Journal of Genetics and Genomics

2011, 38(2) doi: 10.1016/S1673-8527(11)00029-4

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Abstract:

Distinct effects of nuclear membrane localization on gene transcription silencing in Drosophila S2 cells and germ cells

Lu Sui, Yanhong Yang

2011, 38(2): 55-61. doi: 10.1016/j.jcg.2011.01.002

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Abstract:
Nuclear envelope proteins have important roles in chromatin organization and signal-dependent transcriptional regulation. A previous study reported that the inner nuclear membrane protein, Otefin (Ote), was essential for germline stem cell (GSC) maintenance via interaction with Smad complex. The interaction of Ote with the Smad complex recruits the bam locus to the nuclear periphery and subsequently results in bam transcriptional silencing, revealing that nuclear peripheral localization is essential for bam gene regulation. However, it remains unknown whether the nuclear peripheral localization is sufficient for bam silencing. To address this issue, we have established a tethering system, in which the Gal4 DNA binding domain (DBD) of the Flag:Gal4 DBD:Ote▵LEM fusion protein physically interacts with the Gal4 binding sites upstream of bamP-gfp to artificially recruit the reporter gene gfp to the nuclear membrane. Our data demonstrated that the nuclear peripheral localization seemed to affect the expression of the target naked gene in S2 cells. By contrast, in Drosophila germ cells, the nuclear membrane localization was not sufficient for gene silencing.

A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases

Qingshu Meng, Kaifu Chen, Lina Ma, Songnian Hu, Jun Yu

2011, 38(2): 63-70. doi: 10.1016/j.jcg.2011.01.003

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Abstract:
Transposons are sequence elements widely distributed among genomes of all three kingdoms of life, providing genomic changes and playing significant roles in genome evolution.Trichomonas vaginalis is an excellent model system for transposon study since its genome (∼160 Mb) has been sequenced and is composed of ∼65% transposons and other repetitive elements. In this study, we primarily report the identification of Kolobok-type transposons (termed tvBac) in T. vaginalis and the results of transposase sequence analysis. We categorized 24 novel subfamilies of the Kolobok element, including one autonomous subfamily and 23 non-autonomous subfamilies. We also identified a novel H2CH motif in tvBac transposases based on multiple sequence alignment. In addition, we supposed that tvBac and Mutator transposons may have evolved independently from a common ancestor according to our phylogenetic analysis. Our results provide basic information for the understanding of the function and evolution of tvBac transposons in particular and other related transposon families in general.

Identification of two novel missense WFS1 mutations, H696Y and R703H, in patients with non-syndromic low-frequency sensorineural hearing loss

Yi Sun, Jing Cheng, Yanping Lu, Jianzhong Li, Yu Lu, Zhanguo Jin, Pu Dai, Rongguang Wang, Huijun Yuan

2011, 38(2): 71-76. doi: 10.1016/j.jcg.2011.01.001

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Abstract:
Non-syndromic low-frequency sensorineural hearing loss (LFSNHL) is an unusual type of hearing loss in which frequencies ≤2000 Hz predominantly are affected. To date, different mutations in two genes, DIAPH1 and WFS1, have been found to be associated with LFSNHL. Here, we report a five-generation Chinese family with postlingual and progressive LFSNHL. We mapped the disease locus to a 2.5 Mb region on chromosome 4p16 between markers SNP_A-2167174 and D4S431, overlapping with the DFNA6/14/38 locus. Sequencing of candidate gene revealed a heterozygous c.2086C>T substitution in exon 8 ofWFS1, leading to p.H696Y substitution at the C-terminus of Wolframin (WFS1). In addition, we performed mutational screening of WFS1 in 37 sporadic patients, 7–50 years of age, with LFSNHL. We detected a heterozygous c.2108G>A substitution in exon 8 ofWFS1, leading to p.R703H substitution in a patient. The H696 and R703 in WFS1 are highly conserved across species, including human, orangutan, rat, mouse, and frog (Xenopus). Sequence analysis demonstrated the absence of c.2086C>T or c.2108G>A substitutions in theWFS1 genes among 200 unrelated control subjects of Chinese background, supporting the hypothesis that they represent causative mutations, and not rare polymorphisms. Our data provide additional molecular and clinical information for establishing a better genotype–phenotype correlation for LFSNHL.

Identification and characterization of putative CIPK genes in maize

Xifeng Chen, Zhimin Gu, Dedong Xin, Liang Hao, Chengjie Liu, Ji Huang, Bojun Ma, Hongsheng Zhang

2011, 38(2): 77-87. doi: 10.1016/j.jcg.2011.01.005

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Abstract:
Calcium (Ca) plays a crucial role as a second messenger in intracellular signaling elicited by developmental and environmental cues. Calcineurin B-like proteins (CBLs) and their target proteins, CBL-interacting protein kinases (CIPKs) have emerged as a key Ca²⁺-mediated signaling network in response to stresses in plants. Bioinformatic analysis was used to identify 43 putative ZmCIPK (Zea mays CIPK) genes in the genome of maize inbred line B73. Based on gene structures, these ZmCIPKs were divided into intron-rich and intron-poor groups. Phylogenetic analysis indicated that the ZmCIPK family had a high evolutionary relationship with the rice CIPK family of 30 members. Microarray data and RT-PCR assay showed that ZmCIPK genes transcriptionally responded to abiotic stresses, and that 24, 31, 20 and 19 ZmCIPK genes were up-regulated by salt, drought, heat and cold stresses, respectively. There were different expression patterns of ZmCIPKs between cold-tolerant inbred line B73 and cold-sensitive inbred line Mo17 under cold stress. Our findings will aid further molecular dissection of biological functions of the CIPKs in maize, and provide new insight into the CBL–CIPK signaling network in plants.

Synthesizing double haploid hexaploid wheat populations based on a spontaneous alloploidization process

Lianquan Zhang, Li Zhang, Jiangtao Luo, Wenjie Chen, Ming Hao, Baolong Liu, Zehong Yan, Bo Zhang, Huaigang Zhang, Youliang Zheng, Dengcai Liu, Yang Yen

2011, 38(2): 89-94. doi: 10.1016/j.jcg.2011.01.004

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Abstract:
Doubled haploid (DH) populations are useful to scientists and breeders in both crop improvement and basic research. Current methods of producing DHs usually need in vitro culture for extracting haploids and chemical treatment for chromosome doubling. This report describes a simple method for synthesizing DHs (SynDH) especially for allopolyploid species by utilizing meiotic restitution genes. The method involves three steps: hybridization to induce recombination, interspecific hybridization to extract haploids, and spontaneous chromosome doubling by selfing the interspecific F₁s. DHs produced in this way contain recombinant chromosomes in the genome(s) of interest in a homogeneous background. No special equipment or treatments are involved in the DH production and it can be easily applied in any breeding and/or genetic program. Triticum turgidum L. and Aegilops tauschii Coss, the two ancestral species of common wheat (Triticum aestivum L.) and molecular markers were used to demonstrate the SynDH method.

2011 Vol. 38, No. 2