Article
Biochemistry & Molecular Biology
Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky, Tatiana V. Tatarinova
Summary: This study utilized computational approaches to predict genome-wide TSS in four conifer species, laying the groundwork for future research on gene regulatory regions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Kun Wang, Liangzhen Hou, Xin Wang, Xiangwei Zhai, Zhaolian Lu, Zhike Zi, Weiwei Zhai, Xionglei He, Christina Curtis, Da Zhou, Zheng Hu
Summary: PhyloVelo is a computational framework that accurately estimates the velocity of transcriptomic dynamics by using monotonically expressed genes or genes with specific expression patterns. It integrates scRNA-seq data with lineage information to identify key genes and reconstruct the transcriptomic velocity field. PhyloVelo has been validated using simulated and real datasets, and has shown high accuracy and robustness in inferring complex lineage trajectories.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Huifen Cao, Yufei Zhang, Ye Cai, Lu Tang, Fan Gao, Dongyang Xu, Philipp Kapranov
Summary: Single-strand breaks (SSBs) are a common type of DNA damage, and this study found that they exhibit hotspot characteristics in the human genome, with a prominent enrichment near transcriptional start sites (TSSs). These TSS-associated hotspots may be generated by a novel mechanism involving preferential cleavage at specific sites. These findings support recent studies suggesting a complex relationship between DNA damage and gene expression regulation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Microbiology
Devon M. Fitzgerald, Anne M. Stringer, Carol Smith, Pascal Lapierre, Joseph T. Wade
Summary: Genome-scale analyses have found that many transcription factor binding sites are located within genes rather than upstream, but their function remains unclear. In this study, we examined the regulon of the transcription factor PhoB in Escherichia coli and found that the majority of PhoB binding sites are within genes. Surprisingly, these intragenic sites do not regulate transcription and are not conserved evolutionarily, suggesting that they may be genomic noise.
Article
Multidisciplinary Sciences
Yan Ma, Qin Luo, Yao Ou, Yiyun Tang, Wenhui Zeng, Haomiao Wang, Jie Hu, Hanfu Xu
Summary: This study identified proteins interacting with fibroin gene promoters in the silk gland of silkworms, shedding light on their importance in the regulation of silk protein synthesis.
SCIENTIFIC REPORTS
(2021)
Article
Physiology
Satoshi Homma, Akihisa Murata, Masato Ikegami, Masakazu Kobayashi, Maki Yamazaki, Kento Ikeda, Takaaki Daimon, Hideharu Numata, Akira Mizoguchi, Kunihiro Shiomi
Summary: This study investigates the roles of circadian clock genes in temperature-dependent diapause induction in the domestic silkworm. The results show that these genes regulate temperature-induced diapause by acting upstream of cerebral GABAergic and diapause hormone signaling pathways. Furthermore, the temporal expression of clock genes differs significantly between wild-type silkworms and TRPA1 knockout mutants during embryonic development. These findings provide target genes for regulating temperature-dependent diapause induction in silkworms.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Oncology
Yile Sun, Hongmiao Sun, Yuwen Qi, Mengqiao Pan, Na An, Xuejiao Leng, Yun Liu, Zhiwei Chen
Summary: The study found that RNF6 is elevated in several cancers and associated with poor prognosis in patients with lung adenocarcinoma (LUAD). Knockdown of RNF6 in LUAD cells resulted in aberrations in DNA repair genes and increased DNA damage. Furthermore, RNF6 knockdown restored sensitivity to chemotherapy in cisplatin-resistant LUAD cells.
Article
Biochemistry & Molecular Biology
Hitoshi Gotoh, Tatenda Alois Chimhanda, Tadashi Nomura, Katsuhiko Ono
Summary: The transcription factor STAT3 regulates the expression of Gys1 and PygB, key genes in glycogen metabolism, in the developing spinal cord. This finding highlights the importance of STAT3 in the regulation of glycogen metabolism during motor neuron development.
Article
Genetics & Heredity
Pavel A. Makhnovskii, Oleg A. Gusev, Roman O. Bokov, Guzel R. Gazizova, Tatiana F. Vepkhvadze, Evgeny A. Lysenko, Olga L. Vinogradova, Fedor A. Kolpakov, Daniil V. Popov
Summary: This study investigated the role of alternative transcription start sites (TSSs) in the acute stress-induced transcriptome response in human skeletal muscle. The activation of alternative TSSs was found to play a key role in gene expression changes, and the function of these TSSs is predominantly associated with the specific activation of transcription factors. A resource of accurate TSSs and individual promoter regions for each TSS in muscle was created, allowing for accurate prediction of transcription factors involved in the response of skeletal muscle to various stimuli.
