Cloning, transcription and chromosomal localization of the porcine whey acidic protein gene and its expression in HC11 cell line

The whey acidic protein (WAP) is the major whey protein of rodent, rabbit and camel. Recently, it was identified in the milk of swine (Simpson et al., 1998. J. Mol. Endocrinol. 20, 27-35). In this paper, the cloning of the pig WAP cDNA and of bacterial artificial chromosome (BAC) construct containing the entire porcine WAP gene is reported. The comparison of the coding sequence of the pig WAP gene to rodent or lagomorph WAP sequence already published demonstrated that only exon sequences are partially conserved. The porcine WAP gene was localized on the subtelomeric region of the chromosome 18. The estimation of the expression of the swine WAP gene in the mammary gland from lactating animals revealed a high level of expression. In order to compare the expression level of the porcine WAP gene from the large genomic fragment which contained 70 kb downstream and 50 kb upstream the pig WAP gene or the smaller one (1 kb downstream and 2.4 kb upstream), these two genomic fragments were transfected in HC11 cell line. The BAC construct was expressed 15 times higher than the plasmid when reported to the integrated copy number. This report suggests that the HC11 cell line is a useful tool to identify the regulatory sequences of milk protein genes.     

Comparative human-mouse-rat sequence analysis of the ICAM gene cluster on HSA 19p13.2 and a 185-kb porcine region from SSC 2q

The human intercellular adhesion molecule gene (ICAM) cluster is located in a GC-rich and gene-rich region on HSA 19p13.2. We determined the complete DNA sequence of a 185-kb porcine bacterial artificial chromosome (BAC) clone containing parts of the ICAM gene cluster. We used the porcine sequence for a detailed comparative analysis between human, pig, mouse and rat. The 185 kb of porcine sequence covered 220 kb of homologous sequence in the human genome, which adds to the growing evidence that the porcine genome is somewhat smaller than the human genome. The genomic sequences of the four species showed a high level of conserved synteny and no rearrangements in gene order were observed. During evolution, the ICAM3 gene was inactivated by mutation in the mouse and rat genome, whereas it is still present in the human and pig genome. The loss of Icam3 in rodent genomes might be relevant for rodent-specific properties of the T-cell-mediated immune response. All the other investigated genes are conserved across all four investigated sequences.     

Improving the comparative map of SSC2p-q13 by sample sequencing of BAC clones

To improve the comparative map for pig chromosome 2 and increase the gene density on this chromosome, a porcine bacterial artificial chromosome (BAC) library was screened with 17 microsatellite markers and 18 genes previously assigned to pig chromosome 2. Fifty-one BAC clones located in the region of a maternally imprinted quantitative trait locus for backfat thickness (BFT) were identified. From these BACs 372 kb were sample sequenced. The average read length of a subclone was 442 basepair (bp). Contig assembly analysis showed that every bp was sequenced 1.28 times. Subsequently, sequences were compared with sequences in the nucleotide databases to identify homology with other mammalian sequences. Sequence identity was observed with sequences derived from 35 BACs. The average percentage identity with human sequences was 87.6%, with an average length of 143 bp. In total, sample sequencing of all BACs resulted in sequence identity with 29 human genes, 13 human expressed sequence tags (ESTs), 17 human genomic clones, one rat gene, one porcine gene and nine porcine ESTs. Eighteen genes located on human chromosome 11 and 19, and seven genes from other human locations, one rat gene and one porcine gene were assigned to pig chromosome 2 for the first time. The new genes were added to the radiation hybrid map at the same position as the locus from which the BAC that was sequenced was derived. In total 57 genes were placed on the radiation hybrid map of SSC2p-q13.     

Characterization ofAlu family repetitive sequences which flank human β-type globin genes

Heteroduplex mapping has determined the size, location, and orientation of three Alu family sequences from the human beta-type globin gene cluster. Two of these sequences have the same orientation. One (231 bp long) is 2 kb to the 5' side of the B gamma-globin gene and the other (222 bp) is l kb 5' to the pseudo-beta-l-globin gene. The third (300 bp), 3-4 kb 3' to the pseudo-beta-l-globin gene, has the opposite orientation. Their orientations relative to five previously characterized Alu sequences from this cluster have been established. One of these, 2.5 kb 5' to the epsilon-globin gene, was shown by Southern blot hybridization to be similar but not identical to other family members, whereas the region separating it from a neighbouring inverted repeat is not widely distributed in the human genome.     

