Articles

Detect accessible chromatin using ATAC-sequencing, from principle to applications

Chromatin accessibility is crucial for gene expression regulation in specific cells and in multiple biological processes. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) i...

Authors: Yuanyuan Sun, Nan Miao and Tao Sun

Hereditary spastic paraplegia associated with a rare IFIH1 mutation: a case report and literature review

Here, the pathogenesis of an IFIH1 gene mutation is discussed through the analysis of a sporadic case of hereditary spastic paraplegia. Next-generation sequencing was performed for the patient and his family memb...

Authors: Nan Liu, Jiajun Chen, Chuan Xu, Tianji Shi and Jia Li

Expression analysis of Argonaute genes in maize (Zea mays L.) in response to abiotic stress

Argonaute (AGO) protein is a kind of RNA binding protein that plays an integral role in the gene-silencing pathways guided by small RNAs. But there are few studies about the regulation of AGO genes responded t...

Authors: Lihong Zhai, Feng Teng, Kangpeng Zheng, Juan Xiao, Wenbin Deng and Wei Sun

ABCG2 gene polymorphism rs2231142 is associated with gout comorbidities but not allopurinol response in primary gout patients of a Chinese Han male population

One common ATP-binding cassette subfamily G member 2 (ABCG2) gene variant, which is encoded by the single nucleotide polymorphism (SNP) rs2231142, was identified to take an essential part in gouty arthritis. H...

Authors: Keke Zhang and Changgui Li

Integrated identification of key genes and pathways in Alzheimer’s disease via comprehensive bioinformatical analyses

Alzheimer’s disease (AD) is known to be caused by multiple factors, meanwhile the pathogenic mechanism and development of AD associate closely with genetic factors. Existing understanding of the molecular mech...

Authors: Tingting Yan, Feng Ding and Yan Zhao

A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival

Urothelial bladder cancer (BLCA) is one of the most common internal malignancies worldwide with poor prognosis. This study aims to explore effective prognostic biomarkers and construct a prognostic risk score ...

Authors: Zihao Chen, Guojun Liu, Aslam Hossain, Irina G. Danilova, Mikhail A. Bolkov, Guoqing Liu, Irina A. Tuzankina and Wanlong Tan

Identification of serum microRNAs as diagnostic biomarkers for schizophrenia

At present, the schizophrenia diagnoses are based on the clinical symptoms and behaviors neglecting the laboratory test indicators.

Authors: Kuanjun He, Chuang Guo, Meng Guo, Shuping Tong, Qiuli Zhang, Hongjun Sun, Lin He and Yongyong Shi

Mapping and characterization of a quantitative trait locus resistance to the brown planthopper in the rice variety IR64

Rice planthoppers (main brown planthopper, Nilaparvata lugens Stål; BPH) was one of substantial threats to Asia rice production as its serious destruction and difficulties in control under field conditions. Notab...

Authors: Meng Yang, Ling Cheng, Liuhui Yan, Wan Shu, Xinyi Wang and Yongfu Qiu

Proteomic characterization of bovine granulosa cells in dominant and subordinate follicles

Characterization of molecular factors regulating ovarian follicular development is critical to understanding its functional mechanism of controlling the estrous cycle, determining oocyte competency, and regula...

Authors: Qingling Hao, Zhiwei Zhu, Dongmei Xu, Wenzhong Liu, Lihua Lyu and Pengfei Li

Identification of five hub genes as monitoring biomarkers for breast cancer metastasis in silico

Breast cancer is one of the most common endocrine cancers among females worldwide. Distant metastasis of breast cancer is causing an increasing number of breast cancer-related deaths. However, the potential me...

Authors: Yun Cai, Jie Mei, Zhuang Xiao, Bujie Xu, Xiaozheng Jiang, Yongjie Zhang and Yichao Zhu

Association of SYNE1 locus with bipolar disorder in Chinese population

Genome-wide association studies (GWAS) suggest that rs9371601 in the SYNE1 gene is a risk SNP for bipolar disorder (BPD) in populations of European ancestry, but further replication analyses across distinct popul...

Authors: Wenqiang Li, Yongfeng Yang, Binbin Luo, Yan Zhang, Xueqin Song, Ming Li and Luxian Lv

Jérôme Lejeune passed away 25 years ago

Authors: Vicente Soriano

Differentially expressed genes between systemic sclerosis and rheumatoid arthritis

Evidence is accumulating to characterise the key differences between systemic sclerosis (SSc) and rheumatoid arthritis (RA), which are similar but distinct systemic autoimmune diseases. However, the difference...

Authors: Zhenyu Sun, Wenjuan Wang, Degang Yu and Yuanqing Mao

Bread wheat: a role model for plant domestication and breeding

Bread wheat is one of the most important crops in the world. Its domestication coincides with the beginning of agriculture and since then, it has been constantly under selection by humans. Its breeding has fol...

