Journal of Genetics and Genomics

Small RNA transcriptome investigation based on next-generation sequencing technology

Linglin Zhou, Xueying Li, Qi Liu, Fangqing Zhao, Jinyu Wu

2011, 38(11): 505-513. doi: 10.1016/j.jgg.2011.08.006

Abstract (64) HTML PDF (0)

Abstract:
Over the past decade, there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation. With an increased throughput and a reduced cost, next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome. Meanwhile, the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining. To provide some insight into the small RNA transcriptome investigation, this review describes the major small RNA classes, experimental methods to identify small RNAs, and available bioinformatics tools and databases.

Nogo receptor 3, a paralog of Nogo-66 receptor 1 (NgR1), may function as a NgR1 co-receptor for Nogo-66

Lei Zhang, Xia Kuang, Jian Zhang

2011, 38(11): 515-523. doi: 10.1016/j.jgg.2011.10.001

Abstract (48) HTML PDF (2)

Abstract:
Nogo-A is a major myelin associated inhibitor that blocks regeneration of injured axons in the central nervous system (CNS). Nogo-66 (a 66-residue domain of Nogo-A) expressed on the surface of oligodendrocytes has been shown to directly interact with Nogo-66 receptor 1 (NgR1). A number of additional components of NgR1 receptor complex essential for its signaling have been uncovered. However, detailed composition of the complex and its signaling mechanisms remain to be fully elucidated. In this study, we show that Nogo receptor 3 (NgR3), a paralog of NgR1, is a binding protein for NgR1. The interaction is highly specific because other members of the reticulin family, to which Nogo-A belongs, do not bind to NgR3. Neither does NgR3 show any binding activity with Nogo receptor 2 (NgR2), another NgR1 paralog. Majority of NgR3 domains are required for its binding to NgR1. Moreover, a truncated NgR3 with the membrane anchoring domain deleted can function as a decoy receptor to reverse neurite outgrowth inhibition caused by Nogo-66 in culture. These in vitro results, together with previously reported overlapping expression profile between NgR1 and NgR3, suggest that NgR3 may be associated with NgR1in vivo and that their binding interface may be targeted for treating neuronal injuries.

Identification of compatibility between ooplasmic factor and sperm gene in the intersubspecific crosses involving DDK and PWK mice strains

Gendi Song, Tingting Wang, Jie Guo, Jian Lei, Chunli Li, Zhenyu Zheng, Weidong Zhao

2011, 38(11): 525-531. doi: 10.1016/j.jgg.2011.08.008

Abstract (64) HTML PDF (0)

Abstract:
The DDK strain (Mus musculus domesticus) of inbred mouse has a unique peculiarity known as DDK syndrome. The DDK females are mostly infertile when crossed with males of other inbred strains, while DDK males exhibit normal fertility in the reciprocal crosses, as intrastrain matings. This DDK syndrome has been demonstrated to be caused by an incompatibility system between DDK ooplasmic factor and the sperm gene of other strains owing to theovum mutant (Om) locus on mouse Chromosome 11. Recently, it was reported that DDK females are fully fertile when crossed to males of MOM (M. m. molossinus) and CASP (M. m. castaneus) strains, indicating that no incompatibilities exist between DDK ooplasmic factor and sperm gene of MOM or CASP males. In the present study, DDK females were found to be also fully fertile when crossed to the males of PWK wild-derived inbred strain (originated from Czech Republic wild mice, M. m. musculus). The crosses of DDK females×F₁ (DDK♀×PWK♂) males also resulted in normal fertility. Furthermore, the transmission ratios of Om alleles from these F₁ males to their backcross N₂ offspring are 50%:50% as genotyped by microsatellite markers closely linked to Om locus. Moreover, it was demonstrated that PWK females are also fully fertile when crossed to DDK males. All above results indicated that no incompatibility exists between ooplasmic factor and sperm gene in the intersubspecific crosses with DDK and PWK strains. PWK strain would also be useful for further investigations on the DDK syndrome, and DDK strain can be used more widely for various studies in the mouse.

Avian influenza A virus H5N1 causes autophagy-mediated cell death through suppression of mTOR signaling

Jianhui Ma, Qian Sun, Ruifang Mi, Hongbing Zhang

2011, 38(11): 533-537. doi: 10.1016/j.jgg.2011.10.002

Abstract (75) HTML PDF (0)

Abstract:
Of the few avian influenza viruses that have crossed the species barrier to infect humans, the highly pathogenic influenza A (H5N1) strain has claimed the lives of more than half of the infected patients. With largely unknown mechanism of lung injury by H5N1 infection, acute respiratory distress syndrome (ARDS) is the major cause of death among the victims. Here we present the fact that H5N1 caused autophagic cell death through suppression of mTOR signaling. Inhibition of autophagy, either by depletion of autophagy gene Beclin1 or by autophagy inhibitor 3-methyladenine (3-MA), significantly reduced H5N1 mediated cell death. We suggest that autophagic cell death may contribute to the development of ARDS in H5N1 influenza patients and inhibition of autophagy could therefore become a novel strategy for the treatment of H5N1 infection.