Article
Biochemistry & Molecular Biology
Maria Fatima Ladelfa, Leticia Yamila Peche, Gaston Ezequiel Amato, Micaela Carolina Escalada, Stefania Zampieri, Franco Andres Pascucci, Andres Fernandez Benevento, Dario Fernandez Do Porto, Andrea Dardis, Claudio Schneider, Martin Monte
Summary: Cells sustaining a high proliferating rate require enhanced protein synthesis through ribosome production, a hallmark in cancer cells. The nucleolar tumor-protein MageB2 has been found to participate in ribosome biogenesis, interacting with phospho-UBF and affecting rRNA transcription and protein synthesis dynamically. These findings suggest a novel role for MageB2 in enhancing ribosome biogenesis to support cancer cell proliferation.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Plant Sciences
Gurkan Demirkol
Summary: The study found that exogenous PopW treatment significantly improved the growth performance and physiological indicators of alfalfa under drought conditions, promoting the expression of endogenous hormones and related genes, enhancing alfalfa's tolerance to drought stress.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Food Science & Technology
Zhenliang Mou, Runxi Zeng, Nanhui Chen, Zongli Liu, Zexiang Zeng, Yonghua Qin, Wei Shan, Jianfei Kuang, Wangjin Lu, Jianye Chen, Yating Zhao
Summary: In this study, two Dof transcription factors, HpDof1.7 and HpDof5.4, were identified to play roles in sugar accumulation in pitayas. They shared similar expression patterns with sugar metabolism-related genes and sugar transporter genes, and enhanced sugar accumulation by transcriptionally activating sugar metabolic pathway genes.
FOOD QUALITY AND SAFETY
(2022)
Article
Biology
Yumiko Tanaka, Mai Yamagishi, Yasutaka Motomura, Takashi Kamatani, Yusuke Oguchi, Nobutake Suzuki, Tsuyoshi Kiniwa, Hiroki Kabata, Misato Irie, Tatsuhiko Tsunoda, Fuyuki Miya, Keisuke Goda, Osamu Ohara, Takashi Funatsu, Koichi Fukunaga, Kazuyo Moro, Sotaro Uemura, Yoshitaka Shirasaki
Summary: The decision of cell activation is controlled through dynamic molecular networks. However, analyzing the transcriptome of the transition state is challenging due to the low cell population. To address this issue, the Time-Dependent Cell-State Selection (TDCSS) technique combines live-cell imaging and transcriptome analysis to study activation. In this study, TDCSS was used to investigate the activation of ILC2s by analyzing the secretion activity and identifying time-dependent genes.
COMMUNICATIONS BIOLOGY
(2023)
Article
Food Science & Technology
Zhenliang Mou, Runxi Zeng, Nanhui Chen, Zongli Liu, Zexiang Zeng, Yonghua Qin, Wei Shan, Jianfei Kuang, Wangjin Lu, Jianye Chen, Yating Zhao
Summary: Two Dof transcription factors, HpDof1.7 and HpDof5.4, play crucial roles in sugar accumulation in pitayas by enhancing the transcription of sugar metabolic pathway genes, thus affecting fruit quality formation.
FOOD QUALITY AND SAFETY
(2022)
Article
Biochemistry & Molecular Biology
Bo Yan, George Tzertzinis, Ira Schildkraut, Laurence Ettwiller
Summary: ReCappable-seq is a new method that allows the identification of transcription start sites (TSSs) for both Pol II and non-Pol II transcripts at single-nucleotide resolution. It provides a comprehensive understanding of various cell functions involved in eukaryotic transcription.
Article
Biochemistry & Molecular Biology
Kenta Tomihara, Peter Andolfatto, Takashi Kiuchi
Summary: In this study, the efficiency of CRISPR/Cas9-targeted knockouts of pigment-related genes was evaluated to understand their contribution to domestication-associated melanin pigmentation loss in B. mori. The results showed that knocking out certain genes led to lighter body coloration, demonstrating their role in melanin pigment formation. It was also found that the knockout of a specific gene contributed to the evolution of reduced melanin pigmentation in B. mori.
INSECT MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hisashi Tobita, Takashi Kiuchi
Summary: Diapause, an important trait for insects' survival, is determined by the photoperiod which controls the timing of diapause induction. In the silkworm, maternal conditions and core clock genes like period play a crucial role in the regulation of photoperiodic diapause. Knocking out clock genes disrupt normal feedback loops and affect the ability of female moths to induce diapause in response to photoperiod.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Natsuko Izumi, Keisuke Shoji, Takashi Kiuchi, Susumu Katsuma, Yukihide Tomari
Summary: The PIWI-interacting RNA (piRNA) pathway is a protection mechanism against transposons in animal germ cells. Gtsf1 and Gtsf1L promote endonuclease activity of PIWI proteins and bind to specific PIWI proteins, facilitating piRNA amplification.
