m6A Modification and Implications for microRNAs.

Objective: RNA is chemically modified with over 100 distinct reactions. Among these reactions, methylation is probably the most extensively studied modification on the RNA molecule. Studies suggest methylation of Adenine residues (m6A) to be widespread in the transcriptome with potentially important roles in biological processes. Method: Here, we review recent literature on m6A modification and potential implications for microRNA (miRNA) mediated gene expression regulation. These implications involve miRNA biogenesis, mRNA-miRNA interactions and m6A target selection. Conclusion: Understanding the extent and functions of m6A is likely to improve our understanding of the complexities of the transcriptome regulation in normal and in disease states.Food and agriculture sector forms the largest piece of gross world product. Due to the increasing world population, global climate change, environmental deteriorations such as nitrogen pollution and desertification, agriculture sector is expected to face significant problems to supply the drastically increasing demand. Timely and accurate estimation of agricultural crop yields is essential for food security; in addition strategically and economically significant for a wide range of actors on the sector; from singular producers to governments. Remote sensing provides more practical and less costly solutions than conventional methods for crop yield forecasting. Sentinel-2 satellites have a great potential for agricultural remote sensing applications due to its vegetation bands and also having the highest spatial resolution in red, green, blue and NIR bands within the satellites whose data is open and free publicly. In this work, the use of Sentinel-2 vegetation indices for yield estimation of barley is analyzed. Commonly used vegetation indices are calculated from two closely dated Sentinel-2 images acquired before the harvest. Linear regression models are constructed between the indices and actual yields. Correlation coefficients are found promising for the yield estimation of barley. Highest correlation coefficients are obtained by the Modified Simple Ratio index

Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer

Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA), a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A) signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian) compared to normal tissues. Using machine-learning techniques, we further defined specific subsets of APA events to efficiently classify cancer types. Furthermore, APA patterns were associated with altered protein levels in patients, revealed by antibody-based profiling data, suggesting functional significance. Overall, our study offers a computational approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches

N6-methyladenosine modification is not a general trait of viral RNA genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-Seq, an antibody-dependent technique with a high rate of false positives. Here, we address the presence of m6A in CHIKV and DENV RNAs. For this, we combine m6A-Seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we find no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery does not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection has no effect on the m6A machinery’s localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches