Search for: All records

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels in mac5 is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor. 

Abstract The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element. 

High-throughput next generation sequencing of cDNA, i.e. RNA-Seq, presents an unprecedented resource for characterizing the alternative splicing (AS) in complex eukaryotic transcriptomes. Accumulating evidences indicate that AS is developmentally regulated, but the precise responses of AS event to development is not well understood. Here, we describe a new method, based on an adjusted beta-distribution model, for detection of differential AS patterns from RNA-Seq data comparisons. Applying our method to two datasets of RNA-Seq for zika infection in human cells and pollen tissue in Arabidopsis thaliana, we identified 1,871 differentially AS events for 1,394 protein-coding genes in human and 496 differentially AS events for 358 protein-coding genes in Arabidopsis, respectively. The results included known AS events reported before as well as novel events, which demonstrate that the biological replicates are important in the effective identification using β-distribution. With a high accurate rate, our new method in differential AS identification will facilitate future investigation on transcriptomic annotation.