TSA1 interacts with CSN1/CSN and may be functionally involved in Arabidopsis seedling development in darkness

Wenjun Li, Baisheng Zang, Citao Liu, Lu Lu, Ning Wei, Kaiming Cao, Xing Wang Deng, Xiping Wang

2011, 38(11): 539-546. doi: 10.1016/j.jgg.2011.08.007

Abstract (68) HTML PDF (5)

Abstract:
The COP9 signalosome (CSN) is a multiprotein complex which participates in diverse cellular and developmental processes. CSN1, one of the subunits of CSN, is essential for assembly of the multiprotein complex via PCI (proteasome, COP9 signalosome and initiation factor 3) domain in the C-terminal half of CSN1. However, the role of the N-terminal domain (NTD) of CSN1, which is critical for the function of CSN, is not completely understood. Using a yeast two-hybrid (Y2H) screen, we found that the NTD of CSN1 interacts with TSK-associating protein 1 (TSA1), a reported Ca²⁺-binding protein. The interaction between CSN1 and TSA1 was confirmed by co-immunoprecipitation in Arabidopsis. tsa1 mutants exhibited a short hypocotyl phenotype in darkness but were similar to wild-type Arabidopsis under white light, which suggested that TSA1 might regulate Arabidopsis hypocotyl development in the dark. Furthermore, the expression of TSA1 was significantly lower in a csn1 null mutant (fus6), while CSN1 expression did not change in a tsa1 mutant with weak TSA1 expression. Together, these findings suggest a functional relationship between TSA1 and CSN1 in seedling development.

Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

Junzhou Li, Deping Wang, Yan Xie, Hongliang Zhang, Guanglong Hu, Jinjie Li, Anyong Dai, Lifeng Liu, Zichao Li

2011, 38(11): 547-556. doi: 10.1016/j.jgg.2011.08.005

Abstract (56) HTML PDF (2)

Abstract:
Introgression lines (ILs) are valuable materials for identifying quantitative trait loci (QTLs), evaluating genetic interactions, and marker assisted breeding. A set of 430 ILs (BC₅F₃) containing segments from upland tropical japonica cultivar IRAT109 in a lowland temperate japonica cultivar Yuefu background were developed. One hundred and seventy-six polymorphic markers were used to identify introgressed segments. No segment from IRAT109 was found in 160 lines. Introgressed segments of the other 270 lines covered 99.1% of the donor genome. The mean number of introgressed donor segments per individual was 3.3 with an average length of 14.4 cM. QTL analysis was conducted on basal root thickness (BRT) of the 270 ILs grown under irrigated lowland, upland and hydroponic conditions. A total of 22 QTLs affecting BRT were identified, six QTLs (qBRT3.1, qBRT3.2, qBRT6.1, qBRT8.2, qBRT9.1, and qBRT9.2) were consistently expressed under at least two environments (location and water regime), and qBRT7.2 was a new BRT QTL identified under lowland conditions. IL255 containing qBRT9.1 showed an increase of 10.09% and 7.07% BRT over cultivar Yuefu when grown under upland and lowland conditions, respectively. Using a population of 304 F_2:3 lines derived from the cross IL255×Yuefu, qBRT9.1 was validated and mapped to a 1.2 cM interval between RM24271 and RM566. The presence ofqBRT9.1 explained 12% of BRT variation. The results provide upland rice ILs and BRT QTLs for analyzing the genetic basis of drought resistance, detecting favorable genes from upland rice, and rice drought resistance breeding.

A cotton mitogen-activated protein kinase (GhMPK6) is involved in ABA-induced CAT1 expression and H2O2 production

Juan Luo, Li-Li Zhao, Si-Ying Gong, Xiang Sun, Peng Li, Li-Xia Qin, Ying Zhou, Wen-Liang Xu, Xue-Bao Li

2011, 38(11): 557-565. doi: 10.1016/j.jgg.2011.10.003

Abstract (60) HTML PDF (2)

Abstract:
The mitogen-activated protein kinase (MAPK) cascade is one of the major and evolutionally conserved signaling pathways and plays a pivotal role in the regulation of stress and developmental signals in plants. Here, we identified one gene, GhMPK6, encoding an MAPK protein in cotton. GFP fluorescence assay demonstrated that GhMAPK6 is a cytoplasm localized protein. Quantitative RT-PCR analysis revealed that mRNA accumulation of GhMPK6 was significantly promoted by abscisic acid (ABA). Overexpression of GhMPK6 gene in the T-DNA insertion mutant atmkk1 (SALK_015914) conferred a wild-type phenotype to the transgenic plants in response to ABA. Under ABA treatment, cotyledon greening/expansion in GhMPK6 transgenic lines and wild type was significantly inhibited, whereas the atmkk1 mutant showed a relatively high cotyledon greening/expansion ratio. Furthermore, CAT1 expression and H₂O₂ levels in leaves of GhMPK6 transgenic lines and wild type were remarkably higher than those of atmkk1 mutant with ABA treatment. Collectively, our results suggested that GhMPK6 may play an important role in ABA-induced CAT1 expression and H₂O₂ production.

2011 Vol. 38, No. 11