Review
Plant Sciences
Liyang Su, Siqi Wan, Junmei Zhou, Qing Song Shao, Bingcong Xing
Summary: This review discusses the roles of transcription factors (TFs) in regulating plant seed development, noting that different TFs or TF families may have similar functions in this process, and some members of the same TF family may have opposite roles.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Review
Cell Biology
Shringar Rao, Tokameh Mahmoudi
Summary: This review provides an overview of the functions and mechanisms of DEAD-box family proteins in HIV-1 vRNA metabolism. It discusses the implications of these interactions in viral infection, viral latency, and cell death, and speculates on the potential of DEAD-box protein inhibitors as therapeutics for controlling the HIV-1 pandemic.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rachel A. Keuls, Young Sun Oh, Ivanshi Patel, Ronald J. Parchem
Summary: Developmental potential is restricted after germ layer specification, but cranial neural crest cells challenge this by giving rise to both ectodermal and ectomesenchymal lineages. The mechanism behind this cell differentiation is poorly understood. This study demonstrates that cranial neural crest cells have a transient state of increased chromatin accessibility, and the deletion of miR-302 leads to premature specification of the ectomesenchymal lineage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Marleny Garcia-Lozano, Purushothaman Natarajan, Amnon Levi, Ramesh Katam, Carlos Lopez-Ortiz, Padma Nimmakayala, Umesh K. Reddy
Summary: The study revealed that 88% of genes in tetraploid watermelon followed a >1:1 dosage effect, with most genes being upregulated. A large number of hypomethylated regions were identified in an isogenic tetraploid watermelon, localized near transcriptional start sites of upregulated genes, highlighting the importance of methylation in gene regulation. Genome doubling caused changes in higher-order chromatin structures and led to switching of compartments harboring genes associated with growth, development, and stress responses.
Review
Plant Sciences
Takuya Sakamoto, Sachihiro Matsunaga
Summary: Plants exhibit diverse characteristics and functions of chromatin organization, with similarities and differences to animals. The relationship between chromatin organization and transcriptional regulation in response to environmental stresses is becoming clearer. The regulation of specific chromatin positions in the nuclear space plays a crucial role in transcription, and recent findings suggest that local chromatin interactions have a greater impact on gene expression regulation than large-scale chromatin organization. The study highlights the importance of chromatin dynamics and transcriptional regulation in plants and discusses future directions in this field.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Cell Biology
Xin Li, Shanshan Wang, Xilan Yu, Shanshan Li
Summary: Autophagy is a catabolic process that maintains homeostasis and is involved in cell differentiation and development. The chromatin remodeling complex INO80 and histone variant H2A.Z have been identified as new regulators of autophagy, and the histone deacetylase Rpd3L complex plays a role in repressing autophagy by deacetylating Ino80 and H2A.Z. These findings highlight the importance of chromatin remodelers and histone variants in regulating autophagy in response to nutrient availability.
Review
Biochemistry & Molecular Biology
Talha Ijaz, Michael A. Burke
Summary: Heart failure is a complex disease process with neurohormonal system aberrations leading to dysregulated cellular signaling and gene transcription. The BET family epigenetic reader proteins play a key role in regulating gene transcription, influencing cardiac fibrosis and systolic dysfunction. Recent studies also highlight the importance of BRD4 in maintaining cardiomyocyte mitochondrial respiration and define BET bromodomain-independent processes involved in cardiac homeostasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Ka Lung Cheung, Anbalagan Jaganathan, Yuan Hu, Feihong Xu, Alannah Lejeune, Rajal Sharma, Cristina I. Caescu, Jamel Meslamani, Adam Vincek, Fan Zhang, Kyung Lee, Nilesh Zaware, Amina Abdul Qayum, Chunyan Ren, Mark H. Kaplan, John Cijiang He, Huabao Xiong, Ming-Ming Zhou
Summary: This study uncovers a previously unrecognized mechanism of self-directed cell type-specific regulation of the master transcription factor Stat3 through its own transcriptional target Hipk2 in Th17 cell differentiation. These findings provide insights into the regulation of Th17 cell immune functions and suggest a therapeutic strategy for developing targeted therapies for Th17-associated inflammatory disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Cell Biology
