Structure of the RNA‐directed RNA Polymerase from the cystovirus ϕ12

We have determined the structure of P2, the self‐priming RdRp from cystovirus ?12 in two crystal forms (A, B) at resolutions of 1.7 Å and 2.1 Å. Form A contains Mg²⁺ bound at a site that deviates from the canonical noncatalytic position seen in form B. These structures provide insight into the temperature sensitivity of a ts‐mutant. However, the tunnel through which template ssRNA accesses the active site is partially occluded by a flexible loop; this feature, along with suboptimal positioning of other structural elements that prevent the formation of a stable initiation complex, indicate an inactive conformation in crystallo. Proteins 2013; 81:1479–1484. © 2013 Wiley Periodicals, Inc.     

De novo assembly of a chromosome‐level reference genome of red‐spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C

The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future.     

Genome‐wide characterization and developmental expression profiling of long non‐coding RNAs in Sogatella furcifera

The genome‐wide characterization of long non‐coding RNA (lncRNA) in insects demonstrates their importance in fundamental biological processes. Essentially, an in‐depth understanding of the functional repertoire of lncRNA in insects is pivotal to insect resources utilization and sustainable pest control. Using a custom bioinformatics pipeline, we identified 1861 lncRNAs encoded by 1852 loci in the Sogatella furcifera genome. We profiled lncRNA expression in different developmental stages and observed that the expression of lncRNAs is more highly temporally restricted compared to protein‐coding genes. More up‐regulated Sogatella furcifera lncRNA expressed in the embryo, 4th and 5th instars, suggesting that increased lncRNA levels may play a role in these developmental stages. We compared the relationship between the expression of Sogatella furcifera lncRNA and its nearest protein gene and found that lncRNAs were more correlated to their downstream coding neighbors on the opposite strand. Our genome‐wide profiling of lncRNAs in Sogatella furcifera identifies exciting candidates for characterization of lncRNAs, and also provides information on lncRNA regulation during insect development.     

Combined analysis of RNA‐sequence and microarray data reveals effective metabolism‐based prognostic signature for neuroblastoma

The relationship between metabolism reprogramming and neuroblastoma (NB) is largely unknown. In this study, one RNA‐sequence data set (n = 153) was used as discovery cohort and two microarray data sets (n = 498 and n = 223) were used as validation cohorts. Differentially expressed metabolic genes were identified by comparing stage 4s and stage 4 NBs. Twelve metabolic genes were selected by LASSO regression analysis and integrated into the prognostic signature. The metabolic gene signature successfully stratifies NB patients into two risk groups and performs well in predicting survival of NB patients. The prognostic value of the metabolic gene signature is also independent with other clinical risk factors. Nine metabolism‐related long non‐coding RNAs (lncRNAs) were also identified and integrated into the metabolism‐related lncRNA signature. The lncRNA signature also performs well in predicting survival of NB patients. These results suggest that the metabolic signatures have the potential to be used for risk stratification of NB. Gene set enrichment analysis (GSEA) reveals that multiple metabolic processes (including oxidative phosphorylation and tricarboxylic acid cycle, both of which are emerging targets for cancer therapy) are enriched in the high‐risk NB group, and no metabolic process is enriched in the low‐risk NB group. This result indicates that metabolism reprogramming is associated with the progression of NB and targeting certain metabolic pathways might be a promising therapy for NB.