Journal of Genetics and Genomics

Implication of snoRNA U50 in human breast cancer

Xue-Yuan Dong, Peng Guo, Jeff Boyd, Xiaodong Sun, Qunna Li, Wei Zhou, Jin-Tang Dong

2009, 36(8): 447-454. doi: 10.1016/S1673-8527(08)60134-4

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Abstract:
Deletion of chromosome 6q is frequent in breast cancer, and the deletion often involves a region in 6q14-q16. At present, however, theunderlying tumor suppressor gene has not been established. Based on a recent study identifying snoRNA U50 as a candidate for the6q14-16 tumor suppressor gene in prostate cancer, we investigated whether U50 is also involved in breast cancer. PCR-based approachesshowed that U50 underwent frequent genomic deletion and transcriptional downregulation in cell lines derived from breast cancer. Mutation screening identified the same 2-bp deletion of U50 as in prostate cancer in both cell lines and primary tumors from breast cancer, andthe deletion was both somatic and in germline. Genotyping of a cohort of breast cancer cases and controls for the mutation demonstratedthat, while homozygous genotype of the mutation was rare, its heterozygous genotype occurred more frequently in women with breastcancer. Functionally, re-expression of U50 resulted in the inhibition of colony formation in breast cancer cell lines. These results suggestthat noncoding snoRNA U50 plays a role in the development and/or progression of breast cancer.

Characterization of the promoter of phosphate transporter TaPHT1.2 differentially expressed in wheat varieties

Jun Miao, Jinghan Sun, Dongcheng Liu, Bin Li, Aimin Zhang, Zhensheng Li, Yiping Tong

2009, 36(8): 455-466. doi: 10.1016/S1673-8527(08)60135-6

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Abstract:
TaPHT1.2 is a functional, root predominantly expressed and low phosphate (Pi) inducible high-affinity Pi transporter in wheat, whichis more abundant in the roots of P-efficient wheat genotypes (e.g., Xiaoyan 54) than in P-inefficient genotypes (e.g., Jing 411) under bothPi-deficient and Pi-sufficient conditions. To characterize TaPHT1.2 further, we genetically mapped a TaPHT1.2 transporter, TaPHT1.2-D1, on the long arm of chromosome 4D using a recombinant inbred line population derived from Xiaoyan 54 and Jing 411, and isolated a1,302 bp fragment of the TaPHT1.2-D1 promoter (PrTaPHT1.2-D1) from Xiaoyan 54. TaPHT1.2-D1 shows collinearity with OsPHT1.2 that has previously been reported to mediatethe translocation of Pi from roots to shoots.PrTaPHT1.2-D contains a number of Pi-starvation responsive elements, including P1BS, WRKY-binding W-box, and helix-loop-helix-binding elements. PrTaPHT1.2-D1 wasthen used to drive expression of β-glucuronidase (GUS) reporter gene in Arabidopsis through Agrobacterium-mediated transformation. Histochemical analysis of transgenic Arabidopsis plants showed that the reporter gene was specifically induced by Pi-starvation and predominantly expressed in the roots. As there is only one SNP between the TaPHT1.2-D1 promoters of Xiaoyan 54 and Jing 411, and thisSNP does not exist within the Pi-starvation responsive elements, the differential expression of TaPHT1.2 in Xiaoyan 54 and Jing 411 maynot be caused by this SNP.

Effects of age on segregation of the X and Y chromosomes in cultured lymphocytes from Chinese men

Yaxian Song, Qian Chen, Zhen Zhang, Heli Hou, Ding Zhang, Qinghua Shi

2009, 36(8): 467-474. doi: 10.1016/S1673-8527(08)60136-8

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Abstract:
Chromosome malsegregation in binucleated lymphocytes is a useful endpoint to evaluate age effect on genetic stability. However, theinvestigations on chromosome malsegregation in binucleated lymphocytes from Chinese are scarce. In this study, peripheral blood lymphocytes were collected from 14 old (60–70 years) and 10 young (22–26 years) healthy Chinese men. To detect malsegregation of the sexchromosomes, multi-color fluorescence in situ hybridization (FISH) was performed on binucleated lymphocytes, cytokinesis-blocked bycytochalasin B at the first mitosis after phytohaemagglutinin stimulation. Compared with that in young men, a significant increase in frequencies of loss of chromosome X (9.2 ± 3.2‰vs. 1.1 ± 0.9‰, P < 0.001) and Y (2.5 ± 1.9‰ vs. 0.2 ± 0.3‰, P < 0.001) was found inold men. Similarly, nondisjunction of chromosome X (16.5 ± 3.4‰ vs. 3.5 ± 1.1‰, P < 0.001) and Y (7.2 ± 2.6‰ vs. 2.4 ± 1.3‰, P < 0.001) occurred more frequently in old men than in young men. Regardless of donor's age, nondisjunction is more prevalent than loss forboth chromosome X and Y. The frequencies of observed simultaneous malsegregation were relatively higher than the expected, suggesting an association between malsegregation. These results indicated that in Chinese men, malsegregation of the sex chromosomes increases with age in an associated fashion, and nondisjunction accounts for the majority of spontaneous chromosome malsegregation.

