Journal of Genetics and Genomics

A repetitive DNA-directed program of chromosome packaging during mitosis

Shao-Jun Tang

2016, 43(8): 471-476. doi: 10.1016/j.jgg.2016.04.003

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GWAS promotes precision medicine in China

Liangdan Sun, Xuejun Zhang, Lin He

2016, 43(8): 477-479. doi: 10.1016/j.jgg.2016.05.009

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Argonaute: The executor of small RNA function

Azali Azlan, Najat Dzaki, Ghows Azzam

2016, 43(8): 481-494. doi: 10.1016/j.jgg.2016.06.002

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The discovery of small non-coding RNAs – microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) – represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.

Emerging insights into heterotrimeric G protein signaling in plants

Quan Xu, Mingzhu Zhao, Kun Wu, Xiangdong Fu, Qian Liu

2016, 43(8): 495-502. doi: 10.1016/j.jgg.2016.06.004

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Heterotrimeric guanine nucleotide-binding protein (G protein) signaling is an evolutionarily conserved mechanism in diverse eukaryotic organisms. In plants, the repertoire of the heterotrimeric G protein complex, which is composed of the Gα, Gβ, and Gγ subunits, is much simpler than that in metazoans, and the identity of typical G protein-coupled receptors (GPCRs) together with their ligands still remains unclear. Comparative phenotypic analysis in Arabidopsis and rice plants using gain- and loss-of-function mutants of G protein components revealed that heterotrimeric G protein signaling plays important roles in a wide variety of plant growth and developmental processes. Grain yield is a complex trait determined by quantitative trait loci (QTL) and is influenced by soil nitrogen availability and environmental changes. Recent studies have shown that the manipulation of two non-canonical Gγ subunits, GS3 (GRAIN SIZE 3) and DEP1 (DENSE AND ERECT PANICLE 1), represents new strategies to simultaneously increase grain yield and nitrogen use efficiency in rice. This review discusses the latest advances in our understanding of the heterotrimeric G protein signal transduction pathway and its application in improving yield and stress tolerance in crops.

Epigenetic modulations rendering cell-to-cell variability and phenotypic metastability

Shawal Spencer, Agustina Gugliotta, Natascha Gödecke, Hansjörg Hauser, Dagmar Wirth

2016, 43(8): 503-511. doi: 10.1016/j.jgg.2016.05.008

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Tumor cells display phenotypic plasticity and heterogeneity due to genetic and epigenetic variations which limit the predictability of therapeutic interventions. Chromatin modifications can arise stochastically but can also be a consequence of environmental influences such as the microenvironment of cancer cells. A better understanding of the impact and dynamics of epigenetic modulation at defined chromosomal sites is required to get access to the underlying mechanisms. We investigated the epigenetic modulations leading to cell-to-cell heterogeneity in a tumor cell line model. To this end, we analyzed expression variance in 80 genetically uniform cell populations having a single-copy reporter randomly integrated in the genome. Single-cell analysis showed high intraclonal heterogeneity. Epigenetic characterization revealed that expression heterogeneity was accompanied by differential histone marks whereas contribution of DNA methylation could be excluded. Strikingly, some clones revealed a highly dynamic, stochastically altered chromatin state of the transgene cassette which was accompanied with a metastable expression pattern. In contrast, other clones represented a robust chromatin state of the transgene cassette with a stable expression pattern. Together, these results elucidate locus-specific epigenetic modulation in gene expression that contributes to phenotypic heterogeneity of cells and might account for cellular plasticity.

DNA methylation signature of intergenic region involves in nucleosome remodeler DDM1-mediated repression of aberrant gene transcriptional read-through

Xiaojing Yan, Xiaomei Dong, Lei Liu, Yongqing Yang, Jinsheng Lai, Yan Guo

2016, 43(8): 513-523. doi: 10.1016/j.jgg.2016.03.010

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The strict and efficient transcription termination is required to prevent production of aberrant read-through transcripts that may cause transcriptional interference at neighboring genes. However, the exact regulatory mechanism remains poorly understood. Through a genetic screening of a LUCIFERASE (LUC) reporter system, we found that Arabidopsis nucleosome remodeler DECREASE IN DNA METHYLATION1 (DDM1) is a key component of this regulatory machinery and plays an important role in transcription termination, thus limiting transcriptional read-through (TRT). By whole-genome strand-specific RNA sequencing, we identified and confirmed 43 endogenous TRTs between genes, transposable elements (TEs), or genes and TEs in theddm1-10 mutant, which mainly occurred at heterochromatin regions. The DNA methylation analysis of these TRT regions revealed that TRT occurred frequently at the intergenic regions with a higher methylation level in wild type comparing to the regions where TRT did not occur. Our results suggest that the level of intergenic DNA methylation may involve in preventing aberrant gene TRT or producing new gene during evolution.

Molecular insights of organochlorine biocide-induced toxicity in zebrafish: Whole-adult-organism toxicogenomics, targeted gene expression and histological analyses

Eei Yin Lui, Caixia Li, Zhi-Hua Li, Zhiyuan Gong, Siew Hong Lam

2016, 43(8): 525-528. doi: 10.1016/j.jgg.2016.06.001

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Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice

Rongfang Xu, Yachun Yang, Ruiying Qin, Hao Li, Chunhong Qiu, Li Li, Pengcheng Wei, Jianbo Yang

2016, 43(8): 529-532. doi: 10.1016/j.jgg.2016.07.003

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2016 Vol. 43, No. 8