Korean BAC library construction and characterization of HLA-DRA, HLA-DRB3

A human bacterial artificial chromosome (BAC) library was constructed with high molecular weight DNA extracted from the blood of a male Korean. This Korean BAC library contains 100,224 clones of insert size ranging from 70 to 150 kb, with an average size of 86 kb, corresponding to a 2.9-fold redundancy of the genome. The average insert size was determined from 288 randomly selected BAC clones that were well distributed among all the chromosomes. We developed a pooling system and three-step PCR screen for the Korean BAC library to isolate desired BAC clones, and we confirmed its utility using primer pairs designed for one of the clones. The Korean BAC library and screening pools will allow PCR-based screening of the Korean genome for any gene of interest. We also determined the allele types of HLA-DRA and HLA-DRB3 of clone KB55453, located in the HLA class II region on chromosome 6p21.3. The HLA-DRA and DRB3 genes in this clone were identified as the DRA*010202 and DRB3*01010201 types, respectively. The haplotype found in this library will provide useful information in future human disease studies.     

Tissue-specific, high level expression of the rat whey acidic protein gene in transgenic mice.

The importance of intragenic and 3' flanking sequences in the control of the temporal, hormonal and tissue-specific expression of milk whey acidic protein (WAP) has been demonstrated in transgenic mice. Mouse lines carrying a 4.3 kb genomic clone containing the entire rat WAP gene minus 200 bp of the first intron with 0.949 kb of 5' and 1.4 kb of 3' flanking DNA were generated. In eight of nine independent lines of mice analyzed, WAP transgene expression was detected at levels ranging from 1% to 95% (average, 27%) of the endogenous gene. The transgene was expressed preferentially in the mammary gland. Although developmentally regulated during pregnancy and lactation, the temporal pattern of WAP transgene expression differed from the endogenous gene. A precocious increase in expression of the transgene was detected at 7 days of pregnancy, several days earlier in pregnancy than the major increase observed in endogenous mouse WAP mRNA. The rat WAP transgene was translated and secreted into the milk of transgenic mice at levels comparable to the endogenous mouse WAP. This is the first report of a gene that is negatively regulated in dissociated cell cultures as well as in transfected cells, yet is expressed efficiently in the correct multicellular environment of the transgenic mouse.     

新疆细毛羊2倍基因组BAC文库PCR筛选系统的构建与使用

本研究所构建的BAC文库覆盖了8倍新疆细毛羊的基因组,平均插入片段的大小为133kb,同时文库92．5%的克隆插入片段大于100kb,而且有部分克隆甚至大于300kb,假定绵羊的基因组含有3×10~6kb,根据文库的平均插入片段大小为133kb,从文库筛选到目的片段的概率为98．208%。为了验证文库有较好的覆盖率,构建了2倍基因组文库PCR筛选系统,并对位于新疆细毛羊20号染色体MHC基因邻近区段的DMB_EX2、MCMA36、CP73和BM1258 4个分子标记进行了筛选,得到的平均阳性克隆数为1．5个,从筛选结果来看,这与文库插入片段估计的8倍基因组覆盖率相当接近并且没有偏向,这使得本文库成为研究绵羊的功能基因、位置克隆和完善基因组物理图谱的极为有用的资源。     

The mouse secreted gel-forming mucin gene cluster

Using genomic cosmid and BAC clones and genome shotgun supercontigs available in GenBank, we determined the complete gene structure of the four mouse secreted gel-forming mucin genes Muc2, Muc5ac, Muc5b and Muc6 and the organization of the genomic locus harboring these genes. The mouse secreted gel-forming mucin gene is 215 kb on distal chromosome 7 to 69.0 cM from the centromere and organized as: Muc6-Muc2-Muc5ac-Muc5b with Muc2, Muc5ac and Muc5b arranged in the same orientation and Muc6 in opposite. Mouse mucin genes have highly similar genomic organization to each other and to their respective human homologues indicating that they have been well conserved through evolution. Deduced peptides showed striking sequence similarities in their N- and C-terminal regions whereas the threonine/serine/proline-rich central region is specific for each other and for species. Expression studies also showed that they have expression patterns similar to human mucin genes with Muc2 expressed in small and large intestines, Muc5ac and Muc6 in stomach, and Muc5b in laryngo-tracheal tract. These data constitute an important initial step for investigation of mucin gene regulation and mucin function through the use of animal models.     

甘蓝型油菜A基因组候选BAC克隆的筛选及其插入片段大小分析

选择甘蓝型油菜A基因组10个连锁群上特有的85个SSR分子标记,合成其引物序列,采用四维PCR法筛选甘蓝型油菜-新疆野生油菜二体异附加系BAC文库,成功筛选到甘蓝型油菜A基因组39个BAC克隆,其插入片段介于50～300 kb之间,平均为120 kb。甘蓝型油菜A基因组10个连锁群BAC克隆的获得,对后续开展甘蓝型油菜A基因组染色体识别、基因染色体定位、遗传距离与物理距离间关系分析等均具有重要价值。     

Expression of a whey acidic protein transgene during mammary development. Evidence for different mechanisms of regulation during pregnancy and lactation

Expression of the mouse whey acidic protein (WAP) gene is specific to the mammary gland, is induced several thousand-fold during pregnancy, and is under the control of steroid and peptide hormones. To study developmental regulation of the mouse WAP gene, a 7.2-kilobase (kb) WAP transgene, including 2.6 kb of 5'- and 1.6 kb of 3'-flanking sequences, was introduced into mice. Of the 13 lines of mice examined, 6 expressed the transgenes during lactation at levels between 3 and 54% of the endogenous gene. Although expression was dependent on the site of integration, the transgenes within a given locus were expressed in a copy number-dependent manner and were coordinately regulated. The WAP transgenes were expressed specifically in the mammary gland, but showed a deregulated pattern of expression during mammary development. In all six lines of mice, induction of the WAP transgenes during pregnancy preceded that of the endogenous gene. During lactation, expression in two lines increased coordinately with the endogenous gene, and in three other lines of mice, transgene expression decreased to a basal level. These data indicate that the 7.2-kb gene contains some but not all of the elements necessary for correct developmental regulation. At a functional level it appears as if a repressor element, which inactivates the endogenous gene until late pregnancy, and an element necessary for induction during lactation are absent from the transgene. Complementary results from developmental and hormone induction studies suggest that WAP gene expression during pregnancy and lactation is mediated by different mechanisms.     

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

Background

Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?

Results

A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.

Conclusion

We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.     

High-level expression of the rat whey acidic protein gene is mediated by elements in the promoter and 3'' untranslated region.

The high-level expression of the rat whey acidic protein (WAP) gene in transgenic mice depends on the interaction of 5'-flanking promoter sequences and intragenic sequences. Constructs containing 949 bp of promoter sequences and only 70 bp of 3'-flanking DNA were expressed at uniformly high levels, comparable to or higher than that of the endogenous gene. Although this WAP transgene was developmentally regulated, it was expressed earlier during pregnancy than was the endogenous WAP gene. Replacement of 3' sequences, including the WAP poly(A) addition site, with simian virus 40 late poly(A) sequences resulted in an approximately 20-fold reduction in the expression of WAP mRNA in the mammary gland during lactation. Nevertheless, position-independent expression of the transgene was still observed. Further deletion of 91 bp of conserved WAP 3' untranslated region (UTR) led to integration site-dependent expression. Position independence was restored following reinsertion of the WAP 3' UTR into the deleted construct at the same location, but only when the insertion was in the sense orientation. The marked differences observed between the expression levels of the 3'-end deletion constructs in transgenic mice were not seen in transfected CID 9 mammary epithelial cells. In these cells, expression of the endogenous WAP gene was dependent on the interaction of these cells with a complex extracellular matrix. In contrast, the transfected WAP constructs were not dependent on extracellular matrix for expression. Thus, both the abnormal expression of WAP in cells cultured on plastic and the precocious developmental expression of WAP in transgenic mice may reflect the absence of a negative control element(s) within these recombinant constructs.