Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana

Background:Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs.Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3’-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results:Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3’-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3’-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions:The identified IPACs corresponding to novel transcripts, 3’-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants.Funding supports were in part from US National Science Foundation (No. 1541737 to QQL), the Hundred Talent Plans of Fujian Province and Xiamen City (to QQL). This project was also funded by the National Natural Science Foundation of China (Nos. 61201358 and 61174161), the Natural Science Foundation of Fujian Province of China (No. 2012J01154), and the specialized Research Fund for the Doctoral Program of Higher Education of China (Nos. 20120121120038 and 20130121130004), and the Fundamental Research Funds for the Central Universities in China (Xiamen University: Nos. 2013121025, 201412G009, and 2014X0234)

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data

Motivation: Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 30 enriched strategy in library construction, the most commonly used scRNA-seq protocol—10 Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data. Results: Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.This research was supported in part by the Fundamental Research Funds for the Central Universities in China [Xiamen University: 20720170076 and 20720190106], and the National Natural Science Foundation of China [61802323, 31801268 and 61573296]

The Alpha Magnetic Spectrometer (AMS) on the international space station: Part II — Results from the first seven years

The Alpha Magnetic Spectrometer (AMS) is a precision particle physics detector on the International Space Station (ISS) conducting a unique, long-duration mission of fundamental physics research in space. The physics objectives include the precise studies of the origin of dark matter, antimatter, and cosmic rays as well as the exploration of new phenomena. Following a 16-year period of construction and testing, and a precursor flight on the Space Shuttle, AMS was installed on the ISS on May 19, 2011. In this report we present results based on 120 billion charged cosmic ray events up to multi-TeV energies. This includes the fluxes of positrons, electrons, antiprotons, protons, and nuclei. These results provide unexpected information, which cannot be explained by the current theoretical models. The accuracy and characteristics of the data, simultaneously from many different types of cosmic rays, provide unique input to the understanding of origins, acceleration, and propagation of cosmic rays.</p