Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing number of RNA sequencing methods, especially those used for single-cell transcriptome analysis, generate reads close to the polyadenylation site (PAS), termed nearSite reads, hence inherently containing information about APA isoform abundance. Here, we present a probabilistic model-based method named MAAPER to utilize nearSite reads for APA analysis. MAAPER predicts PASs with high accuracy and sensitivity and examines different types of APA events with robust statistics. We show MAAPER's performance with both bulk and single-cell data and its applicability in unpaired or paired experimental designs.

Few-layer black phosphorus (BP) nanosheets were first reported as a 2D material for the application of field-effect transistors in 2014 and have stimulated intense activity among physicists, chemists, and material and biomedical scientists, driving research into novel synthetic techniques to produce BP nanosheets. At present, exfoliation is the main route toward few-layer BP nanosheets via employing bulk BP as raw material. However, this is a complicated and time-consuming process, which is difficult for the large-scale synthesis of BP nanosheets. Moreover, BP degrades rapidly when exfoliated to nanoscale dimensions, resulting in the rapid loss of semiconducting properties. Here, we report the direct wet-chemical synthesis of few-layer BP nanosheets in gram-scale quantities in a bottom-up approach based on common laboratory reagents at low temperature, showing excellent stability due to partial oxidation of surface. Solvent and temperature are two critical factors, controlling not only the formation of BP nanosheets but also the thickness. The as-prepared BP nanosheets can extract hydrogen from pure water (pH = 6.8), exhibiting more than 24-fold higher activity than the well-known C₃N₄ nanosheets. Our results reporting the ability to prepare few-layer BP nanosheets with a facile, scalable, low-cost approach take us a step closer to real-world applications of phosphorene including next-generation metal-free photocatalysts for photosynthesis.

Solar-driven water splitting using powdered catalysts is considered as the most economical means for hydrogen generation. However, four-electron-driven oxidation half-reaction showing slow kinetics, accompanying with insufficient light absorption and rapid carrier combination in photocatalysts leads to low solar-to-hydrogen energy conversion efficiency. Here, we report amorphous cobalt phosphide (Co-P)-supported black phosphorus nanosheets employed as photocatalysts can simultaneously address these issues. The nanosheets exhibit robust hydrogen evolution from pure water (pH = 6.8) without bias and hole scavengers, achieving an apparent quantum efficiency of 42.55% at 430 nm and energy conversion efficiency of over 5.4% at 353 K. This photocatalytic activity is attributed to extremely efficient utilization of solar energy (~75% of solar energy) by black phosphorus nanosheets and high-carrier separation efficiency by amorphous Co-P. The hybrid material design realizes efficient solar-to-chemical energy conversion in suspension, demonstrating the potential of black phosphorus-based materials as catalysts for solar hydrogen production.

Soil-borne wheat mosaic virus (SBWMV) causes a serious viral disease that can significantly reduce grain yield in winter wheat worldwide. Using resistant cultivars is the only feasible strategy to reduce the losses caused by SBWMV. To fine map the resistance gene Sbwm1, 205 wheat accessions was genotyped using wheat Infinium iSelect Beadchips with 90 K SNPs. Association analysis identified 35 SNPs in 12 wheat genes and one intergenic SNP in the Sbwm1 region that showed a significant association with SBWMV resistance. Those SNPs were converted into Kompetitive Allele-Specific Polymerase assays (KASP) and analyzed in two F6-derived recombinant inbred line (RIL) populations derived from the crosses between two resistant cultivars Wesley and Deliver and a susceptible line OK03825-5403-6. Linkage analysis mapped this gene on chromosome 5D at intervals of 5.1 cM and 3.4 cM in the two populations, respectively. The two flanking markers in both populations delimited the gene to a 620 kb region where 19 genes were annotated. Comparative analysis identified a syntenic region of 660 kb in Ae. tauschii with 18 annotated genes and a syntenic region in chromosome 1 of B. distachyon. The candidate region includes several disease resistance related genes and we identified a PTI1-like tyrosine-protein kinase 1 gene as a putative candidate gene for Sbwm1. The two flanking SNPs for Sbwm1 can effectively separate the resistant and susceptible lines in a new diversity panel of 159 wheat germplasm. The results from this study lay a solid foundation for the cloning, functional characterization and marker-assisted selection of Sbwm1.

The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and is disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined central role, and mutations promote malignant transformation. More recently, studies have illuminated the importance of posttranscriptional regulation by RNA-binding proteins (RBPs) in hematopoiesis and leukemia development. However, the RBPs involved and the breadth of regulation are only beginning to be elucidated. Furthermore, the intersection between posttranscriptional regulation and hematopoietic transcription factor function is poorly understood. Here, we studied the posttranscriptional regulation of RUNX1, a key hematopoietic transcription factor. Alternative polyadenylation (APA) of RUNX1 produces functionally antagonistic protein isoforms (RUNX1a vs RUNX1b/c) that mediate HSC self-renewal vs differentiation, an RNA-processing event that is dysregulated in malignancy. Consequently, RBPs that regulate this event directly contribute to healthy and aberrant hematopoiesis. We modeled RUNX1 APA using a split GFP minigene reporter and confirmed the sensitivity of our model to detect changes in RNA processing. We used this reporter in a clustered regularly interspaced short palindromic repeats (CRISPR) screen consisting of single guide RNAs exclusively targeting RBPs and uncovered HNRNPA1 and KHDRBS1 as antagonistic regulators of RUNX1a isoform generation. Overall, our study provides mechanistic insight into the posttranscriptional regulation of a key hematopoietic transcription factor and identifies RBPs that may have widespread and important functions in hematopoiesis.

Long-lasting forms of synaptic plasticity that underlie learning and memory require new transcription and translation for their persistence. The remarkable polarity and compartmentalization of neurons raises questions about the spatial and temporal regulation of gene expression within neurons. Alternative cleavage and polyadenylation (APA) generates mRNA isoforms with different 3' untranslated regions (3'UTRs) and/or coding sequences. Changes in the 3'UTR composition of mRNAs can alter gene expression by regulating transcript localization, stability and/or translation, while changes in the coding sequences lead to mRNAs encoding distinct proteins. Using specialized 3' end deep sequencing methods, we undertook a comprehensive analysis of APA following induction of long-term potentiation (LTP) of mouse hippocampal CA3-CA1 synapses. We identified extensive LTP-induced APA changes, including a general trend of 3'UTR shortening and activation of intronic APA isoforms. Comparison with transcriptome profiling indicated that most APA regulatory events were uncoupled from changes in transcript abundance. We further show that specific APA regulatory events can impact expression of two molecules with known functions during LTP, including 3'UTR APA of Notch1 and intronic APA of Creb1. Together, our results reveal that activity-dependent APA provides an important layer of gene regulation during learning and memory.