Effects of splice sites on the intron retention in histamine H3 receptors from rats and mice

Wenyong Ding, Lin Lin, Feng Ren, Hanfa Zou, Ziyuan Duan, Jianwu Dai

2009, 36(8): 475-482. doi: 10.1016/S1673-8527(08)60137-X

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Abstract:
In the alternative splicing, intron retention, of histamine H₃ receptors in rats and mice, the short transcript isoforms that are excised alternatively spliced introns are easily detected in a very low level in rats and are undetectable in mice using the regular PCR protocol. Theretained introns have common 5′ splice site and different 3′ splice sites. The detailed mechanism for the special alternative splicing remains largely unclear. In this study, we developed a minigene splicing system to recapitulate natural alternative splicing of the receptorsand investigated the effects of 5′ and 3′ splice sites on intron retention in HeLa cells. Mutating weak 5′ and 3′ splice sites of the alternatively spliced introns toward the canonical consensus sequences promoted the splicing of the corresponding introns in rat and mouseminigenes. The effect of splice site strength was context-dependent and much more significant for the 3′ splice site of the longer alternative intron than for the 3′ splice site of the shorter alternative intron and the common 5′ splice sites; it was also more significant in the ratminigene than in the mouse minigene. Mutating the 3′ splice site of the longer alternative intron resulted in almost complete splicing ofthe intron and made the corresponding isoform to become the nearly exclusive transcript in the rat minigene.

vsx1 3′ untranlated region-mediated translation difference at differentdevelopmental stages of goldfish embryos

Jinhui Chen, Ying Tong, Shufang Zhao, Shanshan Ma, Chen Luo

2009, 36(8): 483-490. doi: 10.1016/S1673-8527(08)60138-1

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Abstract:
Visual system homeobox-1 (vsx1) is important in retinal progenitor proliferation, differentiation, and function maintenance of bipolarcells in vertebrates. Recent study in Xenopus laevis has shown that vsx1 3′ untranslated region (3′ UTR) can mediate cell-specific translation of vsx1 mRNA in the bipolar cells of the retinal inner nuclear layer (INL). vsx1 is also transcribed at the early developmental stagesprior to eye formation and its spatiotemporal expression patterns are conserved in allthe examined vertebrates. In order to determinewhether the vsx1 3′ UTR has a role in regulating the spatiotemporal expression of vsx1 during early embryogenesis, we constructed a vsx1 UTR-controlled green fluorescent protein (GFP) reporter gene system and examined the GFP expression pattern in goldfish, Carassiusauratus, at different developmental stages. Our results indicated that both the vsx1 5′ UTR and the vsx1 3′ UTR remarkably repressedGFP expression at transcription level but did not regulate tissue-specific translation at early developmental stages. GFP protein wasubiquitously expressed in the embryos injected with GFP-sensors containing vsx1 UTRs before 60 h post-fertilization (hpf). From hatchingstage (72 hpf) onwards, however, GFP protein was specifically expressed in the bipolar cells of the retinal INL in the vsx1 3′UTR-GFP-sensorembryos, but was still ubiquitously expressed in the embryos injected with GFP-sensor lacking vsx1 3′ UTR. These observations showed asignificant difference of vsx1 3′ UTR-mediated translation between early and late developmental stages and suggested that vsx1 3′ UTR mightnot be involved in regulating the spatiotemporal expression of vsx1 until hatching stage during embryogenesis.

Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers

Xingyu Hu, Jianfei Wang, Ping Lu, Hongsheng Zhang

2009, 36(8): 491-500. doi: 10.1016/S1673-8527(08)60139-3

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Abstract:
The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, wasanalyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles werefound, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content (PIC) was 0.284–0.980 (average, 0.793). The expected heterozygosity (He) varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA (Unweight Pair Group Method with Arithmetic Mean) clustering analysis at thegenetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results wereconsistent with known information on ecological growing areas. Thegenetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. Itindicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site ofPanicum miliaceum.

The construction of a genetic linkage map of non-heading Chinesecabbage (Brassica campestris ssp. chinensis Makino)

Yan Cheng, Jianfeng Geng, Jingyi Zhang, Qian Wang, Qingyu Ban, Xilin Hou

2009, 36(8): 501-508. doi: 10.1016/S1673-8527(08)60140-X

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Abstract:
Non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) is one of the most important vegetables in eastern China. A genetic linkage map was constructed using 127 doubled haploid (DH) lines, and the DH population was derived from a commercial hybrid “Hanxiao” (lines SW-13 × L-118). Out of the 614 polymorphic markers, 43.49% were not assigned to any of the linkage groups(LGs). Chi-square tests showed that 42.67% markers were distorted from expected Mendelian segregation ratios, and the direction ofdistorted segregation was mainly toward the paternal parent L-118. After sequentially removing the markers that had an interval distancesmaller than 1 cM from the upper marker, the overall quality of the linkage map was increased. Two hundred and sixty-eight molecularmarkers were mapped into 10 LGs, which were anchored to the corresponding chromosome of theB. rapa reference map based on common simple sequence repeat (SSR) markers. The map covers 973.38 cM of the genome and the average interval distance between markerswas 3.63 cM. The number of markers on each LG ranged from 18 (R08) to 64 (R07), with an average interval distance within a single LGfrom 1.70 cM (R07) to 6.71 cM (R06). Among these mapped markers, 169 were sequence-related amplified polymorphism (SRAP) molecular markers, 50 were SSR markers and 49 were random amplification polymorphic DNA (RAPD) markers. With further saturation tothe LG, the current map offers a genetic tool for loci analysis for important agronomic traits.

2009 Vol. 36, No. 8