Authors: Eduardo Venske, Railson Schreinert dos Santos, Carlos Busanello, Perry Gustafson and Antonio Costa de Oliveira

Polymorphism of the PPARD Gene and Dynamic Balance Performance in Han Chinese Children

Athletic performances are complex traits with heritability of ~66%. Dynamic balance is one of the most important athletic performances, and there has been little studies for it in sports genomics. The candidate P...

Authors: Yixuan Cao, Qiyue Zhang, Jianhua Chen, Zhiqiang Li, Zhaowei Zhou, Jiawei Shen, Dong Wang, Dun Pan, Zhuo Wang, Dandan Ke, Xiaofei Wang, Dajiang Lu, Ying Zhao, Shulin Cheng and Yongyong Shi

Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

Grapevine is an important fruit crop grown worldwide, and its cultivars are mostly derived from the European species Vitis vinifera, which has genes for high fruit quality and adaptation to a wide variety of clim...

Authors: Ying Zhang, Jia-Long Yao, Hu Feng, Jianfu Jiang, Xiucai Fan, Yun-Fei Jia, Ran Wang and Chonghuai Liu

First report of bicolour FISH of Berberis diaphana and B. soulieana reveals interspecific differences and co-localization of (AGGGTTT)₃ and rDNA 5S in B. diaphana

Berberis consists of approximately 500 species and is the largest genus in Berberidaceae. Most Berberis species lack cytological data, and bicolour fluorescence in situ hybridization (FISH) has never been perform...

Authors: Juncheng Liu and Xiaomei Luo

Transcriptome profiling of the fertile parent and sterile hybrid in tea plant flower buds

The tea plant is a crucial economic crop. The floral organ development consumes a large amount of nutrients, which affects the leaf yield. To understand the mechanism by which the tea plant produces sterile fl...

Authors: Linbo Chen, Hao Qu, Lifei Xia, Yue Liu, Huibing Jiang, Yunnan Sun, Mingzhi Liang and Changjun Jiang

The inhibition of miR-126 in cell migration and invasion of cervical cancer through regulating ZEB1

Cervical cancer is a malignancy that’s common in female with high incidence and mortality worldwide. MicroRNAs (miRNAs) act a pivotal part in human cancer development. Our aim was to investigate the effect of ...

Authors: Jiqin Xu, Hongyun Wang, Huiyan Wang, Qing Chen, Li Zhang, Chao Song, Qianqian Zhou and Ying Hong

Global transcriptome analysis of H5N1 influenza virus-infected human cells

Influenza A virus (IAV) belongs to the Orthomyxoviridae family. IAV causes a highly contagious respiratory disease in humans that exacts severe economic losses globally. The virus uses strategies developed to exp...

Authors: Ying Cao, Kun Zhang, Lirong Liu, Wei Li, Bin Zhu, Shuang Zhang, Ping Xu, Wenjun Liu and Jing Li

Characterization of the Tibet plateau Jerusalem artichoke (Helianthus tuberosus L.) transcriptome by de novo assembly to discover genes associated with fructan synthesis and SSR analysis

Jerusalem artichoke (Helianthus tuberosus L.) is a characteristic crop in the Qinghai-Tibet Plateau which has rapidly developed and gained socioeconomic importance in recent years. Fructans are abundant in tubers...

Authors: Shipeng Yang, Xuemei Sun, Xiaoting Jiang, Lihui Wang, Jie Tian, Li Li, Mengliang Zhao and Qiwen Zhong

Genetic diversity and structure of Elymus tangutorum accessions from western China as unraveled by AFLP markers

Understanding genetic diversity of wild plant germplasm and the relationships between ecogeographic and genetic characteristics may provide insights for better utilizing and conserving genetic resources. Elymus t...

Authors: Wen-Dan Wu, Wen-Hui Liu, Ming Sun, Ji-Qiong Zhou, Wei Liu, Cheng-Lin Zhang, Xing-Quan Zhang, Yan Peng, Lin-Kai Huang and Xiao Ma

Bladder cancer stage-associated hub genes revealed by WGCNA co-expression network analysis

Bladder cancer was a malignant disease in patients, our research aimed at discovering the possible biomarkers for the diseases.

Authors: Yu Di, Dongshan Chen, Wei Yu and Lei Yan

A new model of the mechanism underlying lead poisoning: SNP in miRNA target region influence the AGT expression level

To determine if the rs7079 polymorphism located in the 3′ UTR of the angiotensinogen gene (AGT) altered AGT gene expression and the risk of lead poisoning. A case-control study and luciferase reporter gene assay ...

