The NIEHS Xenopus maternal EST project:: interim analysis of the first 13,879 ESTs from unfertilized eggs

被引:21
作者
Blackshear, PJ
Lai, WS
Thorn, JM
Kennington, EA
Staffa, NG
Moore, DT
Bouffard, GG
Beckstrom-Sternberg, SM
Touchman, JW
Bonaldo, MD
Soares, MB
机构
[1] NIEHS, Off Clin Res, Res Triangle Pk, NC 27709 USA
[2] NIEHS, Lab Signal Transduct, Res Triangle Pk, NC 27709 USA
[3] NIEHS, Informat Technol Support Serv, Res Triangle Pk, NC 27709 USA
[4] Res Genet Inc, Huntsville, AL 35801 USA
[5] NIH Intramural Sequencing Ctr, Gaithersburg, MD 20877 USA
[6] NHGRI, Gaithersburg, MD 20877 USA
[7] Univ Iowa, Dept Pediat, Iowa City, IA 52242 USA
[8] Univ Iowa, Dept Physiol & Biophys, Iowa City, IA 52242 USA
关键词
genomics; allelic variants; gene duplication; sequence tags;
D O I
10.1016/S0378-1119(01)00383-3
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The sequencing of expressed sequence tags (ESTs) from Xenopus laevis has lagged behind efforts on many other common experimental organisms and man, partly because of the pseudotetraploid nature of the Xenopus genome. Nonetheless, large collections of Xenopus ESTs would be useful in gene discovery, oligonucleotide-based knockout studies, gene chip analyses of normal and perturbed development, mapping studies in the related diploid frog X. tropicalis, and for other reasons. We have created a normalized library of cDNAs from unfertilized Xenopus eggs. These cells contain all of the information necessary for the first several cell divisions in the early embryo, as well as much of the information needed for embryonic pattern formation and cell fate determination. To date, we have successfully sequenced 13,879 ESTs out of 16,607 attempts (83.6% success rate), with an average sequence read length of 508 bp. Using a fragment assembly program, these ESTs were assembled into 8,985 'contigs' comprised of up to 11 ESTs each. When these contigs were used to search publicly available databases, 46.2% bore no relationship to protein or DNA sequences in the database at the significance level of 1e-6. Examination of a sample of 100 of the assembled contigs revealed that most (similar to 87%) were comprised of two apparent allelic variants. Expression profiles of 16 of the most prominent contigs showed that 12 exhibited some degree of zygotic expression. These findings have implications for sequence-specific applications for Xenopus ESTs, particularly the use of allele-specific oligonucleotides for knockout studies, differential hybridization techniques such as gene chip analysis, and the establishment of accurate nomenclature and databases for this species. (C) 2001 Published by Elsevier Science B.V. All rights reserved.
引用
收藏
页码:71 / 87
页数:17
相关论文
共 18 条
[1]   Frog genetics:: Xenopus tropicalis jumps into the future [J].
Amaya, E ;
Offield, MF ;
Grainger, RM .
TRENDS IN GENETICS, 1998, 14 (07) :253-255
[2]  
Bantle JA, 1996, J APPL TOXICOL, V16, P517
[3]   Normalization and subtraction: Two approaches to facilitate gene discovery [J].
Bonaldo, MDF ;
Lennon, G ;
Soares, MB .
GENOME RESEARCH, 1996, 6 (09) :791-806
[4]   SINGLE-STEP METHOD OF RNA ISOLATION BY ACID GUANIDINIUM THIOCYANATE PHENOL CHLOROFORM EXTRACTION [J].
CHOMCZYNSKI, P ;
SACCHI, N .
ANALYTICAL BIOCHEMISTRY, 1987, 162 (01) :156-159
[5]   GENETIC INFORMATION IN OOCYTE RNA [J].
DAVIDSON, EH ;
HOUGH, BR .
JOURNAL OF MOLECULAR BIOLOGY, 1971, 56 (03) :491-&
[6]   Identification of four CCCH zinc finger proteins in Xenopus, including a novel vertebrate protein with four zinc fingers and severely restricted expression [J].
De, J ;
Lai, WS ;
Thorn, JM ;
Goldsworthy, SM ;
Liu, XY ;
Blackwell, TK ;
Blackshear, PJ .
GENE, 1999, 228 (1-2) :133-145
[7]   Phase III interlaboratory study of FETAX, part 2: Interlaboratory validation of an exogenous metabolic activation system for Frog Embryo Teratogenesis Assay - Xenopus (FETAX) [J].
Fort, DJ ;
Stover, EL ;
Bantle, JA ;
Rayburn, JR ;
Hull, MA ;
Finch, RA ;
Burton, DT ;
Turley, SD ;
Dawson, DA ;
Linder, G ;
Buchwalter, D ;
Kumsher-King, M ;
Gaudet-Hull, AM .
DRUG AND CHEMICAL TOXICOLOGY, 1998, 21 (01) :1-14
[8]  
GRAF JD, 1991, METHOD CELL BIOL, V36, P663
[9]   OVEREXPRESSION OF CADHERINS AND UNDEREXPRESSION OF BETA-CATENIN INHIBIT DORSAL MESODERM INDUCTION IN EARLY XENOPUS EMBRYOS [J].
HEASMAN, J ;
CRAWFORD, A ;
GOLDSTONE, K ;
GARNERHAMRICK, P ;
GUMBINER, B ;
MCCREA, P ;
KINTNER, C ;
NORO, CY ;
WYLIE, C .
CELL, 1994, 79 (05) :791-803
[10]  
KAY BK, 1991, METHOD CELL BIOL, V36, P663