Journal of Genetics and Genomics

Abstract:
The last couple of years have witnessed an explosion in development of CRISPR-based genome editing technologies in cell lines as well as in model organisms. In this review, we focus on the applications of this popular system in Drosophila. We discuss the effectiveness of the CRISPR/Cas9 systems in terms of delivery, mutagenesis detection, parameters affecting efficiency, and off-target issues, with an emphasis on how to apply this powerful tool to characterize gene functions.

Original research

The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities

Na Li, Li Wang, Hui Wang, Minyue Ma, Xiaohong Wang, Yi Li, Wenke Zhang, Jianguang Zhang, David S. Cram, Yuanqing Yao

2015, 42(4): 151-159. doi: 10.1016/j.jgg.2015.03.001

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Abstract:
Reliable and accurate pre-implantation genetic diagnosis (PGD) of patient's embryos by next-generation sequencing (NGS) is dependent on efficient whole genome amplification (WGA) of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA (15 pg) and single cells, we showed that the two PCR-based WGA systems SurePlex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification (MDA) system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing (CNV-Seq) was applied to single cell WGA products derived by either SurePlex or MALBAC amplification, we showed that known disease CNVs in the range of 3–15 Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either SurePlex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient's cohort for uterine transplantation.

SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes

Chongwu Wang, Yuan Zheng, Yang Zhao, Yi Zhao, Jigang Li, Yan Guo

2015, 42(4): 161-168. doi: 10.1016/j.jgg.2015.02.005

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Abstract:
The STOMATAL CLOSURE-RELATED ACTIN BINDING PROTEIN (SCAB) family is plant-specific, and its members all contain a novel actin binding domain. Here, we report that SCAB3, a homolog of SCAB1, binds, stabilizes and bundles actin filaments. The SCAB3 promoter contains a cis-element which could be bound by the FHY3/FAR1 transcription factors. Consistently, the expression of SCAB3 is induced when plants were transferred from white light to far red light (T-Far Red) conditions. The scab3 mutants show defects in the control of hypocotyl elongation under T-Far Red condition, which may result from an impaired reorganization of actin filaments. Together, our results suggest that SCAB3 plays an important role in plant growth under changes of light conditions possibly by regulating actin filament dynamics.

Letter to the Editor

Mitochondrial DNA as a Risk Factor for False Positives in Case-Control Association Studies

Antonio Salas, Joanna L. Elson

2015, 42(4): 169-172. doi: 10.1016/j.jgg.2015.03.002

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Abstract:

A Positive Correlation between Elevated Altitude and Frequency of Mutant Alleles at the EPAS1 and HBB Loci in Chinese Indigenous Dogs

Ruoxi Fan, Fei Liu, Hong Wu, Shifang Wu, Chunling Zhu, Yan Li, Guodong Wang, Yaping Zhang

2015, 42(4): 173-177. doi: 10.1016/j.jgg.2015.02.006

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Abstract:

Issue 9,

September 2023

Current Issue

JGG Archive