Journal of Genetics and Genomics

Genetic and epigenetic control of transfer cell development in plants

Jing Yuan, Perry Bateman, Jose Gutierrez-Marcos

2016, 43(9): 533-539. doi: 10.1016/j.jgg.2016.08.002

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Abstract:
The inter-cellular translocation of nutrients in plant is mediated by highly specialized transfer cells (TCs). TCs share similar functional and structural features across a wide range of plant species, including location at plant exchange surfaces, rich in secondary wall ingrowths, facilitation of nutrient flow, and passage of select molecules. The fate of endosperm TCs is determined in the TC fate acquisition stage (TCF), before the structure features are formed in the TC differentiation stage (TCD). At present, the molecular basis of TC development in plants remains largely unknown. In this review, we summarize the important roles of the signaling molecules in different development phases, such as sugars in TCF and phytohormones in TCD, and discuss the genetic and epigenetic factors, including TC-specific genes and endogenous plant peptides, and their crosstalk with these signaling molecules as a complex regulatory network in regulation of TC development in plants.

Clinical applications of MARSALA for preimplantation genetic diagnosis of spinal muscular atrophy

Yixin Ren, Xu Zhi, Xiaohui Zhu, Jin Huang, Ying Lian, Rong Li, Hongyan Jin, Yan Zhang, Wenxin Zhang, Yanli Nie, Yuan Wei, Zhaohui Liu, Donghong Song, Ping Liu, Jie Qiao, Liying Yan

2016, 43(9): 541-547. doi: 10.1016/j.jgg.2016.03.011

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Abstract:
Conventional PCR methods combined with linkage analysis based on short tandem repeats (STRs) or Karyomapping with single nucleotide polymorphism (SNP) arrays, have been applied to preimplantation genetic diagnosis (PGD) for spinal muscular atrophy (SMA), an autosome recessive disorder. However, it has limitations in SMA diagnosis by Karyomapping, and these methods are unable to distinguish wild-type embryos with carriers effectively. Mutated allele revealed by sequencing with aneuploidy and linkage analyses (MARSALA) is a new method allowing embryo selection by a one-step next-generation sequencing (NGS) procedure, which has been applied in PGD for both autosome dominant and X-linked diseases in our group previously. In this study, we carried out PGD based on MARSALA for two carrier families with SMA affected children. As a result, one of the couples has given birth to a healthy baby free of mutations in SMA-causing gene. It is the first time that MARSALA was applied to PGD for SMA, and we can distinguish the embryos with heterozygous deletion (carriers) from the wild-type (normal) ones accurately through this NGS-based method. In addition, direct mutation detection allows us to identify the affected embryos (homozygous deletion), which can be regarded as probands for linkage analysis, in case that the affected family member is absent. In the future, the NGS-based MARSALA method is expected to be used in PGD for all monogenetic disorders with known pathogenic gene mutation.

A rare variant in COL11A1 is strongly associated with adult height in Chinese Han population

Changbing Shen, Xiaodong Zheng, Jing Gao, Caihong Zhu, Randy Ko, Xianfa Tang, Chao Yang, Jinfa Dou, Yan Lin, Yuyan Cheng, Lu Liu, Shuangjun Xu, Gang Chen, Xianbo Zuo, Xianyong Yin, Liangdan Sun, Yong Cui, Sen Yang, Xuejun Zhang, Fusheng Zhou

2016, 43(9): 549-554. doi: 10.1016/j.jgg.2016.04.002

Abstract (120) HTML PDF (1)

Abstract:
Human height is a highly heritable trait in which multiple genes are involved. Recent genome-wide association studies (GWASs) have identified that COL11A1 is an important susceptibility gene for human height. To determine whether the variants of COL11A1 are associated with adult and children height, we analyzed splicing and coding single-nucleotide variants across COL11A1 through exome-targeted sequencing and two validation stages with a total 20,426 Chinese Han samples. A total of 105 variants were identified by exome-targeted sequencing, of which 30 SNPs were located in coding region. The strongest association signal was chr1_103380393 with P value of 4.8 × 10⁻⁷. Chr1_103380393 also showed nominal significance in the validation stage (P = 1.21 × 10⁻⁶). Combined analysis of 16,738 samples strengthened the original association of chr1_103380393 with adult height (P = 3.1 × 10⁻⁸), with an increased height of 0.292sd (standard deviation) per G allele (95% CI: 0.19–0.40). There was no evidence (P = 0.843) showing that chr1_103380393 altered child height in 3688 child samples. Only the group of 12–15 years showed slight significance with P value of 0.0258. This study firstly shows that genetic variants of COL11A1 contribute to adult height in Chinese Han population but not to children height, which expand our knowledge of the genetic factors underlying height variation and the biological regulation of human height.

The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis

Chuang-Qi Wei, Chih-Wei Chien, Lian-Feng Ai, Jun Zhao, Zhenzhen Zhang, Kathy H. Li, Alma L. Burlingame, Yu Sun, Zhi-Yong Wang

2016, 43(9): 555-563. doi: 10.1016/j.jgg.2016.05.007

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Abstract:
Plant growth is controlled by integration of hormonal and light-signaling pathways. BZS1 is a B-box zinc finger protein previously characterized as a negative regulator in the brassinosteroid (BR)-signaling pathway and a positive regulator in the light-signaling pathway. However, the mechanisms by which BZS1/BBX20 integrates light and hormonal pathways are not fully understood. Here, using a quantitative proteomic workflow, we identified several BZS1-associated proteins, including light-signaling components COP1 and HY5. Direct interactions of BZS1 with COP1 and HY5 were verified by yeast two-hybrid and co-immunoprecipitation assays. Overexpression of BZS1 causes a dwarf phenotype that is suppressed by thehy5 mutation, while overexpression of BZS1 fused with the SRDX transcription repressor domain (BZS1-SRDX) causes a long-hypocotyl phenotype similar to hy5, indicating that BZS1's function requires HY5. BZS1 positively regulates HY5 expression, whereas HY5 negatively regulates BZS1 protein level, forming a feedback loop that potentially contributes to signaling dynamics. In contrast to BR, strigolactone (SL) increases BZS1 level, whereas the SL responses of hypocotyl elongation, chlorophyll and HY5 accumulation are diminished in the BZS1-SRDX seedlings, indicating that BZS1 is involved in these SL responses. These results demonstrate that BZS1 interacts with HY5 and plays a central role in integrating light and multiple hormone signals for photomorphogenesis in Arabidopsis.

Estrogen-estrogen receptor signaling suppresses the transcription of ERRF in breast cancer cells

Ang Luo, Dan Su, Xuan Zhang, Leilei Qi, Liya Fu, Jin-Tang Dong

2016, 43(9): 565-567. doi: 10.1016/j.jgg.2016.06.003

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Abstract:

Literature-based knowledgebase of pancreatic cancer gene to prioritize the key genes and pathways

Yining Liu, Jingchun Sun, Min Zhao

2016, 43(9): 569-571. doi: 10.1016/j.jgg.2016.04.006

Abstract (107) HTML PDF (2)

Abstract:

Establishment and characterization of new wheat-Thinopyrum ponticum addition and translocation lines with resistance to Ug99 races

Hongwei Li, Qi Zheng, Zacharias A. Pretorius, Bin Li, Dingzhong Tang, Zhensheng Li

2016, 43(9): 573-575. doi: 10.1016/j.jgg.2016.07.004

Abstract (78) HTML PDF (2)

Abstract:

2016 Vol. 43, No. 9