Journal of Genetics and Genomics

The Role of RNA Structure in Posttranscriptional Regulation of Gene Expression

Elina Jacobs, James D. Mills, Michael Janitz

2012, 39(10): 535-543. doi: 10.1016/j.jgg.2012.08.002

Abstract (63) HTML PDF (1)

Abstract:
As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one such regulatory process that until recently it has not been analysed in depth. Formation of these mRNA structures has the potential to enhance and inhibit alternative splicing of transcripts, and regulate rates and amount of translation. As this regulatory mechanism potentially impacts at both the transcriptional and translational level, while also potentially utilising the vast array of non-coding RNAs, it warrants further investigation. Currently, a variety of high-throughput sequencing techniques including parallel analysis of RNA structure (PARS), fragmentation sequencing (FragSeq) and selective 2-hydroxyl acylation analysed by primer extension (SHAPE) lead the way in the genome-wide identification and analysis of mRNA structure formation. These new sequencing techniques highlight the diversity and complexity of the transcriptome, and demonstrate another regulatory mechanism that could become a target for new therapeutic approaches.

Effect of Genome-Wide Genotyping and Reference Panels on Rare Variants Imputation

Hou-Feng Zheng, Martin Ladouceur, Celia M.T. Greenwood, J. Brent Richards

2012, 39(10): 545-550. doi: 10.1016/j.jgg.2012.07.002

Abstract (73) HTML PDF (0)

Abstract:
Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms (SNPs), to two different reference panels: HapMap2 and 1000 Genomes pilot March 2010 release (1KGpilot) by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy (info > 0.4) in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants (minor allele frequency (MAF) ≤5%), the proportion of well-imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study (GWAS) datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants (MAF ≤ 0.3%) were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.

Molecular Evolution of the TAC1 Gene from Rice (Oryza sativa L.)

Jiahuan Jiang, Lubin Tan, Zuofeng Zhu, Yongcai Fu, Fengxia Liu, Hongwei Cai, Chuanqing Sun

2012, 39(10): 551-560. doi: 10.1016/j.jgg.2012.07.011

Abstract (105) HTML PDF (6)

Abstract:
Tiller angle is a key feature of the architecture of cultivated rice (Oryza sativa), since it determines planting density and influences rice yield. Our previous work identified Tiller Angle Control 1 (TAC1) as a major quantitative trait locus that controls rice tiller angle. To further clarify the evolutionary characterization of the TAC1 gene, we compared a TAC1-containing 3164-bp genomic region among 113 cultivated varieties and 48 accessions of wild rice, including 43 accessions of O. rufipogon and five accessions of O. nivara. Only one single nucleotide polymorphism (SNP), a synonymous substitution, was detected in TAC1 coding regions of the cultivated rice varieties, whereas one synonymous and one nonsynonymous SNP were detected among the TAC1 coding regions of wild rice accessions. These data indicate that little natural mutation and modification in the TAC1 coding region occurred within the cultivated rice and its progenitor during evolution. Nucleotide diversities in the TAC1 gene regions of O. sativa and O. rufipogon of 0.00116 and 0.00112, respectively, further indicate that TAC1 has been highly conserved during the course of rice domestication. A functional nucleotide polymorphism (FNP) of TAC1 was only found in the japonica rice group. A neutrality test revealed strong selection, especially in the 3′-flanking region of the TAC1 coding region containing the FNP in the japonica rice group. However, no selection occurred in the indica and wild-rice groups. A phylogenetic tree derived from TAC1 sequence analysis suggests that the indica and japonica subspecies arose independently during the domestication of wild rice.

Establishment of a Genetic Transformation System and Its Application in Thermoanaerobacter tengcongensis

Bo Liu, Chuan Wang, Haihua Yang, Huarong Tan

2012, 39(10): 561-570. doi: 10.1016/j.jgg.2012.07.003

Abstract (74) HTML PDF (0)

Abstract:
The whole-genome sequence of Thermoanaerobacter tengcongensis, an anaerobic thermophilic bacterium isolated from the Tengchong hot spring in China, was completed in 2002. However, in vivo studies on the genes of this strain have been hindered in the absence of genetic manipulation system. In order to establish such a system, the plasmid pBOL01 containing the replication origin of the T. tengcongensis chromosome and a kanamycin resistance cassette, in which kanamycin resistance gene expression was controlled by the tte1482 promoter from T. tengcongensis, was constructed and introduced into T. tengcongensis via electroporation. Subsequently, the high transformation efficiency occurred when using freshly cultured T. tengcongensis cells without electroporation treatment, suggesting that T. tengcongensis is naturally competent under appropriate growth stage. A genetic transformation system for this strain was then established based on these important components, and this system was proved to be available for studying physiological characters ofT. tengcongensis in vivo by means of hisG gene disruption and complementation.

Atypical Deletion in Williams–Beuren Syndrome Critical Region Detected by MLPA in a Patient with Supravalvular Aortic Stenosis and Learning Difficulty

Rachel Sayuri Honjo, Roberta Lelis Dutra, Michele Moreira Nunes, Israel Gomy, Leslie Domenici Kulikowski, Fernanda Sarquis Jehee, Chong Ae Kim

2012, 39(10): 571-574. doi: 10.1016/j.jgg.2012.07.001

Abstract (71) HTML PDF (1)

Abstract:

2012 Vol. 39, No. 10