

zu-154* and zu-127*: Embryonic Lethal, Excess Pharyngeal or Intestinal Cells zu-127*: Cell Fate Transformation, muscle excess, P granule localization abnormal and equal in both daughter cells niDf71(III)(poss deletion), pas49287 (deletion AT), pas31245 (sub A/T), t1682 *, zu-177* (WB) * Unknown mutation Mutations (Alleles)

BLASTP Matches ● C. briggsae BP:CBP22586 E= 6.3e-60 L=88% ● C. remanei RP05838 E= 7.2e-47 L= 39% (pred) ● C. elegans pos-1 E= 9.8e-11 L= 30.4% ● M. musculus TTP E= 8e-10 L= 42.4% ● H. sapiens ENSG E=8.2e-10 L=38.2% ENSG ● Possibly related Zinc Finger Protein Family

Protein Function -1 ● Encodes protein PIE-1 contains 2 -C3H1 Zinc finger (99-123, ) ● Essential for Cell Fate Determination ● Stops germline cell from differentiating into somatic cells ● Blocks mRNA transcription until about 100 cell level in germline cell ● Blocks phosphorylation of RNA polymerase of RNA polymerase II ● Eliminates remaining PIE-1 in somatic cells ZF1 ● Batchelor et al (1)

Required for efficient expression of nos-2 Promotes primordial germ cell development Possible action of ZF2 Tenenhaus, et al (2) Protein Function -2

Zinc Finger motif Large super family of protein domains bind dna (regulatory proteins, transcription factors). Contains 2 anti parallel β strands, 1 α helix 2 Cysteine and 2 Histidine residues bind Zn. If looses zinc it unfolds (Wikipedia)

Wallenfang(7) Polarization of PIE-1

Mello (12) Hubbard (9)

Mello Lab: GLP Tagged PIE-1 (8) and Monoclonal Antibody (8)

DataBases Used ● Wormbase ● Ensembl ● Embl ● Entrez ● UniGene

References 1. Transcriptional repression by the Caenorhabditis elegans germ-line protein PIE-1, Ceri Batchelder, Melanie A. Dunn, Bob Choy, Yong Suh, Conrad Cassie, Eun Yong Shim, Tae Ho Shin, Craig Mello, Geraldine Seydoux and T. Keith Blackwell, Genes & Dev : PIE-1 is a bifunctional protein that regulates maternal and zygotic gene expression in the embryonic germ line of Caenorhabditis elegansm Christina Tenenhaus, Kuppuswamy Subramaniam, Melanie A. Dunn and Geraldine Seydoux, Genes & Dev : Asymmetric Segregation of PIE-1 in C. elegans Is Mediated by Two Complementary Mechanisms that Act through Separate PIE-1 Protein Domains, Kimberly J. Reese, Melanie A. Dunn, James A. Waddle, Geraldine Seydoux, Molecular Cell, Vol. 6, August, 2000, 445– The pie-1 and mex-1 Genes and Maternal Control of Blastomere Identity In Early C. elegans Embryos, Craig C. Mello, Bruce W. Draper, Michael Krause, Harold Weintraub, James R. Priess, Cell, Vol. 70, 1992,

References- Cont. 6. Identification of genes required for cytoplasmic localization in early C. elegans embryos, Kemphues, KJ, Priess, JR, Morton, DG, Cheng, NS, Cell, 1988,Feb12;52(3): Polarization of the anterior–posterior axis of C. elegans is a microtubule-directed process, Matthew R. Wallenfang & Geraldine Seydoux, NATURE, VOL 408, 2 NOVEMBER 2000 | Introduction To The Germline, E. Jane Albert Hubbard, David Greenstein, WormBook.org, Cellular Interactions in early C. elegans embryos, Priess, JR, Thomson, JN, Cell, 48, 1987, Repression of Gene Expression in embryonic germ lineage of C. elegans, G Seydoux, C Mello, J Pettitt, WB Wood, JR Priess, A Fire, Nature, 382, 22 August 1996, The PIE-1 protein and germline specification in C. elegans embryos, Letters to Nature, Nature, Vol 382, 22 August 1996,

Quick Time Movie Reese (3)