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Genomics, Proteomics & Bioinformatics (GPB; ISSN 1672-0229, CN11-4926/Q), a peer-reviewed international journal in English, is sponsored by Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China, and jointly published by Elsevier and Science Press bi-monthly.

The publications of the journal are high-quality papers from all over the world in the fields of genomics, proteomics, and bioinformatics. For manuscripts submitted to GPB, direct rejection, direct acceptance or further review will be decided within 5 days. Besides, GPB offers Article-in-Press, by which all the accepted manuscripts can be available online ahead of its printed issue print for fast dissemination.

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Recent Articles (Volume:16, Issue:6)

1. A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG, CAS

Jun Yu

Page 387-388


2. From Basic Research to Molecular Breeding — Chinese Scientists Play A Central Role in Boosting World Rice Production

Ding Tang, Zhukuan Cheng

On November 18, 2018, the Future Science Prize Awarding Ceremony was held in Beijing. In the area of life science, Professors Jiayang Li, Longping Yuan, and Qifa Zhang shared the prize for their pioneering contributions in producing high-yield, superior-quality rice through systematic study of molecular mechanisms associated with specific rice features and application of novel approaches in rice breeding. The Future Science Prize is also touted as “China’s Nobel Prize”, fully affirming their achievements in rice basic research and breeding.

Page 389-392


3. Development of the “Third-Generation” Hybrid Rice in China

Haiyang Wang, Xing Wang Deng

Rice is a major cereal crop for China. The development of the “three-line” hybrid rice system based on cytoplasmic male sterility in the 1970s (first-generation) and the “two-line” hybrid rice system based on photoperiod- and thermo-sensitive genic male-sterile lines (second-generation) in the 1980s has contributed significantly to rice yield increase and food security in China. Here we describe the development and implementation of the “third-generation” hybrid rice breeding system that is based on a transgenic approach to propagate and utilize stable recessive nuclear male sterile lines, and as such, the male sterile line and hybrid rice produced using such a system is non-transgenic. Such a system should overcome the intrinsic problems of the “first-generation” and “second-generation” hybrid rice systems and hold great promise to further boost production of hybrid rice and other crops.

Page 393-396


4. Rice Genomics: over the Past Two Decades and into the Future

Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu

Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future.
水稻是全球重要的粮食作物,也是最早开展基因组学研究的模式作物,随着高通量基因组测序技术的发展,水稻基因组学研究取得了突破性进展。本文简要回顾了近二十年水稻基因组测序计划、基因组学特征及相关科学问题、水稻杂种优势和重要农艺性状的遗传基础、同属基因组测序概况及基因组多样性和驯化历史、水稻功能基因的克隆等方面的研究进展和取得的成果。最后,对水稻基因组学研究的未来和挑战进行了展望。

Page 397-404


5. Recent Advances in Function-based Metagenomic Screening

Tanyaradzwa Rodgers Ngara, Houjin Zhang

Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.

Page 405-415


6. Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays

Wenfang Zhou, Mojie Duan, Weitao Fu, Jinping Pang, Qin Tang, Huiyong Sun, Lei Xu, Shan Chang, Dan Li, Tingjun Hou

Androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of many severe diseases such as prostate cancer, muscle atrophy, and osteoporosis. Binding of ligands to AR triggers the conformational changes in AR that may affect the recruitment of coactivators and downstream response of AR signaling pathway. Therefore, AR ligands have great potential to treat these diseases. In this study, we searched for novel AR ligands by performing a docking-based virtual screening (VS) on the basis of the crystal structure of the AR ligand binding domain (LBD) in complex with its agonist. A total of 58 structurally diverse compounds were selected and subjected to LBD affinity assay, with five of them (HBP1-3, HBP1-17, HBP1-38, HBP1-51, and HBP1-58) exhibiting strong binding to AR-LBD. The IC50 values of HBP1-51 and HBP1-58 are 3.96 µM and 4.92 µM, respectively, which are even lower than that of enzalutamide (Enz, IC50 = 13.87 µM), a marketed second-generation AR antagonist. Further bioactivity assays suggest that HBP1-51 is an AR agonist, whereas HBP1-58 is an AR antagonist. In addition, molecular dynamics (MD) simulations and principal components analysis (PCA) were carried out to reveal the binding principle of the newly-identified AR ligands toward AR. Our modeling results indicate that the conformational changes of helix 12 induced by the bindings of antagonist and agonist are visibly different. In summary, the current study provides a highly efficient way to discover novel AR ligands, which could serve as the starting point for development of new therapeutics for AR-related diseases.
雄激素受体(AR)是配体依赖的转录因子,在前列腺癌、肌肉萎缩和骨质疏松等重大疾病的发生和发展中扮演重要角色。被配体激活后,AR的构型发生变化,募集共激活剂,引起AR信号通路下游的一系列反应。因此,AR配体对于这些疾病的治疗具有极高的潜在价值。该研究基于AR与其激动剂的复合物晶体结构,通过以对接为主要手段的虚拟筛选寻找AR的新型配体。58个结构各异的化合物被筛选出来。其中HBP1-3,HBP1-17,HBP1-38,HBP1-51和HBP1-58等5个化合物在竞争性结合实验中展现出对AR配体结合域的很强的结合能力。HBP1-51和HBP1-58的IC50值分别为3.96 µM和4.92 µM,低于已上市的第二代AR拮抗剂比卡鲁胺(IC50 = 13.87 µM)。进一步的生物实验证明:HBP1-51是AR激动剂,而HBP1-58是AR拮抗剂。此外,该研究进行了分子动力学模拟(MD)和主成分分析(PCA),揭示了这些新型小分子配体与AR的结合原理。建立的模型结构显示,当与激动剂和拮抗剂结合时,AR的H12构型变化明显不同。该研究提供了一条高效筛选AR配体的途径,同时为治疗AR相关疾病的新型药物的开发提供了素材。

Page 416-427


7. RNF126 Quenches RNF168 Function in the DNA Damage Response

Lianzhong Zhang, Zhenzhen Wang, Ruifeng Shi, Xuefei Zhu, Jiahui Zhou, Bin Peng, Xingzhi Xu

DNA damage response (DDR) is essential for maintaining genome stability and protecting cells from tumorigenesis. Ubiquitin and ubiquitin-like modifications play an important role in DDR, from signaling DNA damage to mediating DNA repair. In this report, we found that the E3 ligase ring finger protein 126 (RNF126) was recruited to UV laser micro-irradiation-induced stripes in a RNF8-dependent manner. RNF126 directly interacted with and ubiquitinated another E3 ligase, RNF168. Overexpression of wild type RNF126, but not catalytically-inactive mutant RNF126 (CC229/232AA), diminished ubiquitination of H2A histone family member X (H2AX), and subsequent bleomycin-induced focus formation of total ubiquitin FK2, TP53-binding protein 1 (53BP1), and receptor-associated protein 80 (RAP80). Interestingly, both RNF126 overexpression and RNF126 downregulation compromised homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs). Taken together, our findings demonstrate that RNF126 negatively regulates RNF168 function in DDR and its appropriate cellular expression levels are essential for HR-mediated DSB repair.
DNA损伤应答(DDR)对于维持基因组的稳定性和保护细胞免于癌变是至关重要的。泛素化和类泛素化修饰从DNA损伤的信号传递到DNA修复的过程中都发挥着重要作用。在本研究中,我们发现E3连接酶环指蛋白126(RNF126)以RNF8依赖的方式被募集到紫外激光微辐射诱导的DNA损伤条带中。RNF126与另一个E3连接酶RNF168发生直接相互作用,并且对RNF168进行泛素化修饰。过表达野生型RNF126,而不是催化失活突变型RNF126(CC229/232AA),减少了H2A组蛋白家族成员X(H2AX)的泛素化修饰,以及随后博莱霉素诱导的FK2、53BP1和RAP80的聚焦形成。有趣的是,过表达和抑制RNF126都不利于同源重组(HR)介导的DNA双链断裂(DSB)的修复。总之,我们的研究结果表明RNF126在DNA损伤应答反应中负性调节RNF168的功能,其适当的细胞表达水平对于同源重组介导的DNA双链断裂(DSB)修复是必需的。