Authors: Yu Wu, Miaomiao Wang, Jinlong Zhang, Na Sun and Chunping Li

The evolution of transcriptional repressors in the Notch signaling pathway: a computational analysis

The Notch signaling pathway governs the specification of different cell types in flies, nematodes and vertebrates alike. Principal components of the pathway that activate Notch target genes are highly conserve...

Authors: Dieter Maier

Common variants in the SLC28A2 gene are associated with serum uric acid level and hyperuricemia and gout in Han Chinese

Serum uric acid (SUA), hyperuricemia (HUA) and gout are complex traits with relatively high heritability. This study aims to identify whether a candidate gene, SLC28A2, exerts susceptibility for SUA fluctuation a...

Authors: Zhaowei Zhou, Zhiqiang Li, Can Wang, Xinde Li, Xiaoyu Cheng, Changgui Li and Yongyong Shi

Global mapping of binding sites for phic31 integrase in transgenic maden-darby bovine kidney cells using ChIP-seq

ΦC31 integrase, a site-specific recombinase, can efficiently target attB-bearing transgenes to endogenous pseudo attP sites within mammalian genomes. The sequence features of endogenous binding sites will help...

Authors: Lijuan Qu, Lei Wang, Xueyuan Zhu, Yan Zhang, Qiang Ou, Aying Ma, Fengying Sheng, Xiaoqing Wei, Yue Dai, Guoting Li and Shuwu Xie

Genetic characterization of maize germplasm derived from Suwan population and temperate resources

The Suwan population is a well-known maize germplasm that has greatly contributed to the development of maize breeding in tropical and subtropical regions, especially in southern China. Inbred lines derived fr...

Authors: Xun Wu, Angui Wang, Xiangyang Guo, Pengfei Liu, Yunfang Zhu, Xiushi Li and Zehui Chen

Natural selection and local adaptation of blood pressure regulation and their perspectives on precision medicine in hypertension

Prevalence of hypertension (HTN) varies substantially across different populations. HTN is not only common – affecting at least one third of the world’s adult population – but is also the most important driver...

Authors: Boon-Peng Hoh, Thuhairah Abdul Rahman and Khalid Yusoff

Differences in the Neanderthal BRCA2 gene might be related to their distinctive cognitive profile

The unique divergence of the BRCA2 gene in Neanderthals compared to modern humans has been hypothesized to account for a differential susceptibility to cancer. However, the role of the gene in brain development a...

Authors: Antonio Benítez-Burraco

Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Colored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed co...

Authors: Xiaohua Yao, Kunlun Wu, Youhua Yao, Yixiong Bai, Jingxiu Ye and Dezhao Chi

De novo transcriptome assembly of brackish water flea Diaphanosoma celebensis based on short-term cadmium and benzo[a]pyrene exposure experiments

To develop a brackish water flea as a promising model for marine monitoring, Diaphanosoma celebensis were exposed to two pollutants, cadmium (Cd) and benzo[a]pyrene (BaP), which have different chemical characteri...

Authors: Bo-Mi Kim, Seunghyun Kang, Ryeo-Ok Kim, Jee-Hyun Jung, Kyun-Woo Lee, Jae-Sung Rhee and Young-Mi Lee

Genetic diversity of Bletilla striata assessed by SCoT and IRAP markers

Bletilla striata is a well-known traditional Chinese herb with varieties of functions. In China, the natural resources of Bletilla striata have been severely damaged because of the excessive exploitation and dest...

Authors: Yan Guo, Lina Zhai, Hao Long, Nipi Chen, Chengxian Gao, Zhishan Ding and Bo Jin

Unique divergence of the breast cancer 2 (BRCA2) gene in Neanderthals

Unique divergence of the BRCA2, a tumor suppressor gene, in Neanderthals relative to other primates, including modern humans, is highlighted. This divergence with potentially pathogenic consequences raises a q...

Authors: Pawel Michalak and Lin Kang

Enhancement of grain number per spike by RNA interference of cytokinin oxidase 2 gene in bread wheat

This study aimed to validate the function of CKX gene on grain numbers in wheat.

Authors: Yulian Li, Guoqi Song, Jie Gao, Shujuan Zhang, Rongzhi Zhang, Wei Li, Mingli Chen, Min Liu, Xianchun Xia, Thierry Risacher and Genying Li

Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis

For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to ...

Authors: Hefan Miao, Jiapeng Zhou, Qi Yang, Fan Liang, Depeng Wang, Na Ma, Bodi Gao, Juan Du, Ge Lin, Kai Wang and Qianjun Zhang

Variations in morphological traits of bermudagrass and relationship with soil and climate along latitudinal gradients

This complex environmental heterogeneity coupled with the long-standing history offers scenario suitable for and favoring the evolution and existence of variation of morphological traits.

