Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes.

RNA degradation is one of the critical steps for control of gene expression, and endonucleolytic cleavage-dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the Cap analysis of gene expression (CAGE) method. Although uncapped cleavage sites are widespread in eukaryotes, comparatively little information has been obtained about these sites using CAGE-based degradome analysis.

Methods for detecting RNA degradation intermediates in plants.

RNA degradation is an important process for controlling gene expression and is mediated by decapping / deadenylation-dependent or endonucleolytic cleavage-dependent RNA degradation mechanisms. High-throughput sequencing of RNA degradation intermediates was initially developed in Arabidopsis thaliana and similar RNA degradome sequencing methods were conducted in other eukaryotes. However, interpreting results obtained by these sequencing methods is fragmented, and an overview is needed.

Depression of Bone Density at the Weight-Bearing Joints in Wistar Hannover Rats by a Simulated Mechanical Stress Associated With Partial Gravity Environment.

The partial gravity environment in space can negatively affect bone health. This survey aimed to study the reaction of different parts of the lower limb bones of rats to partial gravity and the effects of different degrees of gravity on these bony parts. We used 15 8-week-old male Wistar Hannover rats were used at the beginning of the experiment.

Feature selection for RNA cleavage efficiency at specific sites using the LASSO regression model in Arabidopsis thaliana.

Background: RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-dependent RNA degradation has not been studied in detail. Here, we developed truncated RNA end sequencing in Arabidopsis thaliana to identify cleavage sites and evaluate the efficiency of cleavage at each site.

Changes in mRNA Degradation Efficiencies under Varying Conditions Are Regulated by Multiple Determinants in Arabidopsis thaliana.

Multiple mechanisms are involved in gene expression, with mRNA degradation being critical for the control of mRNA accumulation. In plants, although some trans-acting factors and motif sequences have been identified in deadenylation-dependent mRNA degradation, endonucleolytic cleavage-dependent mRNA degradation has not been studied in detail. Previously, we developed truncated RNA-end sequencing (TREseq) in Arabidopsis thaliana and detected G-rich sequence motifs around 5' degradation intermediates.

Identification of 5'-untranslated regions that function as effective translational enhancers in monocotyledonous plant cells using a novel method of genome-wide analysis.

High expression of a transgene is often necessary to produce useful substances in plants. The efficiency of mRNA translation is an important determinant of the level of transgene expression. In dicotyledonous plants, the 5'UTR of certain mRNAs act as translational enhancers, dramatically improving transgene expression levels.

Different Plant Species Have Common Sequence Features Related to mRNA Degradation Intermediates.

mRNA degradation is an important cellular mechanism involved in the control of gene expression. Several genome-wide profiling methods have been developed for detecting mRNA degradation in plants and animals. However, because many of these techniques use poly (A) mRNA for library preparation, degradation intermediates are often only detected near the 3'-ends of transcripts.

Comprehensive analysis of mRNA internal cleavage sites in Arabidopsis thaliana.

The major obstacle of efficient transgene expression seems to be gene silencing, and one of the important factors in gene silencing is mRNA stability. Regulation of mRNA stability is an important aspect of the control of gene expression. mRNAs are degraded by both exonucleolytic digestion and endonucleolytic cleavage.

Arabidopsis thaliana cold-regulated 47 gene 5'-untranslated region enables stable high-level expression of transgenes.

Transgene expression is regulated through several steps, this study focuses on the mRNA translation step. The expression level of transgenes can be increased by 5'-untranslated region (5'UTR) sequences in certain genes which act as translational enhancers. On the other hand, translation in most mRNA species is repressed by growth, development, and stress events.