Journal of Genetics and Genomics

Reviewer Acknowledgements

2011, 38(1): I-II. doi: 10.1016/S1673-8527(11)00013-0

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Inside Front Cover - Editorial Board

2011, 38(1) doi: 10.1016/S1673-8527(11)00008-7

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TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance

Song Song, Qinglan Ge, Jinbo Wang, Haiyang Chen, Sanyuan Tang, Junfeng Bi, Xia Li, Qi Xie, Xun Huang

2011, 38(1): 1-11. doi: 10.1016/j.jcg.2010.12.004

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TRIpartite Motif (TRIM) family proteins are ring finger domain-containing, multi-domain proteins implicated in many biological processes. Members of the TRIM-9/C-I subfamily of TRIM proteins, including TRIM-9, MID1 and MID2, have neuronal functions and are associated with neurological diseases. To explore whether the functions of C-I TRIM proteins are conserved in invertebrates, we analyzed Caenorhabditis elegans and Drosophila trim-9 mutants. C. elegans trim-9 mutants exhibit defects in the ventral guidance of hermaphrodite specific neuron (HSN) and the touch neuron AVM. Further genetic analyses indicate that TRIM-9 participates in the UNC-6-UNC-40 attraction pathway. Asymmetric distribution of UNC-40 during HSN development is normal in trim-9 mutants. However, the asymmetric localization of MIG-10, a downstream effector of UNC-40, is abolished in trim-9 mutants. These results suggest that TRIM-9 functions upstream of MIG-10 in the UNC-40 pathway. Moreover, we showed that TRIM-9 exhibits E3 ubiquitin ligase activity in vitro and this activity is important for TRIM-9 function in vivo. Additionally, we found that Drosophila trim-9 is required for the midline attraction of a group of sensory neuron axons. Over-expression of the Netrin/UNC-6 receptor Frazzled suppresses the guidance defects in trim-9 mutants. Our study reveals an evolutionarily conserved function of TRIM-9 in the UNC-40/Frazzled-mediated UNC-6/Netrin attraction pathway.

Derivation and characterization of human embryonic stem cell lines from the Chinese population

Zhao Wu, Hui Li, Lingjun Rao, Lixiazi He, Lei Bao, Jing Liao, Chun Cui, Zhenyu Zuo, Qiao Li, Huimin Dai, Lei Qian, Qing Tian, Lei Xiao, Xiaojun Tan

2011, 38(1): 13-20. doi: 10.1016/j.jcg.2010.12.006

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Human embryonic stem cells (hESCs) can self-renew indefinitely and differentiate into all cell types in the human body. Therefore, they are valuable in regenerative medicine, human developmental biology and drug discovery. A number of hESC lines have been derived from the Chinese population, but limited of them are available for research purposes. Here we report the derivation and characterization of two hESC lines derived from human blastocysts of Chinese origin. These hESCs express alkaline phosphatase and hESC-specific markers, including Oct4, Nanog, SSEA-3, SSEA-4, TRA-1-60 and TRA-1-81. They also have high levels of telomerase activity and normal karyotypes. These cells can form embryoid body in vitro and can be differentiated into all three germ layers in vivo by teratoma formation. The newly established hESCs will be distributed for research purposes. The availability of hESC lines from the Chinese population will facilitate studies on the differences in hESCs from different ethnic groups.

Association between mitochondrial DNA haplotype compatibility and increased efficiency of bovine intersubspecies cloning

Hao Yan, Zhonghai Yan, Qingwen Ma, Fei Jiao, Shuzhen Huang, Fanyi Zeng, Yitao Zeng