Authors: Jingxue Zhang, Miaoli Wang, Zhipeng Guo, Yongzhuo Guan, Yuxia Guo and Xuebing Yan

Development of 17 polymorphic microsatellite loci from Jeju striped field mouse, Apodemus agrarius chejuensis (Rodentia: Muridae), by 454 pyrosequencing

The striped field mouse, Apodemus agrarius, is the most common mammal in Korea. Although microsatellite loci for the species have been identified from populations in southwestern China, amplification of those mar...

Authors: Han-Na Kim, Han-Ul Kim, Yeong-Seok Jo and Jongwoo Jung

Comparative analysis of the genetic variability within the Q-type C2H2 zinc-finger transcription factors in the economically important cabbage, canola and Chinese cabbage genomes

Brassica oleracea, B. rapa and B. napus encompass many economically important vegetable and oil crops; such as cabbage, broccoli, canola and Chinese cabbage. The genome sequencing of these species allows for gene...

Authors: Susan D. Lawrence and Nicole G. Novak

Seeing is believing: the Bicoid protein reveals its path

In this commentary, I will review the latest findings on the Bicoid (Bcd) morphogen in Drosophila, a paradigm for gradient formation taught to biology students for more than two decades. “Seeing is believing” als...

Authors: Stefan Baumgartner

Overexpression of the Drosophila ATR homologous checkpoint kinase Mei-41 induces a G2/M checkpoint in Drosophila imaginal tissue

DNA damage generally results in the activation of ATM/ATR kinases and the downstream checkpoint kinases Chk1/Chk2. In Drosophila melanogaster, the ATR homologue meiotic 41 (mei-41) is pivotal to DNA damage repair...

Authors: Fabienne E. Bayer, Mirjam Zimmermann, Anette Preiss and Anja C. Nagel

Characterization of TaDREB1 in wheat genotypes with different seed germination under osmotic stress

The cis-acting element DRE/CRT plays an important role in activating gene expression responsive to osmotic stress, low temperature and high-salinity. DREB1/CBF genes encode DRE-binding proteins with the function ...

Authors: Meng Liu, Zeng Wang, Hong-mei Xiao and Yan Yang

The genetic locus underlying red foliage and fruit skin traits is mapped to the same location in the two pear bud mutants ‘Red Zaosu’ and ‘Max Red Bartlett’

Red-skinned pears are attractive to consumers because of their aesthetic appeal and the antioxidant-associated health benefits provided by the anthocyanins in their red skin. In China, the ‘Red Zaosu’ (RZS) re...

Authors: Huabai Xue, Suke Wang, Jia-Long Yao, Xiaoli Zhang, Jian Yang, Long Wang, Yanli Su, Lei Chen, Huirong Zhang and Xiugen Li

A novel RASA1 mutation causing capillary malformation-arteriovenous malformation (CM-AVM): the first genetic clinical report in East Asia

Capillary malformation-arteriovenous malformation (CM-AVM) is a clinical entity newly identified in 2003 that is caused by mutation of the RASA-1 gene, which encodes the protein p120-RasGAP. To date, most of t...

Authors: Ren Cai, Fatao Liu, Chen Hua, Zhang Yu, Michele Ramien, Claudia Malic, Wenxin Yu, Xiaolin Zhang, Yun Liu, Yunbo Jin, Xun Hu and Xiaoxi Lin

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

Clematis is the biggest genus in the family Ranunculaceae with about 300 species. Clematis is also a globally important commercial group of flowers, especially in the United States and European countries. Their p...

Authors: Zhigao Liu, Weili Shao, Yamei Shen, Mengcheng Ji, Wenchao Chen, Ying Ye and Yongbao Shen

Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers

Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea p...

Authors: Yu Zhang, Xiaojuan Zhang, Xi Chen, Wang Sun and Jiao Li

Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma

This study aimed to identify potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma by comprehensive bioinformatics analysis.

Authors: Yue Pan, Lingyun Lu, Junquan Chen, Yong Zhong and Zhehao Dai

Molecular markers associated with aluminium tolerance in Sorghum bicolor

Sorghum (Sorghum bicolor, L. Moench) production in many agro-ecologies is constrained by a variety of stresses, including high levels of aluminium (Al) commonly found in acid soils. Therefore, for such soils, gro...

Authors: Emily Jepkosgei Too, Augustino Osoro Onkware, Beatrice Ang’iyo Were, Samuel Gudu, Anders Carlsson and Mulatu Geleta

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations

Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent ...

Authors: Yuchen Wang, Dongsheng Lu, Yeun-Jun Chung and Shuhua Xu

Comparative transcriptome reveal the potential adaptive evolutionary genes in Andrias davidianus

To search the evidence of molecular evolution mechanism for aquatic and cave habitat in Andrias davidianus, the evolution analysis was carried out among several species transcriptome data. The transcriptome data ...

Authors: Qiaomu Hu, Quanhe Wang, Yan Meng, Haifeng Tian and Hanbing Xiao