Unequal usage of synonymous codons is known as codon usage bias (CUB), which is generally different between the high-expression genes (HEG) and low-expression genes (LEG) in organisms is not yet adequately reported across different bacteria. In this study, a machine learning-based approach was implemented initially to find out codons that are significantly different between the HEG and LEG in Escherichia coli. It identified Cys codons such as UGU and UGC, Lys codons such as AAA and AAG that were least influenced by gene expression. Codons such as UCU (Ser), CUG (Leu), GGG (Gly), CGG (Arg) etc. were identified to be influenced maximum by the gene expression. The study was extended to analyze codon usage in 683 other bacterial species. Cys (UGU/UGC) and Ser (AGU/AGC) codons were identified being the least different between the two groups of genes across these bacterial species. Codons such as CGA, CUG, GGG, GCC, ACC, AUA, and AUC were identified to be influenced by the gene expression across majority of these species. This study supports the role of CUB on gene expression across bacteria and demonstrates a commonality among bacteria regarding behavior of certain codons with regard to gene expression.

Pre-mRNA splicing imprints mRNAs by depositing multi-protein complexes, termed exon junction complexes (EJCs). The EJC core consists of four proteins, eIF4AIII, MLN51, Y14 and Magoh. Magoh is a human homolog of Drosophila mago nashi protein, which is involved in oskar mRNA localization in Drosophila oocytes. Here we determined the effects of Magoh mutations equivalent to those of Drosophila mago nashi mutant proteins that cause mis-localization of oskar mRNA. We found that Magoh I90T mutation caused mis-localization of Magoh protein in the cytoplasm by reducing its binding activity to Y14. On the other hand, G18R mutation did not affect its binding to Y14, but this mutation reduced its association with spliced mRNAs. Our results strongly suggest that Magoh mutations equivalent to Drosophila mago nashi mutants cause improper EJC formation by reducing incorporation of Magoh into EJC.

Dicer-like 1 (DCL1) is a core component of the plant microRNA (miRNA) biogenesis machinery. MiRNA is transcribed as a precursor RNA, termed primary miRNA (pri-miRNA), which is cleaved by DCL1 in two steps to generate miRNA/miRNA* duplex. Pri-miRNA is a single-stranded RNA that forms a hairpin structure with a number of unpaired bases, hereafter called mismatches, on its stem. In the present study, by using purified recombinant Arabidopsis DCL1, we presented evidence that mismatches on the stem of pri-miRNA are important for precise DCL1cleavage. We showed that a mismatch at the loop-distal side of the end of miRNA/miRNA* duplex is important for efficient cleavage of pri-miRNA in vitro, as previously suggested in planta. On the contrary, mismatches distant from the miRNA/miRNA* duplex region are important for determining the cleavage position by DCL1. The purified DCL1 proteins cleaved mutant pri-miRNA variants without such mismatches at a position at which wild-type pri-miRNA variants are not usually cleaved, resulting in an increased accumulation of small RNA different from miRNA. Therefore, our results suggest that, in addition to the distance from the ssRNA-dsRNA junction, mismatches on the stem of pri-miRNA function as a determinant for precise processing of pri-miRNA by DCL1 in plants.

Abstract A newly formed memory is initially unstable. However, if it is consolidated into the brain, the consolidated memory is stored as stable long‐term memory (LTM). Despite the recent progress, the molecular and cellular mechanisms of LTM have not yet been fully elucidated. The fruitfly Drosophila melanogaster, for which various genetic tools are available, has been used to clarify the molecular mechanisms of LTM. Using the Drosophila courtship‐conditioning assay as a memory paradigm, we previously identified that the circadian clock gene period (per) plays a vital role in consolidating LTM, suggesting that per‐expressing clock neurons are critically involved in LTM. However, it is still incompletely understood which clock neurons are essential for LTM. Here, we show that dorsal–lateral clock neurons (LNds) play a crucial role in LTM. Using an LNd‐specific split‐GAL4 line, we confirmed that disruption of synaptic transmission in LNds impaired LTM maintenance. On the other hand, induction of per RNAi or the dominant‐negative transgene of Per in LNds impaired LTM consolidation. Our results reveal that transmitter release and Per function in LNds are involved in courtship memory processing.