2011, 38(1): 21-28. doi: 10.1016/j.jcg.2010.12.003

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Reconstructed embryos derived from intersubspecies somatic cell nuclear transfer (SCNT) have poorer developmental potential than those from intrasubspecies SCNT. Based on our previous study that Holstein dairy bovine (HD) mitochondrial DNA (mtDNA) haplotype compatibility between donor karyoplast and recipient cytoplast is crucial for SCNT embryo development, we performed intersubspecies SCNT using HD as donor karyoplast and Luxi yellow heifer (LY) as recipient cytoplast according to mtDNA haplotypes determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The results demonstrated that intersubspecies mtDNA homotype SCNT embryos had higher pre- and post-implantation developmental competence than intrasubspecies mtDNA heterotype embryos as well as improved blastocyst reprogramming status, including normal H3K9 dimethylation pattern and promoter hypomethylation of pluripotent genes such as Oct4 and Sox2, suggesting that intersubspecies SCNT using LY oocytes maintains HD cloning efficiency and may reprogram HD nuclei to develop into a normal cloned animal ultimately. Our results indicated that karyoplast–cytoplast interactions and mtDNA haplotype compatibility may affect bovine intersubspecies SCNT efficiency. This study on bovine intersubspecies SCNT is valuable for understanding the mechanisms of mtDNA haplotype compatibility between karyoplast and cytoplast impacting the bovine SCNT efficiency, and provides an alternative and economic resource for HD cloning.

RLIN1, encoding a putative coproporphyrinogen III oxidase, is involved in lesion initiation in rice

Changhui Sun, Linchuan Liu, Jiuyou Tang, Aihong Lin, Fantao Zhang, Jun Fang, Genfa Zhang, Chengcai Chu

2011, 38(1): 29-37. doi: 10.1016/j.jcg.2010.12.001

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Lesion mimic is necrotic lesions on plant leaf or stem in the absence of pathogenic infection, and its exact biological mechanism is varied. By a large-scale screening of our T-DNA mutant population, we identified a mutant rice lesion initiation 1 (rlin1), which was controlled by a single nuclear recessive gene. Map-based cloning revealed that RLIN1 encoded a putative coproporphyrinogen III oxidase in tetrapyrrole biosynthesis pathway. Sequencing results showed that a G to T substitution occurred in the second exon of RLIN1 and led to a missense mutation from Asp to Tyr. Ectopic expression of RLIN1 could rescue rlin1 lesion mimic phenotype. Histochemical analysis demonstrated that lesion formation inrlin1 was light-dependent accompanied by reactive oxygen species accumulated. These results suggest that tetrapyrrole participates in lesion formation in rice.

Comparison of the distribution of the repetitive DNA sequences in three variants of Cucumis sativus reveals their phylogenetic relationships

Xin Zhao, Jingyuan Lu, Zhonghua Zhang, Jiajin Hu, Sanwen Huang, Weiwei Jin

2011, 38(1): 39-45. doi: 10.1016/j.jcg.2010.12.005

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Repetitive DNA sequences with variability in copy number or/and sequence polymorphism can be employed as useful molecular markers to study phylogenetics and identify species/chromosomes when combined with fluorescence in situ hybridization (FISH). Cucumis sativus has three variants, Cucumis sativus L. var. sativus, Cucumis sativus L. var. hardwickii and Cucumis sativus L. var. xishuangbannesis. The phylogenetics among these three variants has not been well explored using cytological landmarks. Here, we concentrate on the organization and distribution of highly repetitive DNA sequences in cucumbers, with emphasis on the differences between cultivar and wild cucumber. The diversity of chromosomal karyotypes in cucumber and its relatives was detected in our study. Thereby, sequential FISH with three sets of multi-probe cocktails (combined repetitive DNA with chromosome-specific fosmid clones as probes) were conducted on the same metaphase cell, which helped us to simultaneously identify each of the 7 metaphase chromosomes of wild cucumber C. sativus var. hardwickii. A standardized karyotype of somatic metaphase chromosomes was constructed. Our data also indicated that the relationship between cultivar cucumber and C. s. var. xishuangbannesis was closer than that of C. s. var. xishuangbannesis and C. s. var. hardwickii.

Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

Tae-Ho Park, Beom-Seok Park, Jin-A. Kim, Joon Ki Hong, Mina Jin, Young-Joo Seol, Jeong-Hwan Mun

2011, 38(1): 47-53. doi: 10.1016/j.jcg.2010.12.002

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As a part of the Multinational Genome Sequencing Project ofBrassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.

2011 Vol. 38, No. 1