Article
Biochemistry & Molecular Biology
Wei Liu, Keisuke Shoji, Masahiro Naganuma, Yukihide Tomari, Hiro-oki Iwakawa
Summary: Biochemical investigation reveals that Arabidopsis AGO4 and AGO6 selectively load 24A siRNAs through different mechanisms, and their 5' A specificity is determined by the coordination of the MID and PIWI domains, rather than the known nucleotide specificity loop in the MID domain.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Susumu Katsuma, Kanako Hirota, Noriko Matsuda-Imai, Takahiro Fukui, Tomohiro Muro, Kohei Nishino, Hidetaka Kosako, Keisuke Shoji, Hideki Takanashi, Takeshi Fujii, Shin-ichi Arimura, Takashi Kiuchi
Summary: This study identifies a Wolbachia protein that interacts with a host masculinization factor and leads to male killing in lepidopteran insects, providing insights into the mechanism by which Wolbachia manipulate the sexual development and reproduction of their insect hosts.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kenta Tomihara, Saori Tanaka, Susumu Katsuma, Toru Shimada, Jun Kobayashi, Takashi Kiuchi
Summary: In this study, two embryonic lethal mutations, l-t04 and l-m04, were discovered in semiconsomic strains T04 and M04. The mutations responsible for these lethalities were identified as the Bombyx homolog of imaginal discs arrested (Bmida) and TATA box binding protein-associated factor 5 (BmTaf5) through positional cloning and CRISPR/Cas9 mediated knockout screening. These genes were found to play important roles in late embryogenesis of B. mori.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Takahiro Fukui, Keisuke Shoji, Takashi Kiuchi, Yutaka Suzuki, Susumu Katsuma
Summary: Lepidopteran insects show a different mechanism of sex determination compared to most insect species. The silkworm Bombyx mori, a model species in this group, has a sex-determining gene called Feminizer (Fem) on the female-specific W chromosome. Fem is a precursor of PIWI-interacting small RNA (piRNA) that cleaves the mRNA of the male-determining gene Masc, leading to female development. However, this piRNA-dependent sex determination strategy is not observed in the Asian corn borer, Ostrinia furnacalis. Despite previous findings of masculinizing function of the Masc gene (OfMasc) in O. furnacalis embryos, there was no difference in the expression level of OfMasc between males and females during sex determination. Furthermore, deep sequencing analysis did not identify any female-specific small RNAs mapped onto OfMasc mRNA. Knockdown of two PIWI genes also did not affect the expression level of OfMasc in either sex. These findings suggest the possibility of divergent evolution of sex determinants in Lepidoptera.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kenta Tomihara, Takashi Kiuchi
Summary: In this study, the role of the Bmmamo gene in the bd phenotype of the silkworm Bombyx mori was investigated. The expression of Bmmamo was found to be downregulated in bd mutants, leading to the grayish-black color in the larval integument. Knockout mutants of Bmmamo also exhibited the bd phenotype, suggesting its involvement in pigmentation changes in the silkworm.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2023)
Article
Ecology
Tomohiro Muro, Hiroyuki Hikida, Takeshi Fujii, Takashi Kiuchi, Susumu Katsuma
Summary: This study determined the complete genome sequences of two male-killing Wolbachia strains in Ostrinia moths. The two genomes showed high homology and minimal evolution, but frequent genome rearrangements and rapid evolution of ankyrin repeat-containing proteins were observed. Additionally, mitochondrial genome comparison suggested recent Wolbachia introgression between infected Ostrinia species. These findings shed light on the evolutionary dynamics of host-symbiont interaction.
Article
Biochemistry & Molecular Biology
Takahiro Fukui, Takashi Kiuchi, Kenta Tomihara, Tomohiro Muro, Noriko Matsuda-Imai, Susumu Katsuma
Summary: Wolbachia, an intracellular bacteria in insects, can manipulate sexual development and reproduction. A recently identified protein, Oscar, interacts with the Masc protein and interferes with dosage compensation, leading to male killing in lepidopteran insects.
Article
Biology
Kenta Tomihara, Munetaka Kawamoto, Yutaka Suzuki, Susumu Katsuma, Takashi Kiuchi
Summary: The evolution of dosage compensation leads to the transcriptional downregulation of both Z chromosomes in male silkworms.
Article
Mathematical & Computational Biology
Munetaka Kawamoto, Takashi Kiuchi, Susumu Katsuma
Summary: SilkBase is an integrated database for transcriptomic and genomic resources of the silkworm and related species. It provides various data including gene expression, alternative splicing, and histone modifications, and can be used for comparative studies among closely related lepidopteran insects.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)