In pregnant mice, the maternal liver expands drastically during gestation, which is believed to be essential to accommodate various metabolic demands caused by physiological changes and fetal growth. Although hepatocyte proliferation and hypertrophy have been reported, little is known about the dynamics of biliary epithelial cells (BECs), which comprise the bile duct epithelium in the liver. Here, we show that BECs transiently proliferate during the early stage of gestation. Lineage tracing revealed that BEC progeny were retained in the bile duct epithelium and did not differentiate into hepatocytes, indicating BEC self-replication during pregnancy. RNA-sequencing analysis of BECs identified their early pregnancy-signature transcriptomes, which highlighted Yes-associated protein (YAP) signaling-related genes. Nuclear accumulation of YAP was enhanced in BECs during pregnancy but was barely detectable in hepatocytes. In addition, the pharmacological inhibition of YAP attenuated BEC proliferation and liver weight gain during pregnancy. Our results delineate the proliferation and transcriptomic dynamics of BECs during pregnancy and suggest the relevance of YAP-mediated signals.

Ectopic gene expression is an indispensable tool in biology and medicine, but is often limited by the low efficiency of DNA transfection. We previously reported that depletion of the autophagy receptor p62/SQSTM1 enhances DNA transfection efficiency by preventing the degradation of transfected DNA. Therefore, p62 is a potential target for drugs to increase transfection efficiency. To identify such drugs, a nonbiased high-throughput screening was applied to over 4,000 compounds from the Osaka University compound library, and their p62 dependency was evaluated. The top-scoring drugs were mostly microtubule inhibitors, such as colchicine and vinblastine, and all of them showed positive effects only in the presence of p62. To understand the p62-dependent mechanisms, the time required for p62-dependent ubiquitination, which is required for autophagosome formation, was examined using polystyrene beads that were introduced into cells as materials that mimicked transfected DNA. Microtubule inhibitors caused a delay in ubiquitination. Furthermore, the level of phosphorylated p62 at S405 was markedly decreased in the drug-treated cells. These results suggest that microtubule inhibitors inhibit p62-dependent autophagosome formation. Our findings demonstrate for the first time that microtubule inhibitors suppress p62 activation as a mechanism for increasing DNA transfection efficiency and provide solutions to increase efficiency.

Front cover: The night of Tanabata (Star Festival) on July 7th. A heat map of metabolic reactions in each tissue of C. elegans, derived from single-cell transcriptome analysis, illuminates the surface of the sea. And the metabolic networks of each tissue drawn based on the heat map decorate the night sky like constellations fl oating in the Milky Way. For drawing this image, we referred to Yilmaz et al. (2020) Mol. Syst. Biol. 16:e9649, DOI: 10.15252/msb.20209649. Designed by TRAIS Co., Ltd. (Kobe, Japan). The heat map: Adapted from Figure 3(C) of © Yilmaz et al. (2020) Mol. Syst. Biol. 16:e9649, DOI: 10.15252/msb.20209649. Licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).

Single-cell RNA-sequencing analysis is one of the most effective tools for understanding specific cellular states. The use of single cells or pooled cells in RNA-seq analysis requires the isolation of cells from a tissue or culture. Although trypsin or more recently cold-active protease (CAP) has been used for cell dissociation, the extent to which the gene expression changes are suppressed has not been clarified. To this end, we conducted detailed profiling of the enzyme-dependent gene expression changes in mouse skeletal muscle progenitor cells, focusing on the enzyme treatment time, amount and temperature. We found that the genes whose expression was changed by the enzyme treatment could be classified in a time-dependent manner and that there were genes whose expression was changed independently of the enzyme treatment time, amount and temperature. This study will be useful as reference data for genes that should be excluded or considered for RNA-seq analysis using enzyme isolation methods.

Lymphatic recanalization failure after lymphadenectomy constitutes a major risk of lymphedema in cancer surgery. It has been reported that GATA2, a zinc finger transcription factor, is expressed in lymphatic endothelial cells and is involved in the development of fetal lymphatic vessels. GATA3, another member of the GATA family of transcription factors, is required for the differentiation of lymphoid tissue inducer (LTi) cells and is essential for lymph node formation. However, how GATA2 and GATA3 function in recanalization after the surgical extirpation of lymphatic vessels has not been elucidated. Employing a new model of lymphatic recanalization, we examined the lymphatic reconnection process in Gata2 heterozygous deficient (Gata2+/- ) and Gata3 heterozygous deficient (Gata3+/- ) mice. We found that lymphatic recanalization was significantly impaired in Gata2+/- mice, while Gata3+/- mice rarely showed such abnormalities. Notably, the perturbed lymphatic recanalization in the Gata2+/- mice was partially restored by crossing with the Gata3+/- mice. Our results demonstrate for the first time that GATA2 participates in the regeneration of damaged lymphatic vessels and the unexpected suppressive activity of GATA3 against lymphatic recanalization processes.

Aims and