Page 428-438


8. An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants

Shangang Jia, Kyla Morton, Chi Zhang, David Holding

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ~200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding the RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.
尽管有很多玉米研究的基因组和转录组资源,但是对于发育和生化过程中基因功能,我们的理解还不够,仍然有很多方面需要进行研究。本研究中,我们首先用伽马射线创造了一些玉米突变体,当我们将它们与玉米Mo17株系杂交得到F1代,在F1代自交获得的F2代中,发现其玉米籽粒有非常明显的性状分离。为了更好地理解玉米籽粒发育中的功能基因组学,我们开发出一个基因定位和鉴定的流程,叫作bulked segregant exome sequencing (BSEx-seq),在不透明籽粒和小籽粒表型的玉米突变体中,成功进行了定位分析。BSEx-seq在性状分离为突变体表型和正常表型的F2代植株中,提取叶子中的基因组DNA,开展外显子测序,并进行比较分析。这种比较分析可以得到定位峰,进而在定位峰中找到缺失突变,最后在缺失区域中确定候选基因。然后,我们利用已发表的玉米籽粒中特异表达的基因数据,来缩小候选基因/变异的数量,同时也识别出长度从几个kb到大于1Mb的缺失。我们在籽粒不透明突变体531中,发现Opaque-2基因完全缺失了,这个缺失长度大约为200kb。在籽粒不透明突变体1486中,我们在定位区间中发现了一个6248bp的缺失,这个缺失涉及到两个基因,分别编码RNA-directed DNA methylation 4 (RdDM4)和AMP-binding protein。本研究中,BSEx-seq可以有效地定位突变变异位点和突变基因,其成本也很低,这为玉米功能基因组学研究,提供了新的测序定位方法。

Page 439-450


9. Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites

Zhen Chen, Ningning He, Yu Huang, Wen Tao Qin, Xuhan Liu, Lei Li

As a newly-identified protein post-translational modification, malonylation is involved in a variety of biological functions. Recognizing malonylation sites in substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein malonylation. In this study, we constructed a deep learning (DL) network classifier based on long short-term memory (LSTM) with word embedding (LSTMWE) for the prediction of mammalian malonylation sites. LSTMWE performs better than traditional classifiers developed with common pre-defined feature encodings or a DL classifier based on LSTM with a one-hot vector. The performance of LSTMWE is sensitive to the size of the training set, but this limitation can be overcome by integration with a traditional machine learning (ML) classifier. Accordingly, an integrated approach called LEMP was developed, which includes LSTMWE and the random forest classifier with a novel encoding of enhanced amino acid content. LEMP performs not only better than the individual classifiers but also superior to the currently-available malonylation predictors. Additionally, it demonstrates a promising performance with a low false positive rate, which is highly useful in the prediction application. Overall, LEMP is a useful tool for easily identifying malonylation sites with high confidence. LEMP is available at http://www.bioinfogo.org/lemp.
蛋白质丙二酰化(Malonylation)是一种近年来新发现的蛋白质翻译后修饰,发生在蛋白质的赖氨酸(Lysine)的侧链上,它在多种代谢调控过程中都发挥着重要的作用。最近的研究表明,丙二酰化通过糖酵解途径来调控能量循环,在葡萄糖和脂肪酸代谢过程中起关键作用,与2 型糖尿病也密切相关。因此,在修饰底物上精确鉴定修饰位点是研究其分子机制的一个非常关键的步骤。在本研究中,我们首先采用长短期记忆(LSTM)模型算法构建了一个基于的深度学习的模型—LSTMWE,用于对哺乳动物中的丙二酰化修饰位点进行预测。测试结果表明,LSTMWE的性能对训练集数据量敏感,当训练数据集足够大的时候,LSTMWE的预测性相对于传统的基于预定义的特征编码的分类模型有着绝对优势,但当数据量较小的时候,这种优势消失。为了使我们的预测框架能够应用在不同量级的数据集中,我们通过整合LSTMWE和一种使用增强氨基酸含量的新型编码的随机森林分类模型构建了一个集成的模型—LEMP。LEMP不仅在不同大小的数据集中都具有较稳定的预测性能,而且优于目前已经发表的丙二酰化预测方法。总的来说,LEMP是一个对丙二酰化修饰进行预测的有效工具。目前,LEMP可以通过http://www.bioinfogo.org/lemp访问。

Page 451-459


10. The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway

Yiheng Hu, Ran Zhao, Peng Xu, Yuannian Jiao

Page 460-462


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