Brittany Cain, Brian Gebelein
Summary: Metazoans express multiple Hox transcription factors to specify cell fate along the anterior-posterior axis. Understanding how Hox factors regulate target genes for morphogenesis poses challenges on distinguishing their roles in activating/repressing genes for distinct segment identities and impacting organ development in a cell type-specific manner. Recent studies suggest Hox factors modify gene chromatin and utilize interactions with co-activators and co-repressors for accurate transcriptional outcomes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Wei Yu, V. Praveen Chakravarthi, Shaon Borosha, Iman Dilower, Eun Bee Lee, Anamika Ratri, Rebekah R. Starks, Patrick E. Fields, Michael W. Wolfe, M. Omar Faruque, Geetu Tuteja, M. A. Karim Rumi
Summary: The study reveals that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping mediated by an enhancer that interacts with ELF5 and SATB proteins, contributing to the maintenance of cell state.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ester Marina-Zarate, Ana Rodriguez-Ronchel, Manuel J. Gomez, Fatima Sanchez-Cabo, Almudena R. Ramiro
Summary: CTCF is a DNA-binding protein that plays important roles in chromatin structure organization and transcriptional regulation; however, the functional determinants of different CTCF-binding sites (CBS) are not well characterized. Using a conditional mouse model, we identified a set of CBSs that are lost upon CTCF depletion (lost CBSs) and another set that persists (retained CBSs). Retained CBSs are more similar to the consensus CTCF-binding sequence and usually span tandem CTCF peaks. Lost CBSs are enriched at enhancers and promoters and associated with active chromatin marks and higher transcriptional activity. In contrast, retained CBSs are enriched at TAD and loop boundaries, acting as chromatin barriers between distinct chromatin states.
Article
Immunology
Noam Kadouri, Tal Givony, Shir Nevo, Joschka Hey, Shifra Ben Dor, Golda Damari, Bareket Dassa, Jan Dobes, Dieter Weichenhan, Marion Bahr, Michelle Paulsen, Rebecca Haffner-Krausz, Marcus A. Mall, Christoph Plass, Yael Goldfarb, Jakub Abramson
Summary: This study reveals the importance of FOXN1 in the development of thymic epithelial cells and hair follicle cells, and identifies key regulatory regions and transcription factors involved in its expression.
SCIENCE IMMUNOLOGY
(2022)
Review
Cell Biology
Ming-Ming Chen, Yi-Ping Zhao, Yue Zhao, Shou-Long Deng, Kun Yu
Summary: Myostatin, a member of the TGF-β superfamily, negatively regulates skeletal muscle growth and development through autocrine or paracrine signaling, with mutations leading to increased muscle mass. It regulates myogenic differentiation, protein synthesis, and oxidative stress in skeletal muscle.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hongxu Ding, Ying Yang, Yuanqing Xue, Lucas Seninge, Henry Gong, Rojin Safavi, Andrea Califano, Joshua M. Stuart
Summary: This study demonstrates that the dynamic changes of biological states are controlled by coordinated transcription factors within gene regulatory networks, and TFs responsible for these changes can be prioritized and extended through temporal PageRank and multiplex PageRank, integrating gene regulatory networks reverse engineered from multi-omics profiles.
Article
Chemistry, Medicinal
Kentaro Takayama, Keisuke Hitachi, Hideyuki Okamoto, Mariko Saitoh, Miki Odagiri, Rina Ohfusa, Takahiro Shimada, Akihiro Taguchi, Atsuhiko Taniguchi, Kunihiro Tsuchida, Yoshio Hayashi
Summary: A new myostatin inhibitory peptide, MID-35, has been developed with improved stability and resistance to biodegradation. It significantly increases the tibialis anterior muscle mass in mice and can be used for prolonged inactivation of myostatin in skeletal muscle.
ACS MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Cell Biology
Setsuko Komatsu, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida
Summary: The mixture of silver nanoparticles, nicotinate, and potassium nitrate was found to have positive effects on wheat seedlings by regulating pathogen-related protein and reactive-oxygen species scavenging. Additionally, increasing starch content and decreasing lipoxygenase could promote wheat growth.
Article
Oncology
Haitao Gu, Wensheng Deng, Yi Zhang, Yu Chang, Vishal G. Shelat, Kunihiro Tsuchida, Leonardo S. Lino-Silva, Zhaowen Wang
Summary: In this study, we found that NLRP3 plays an important role in the polarization of macrophages in lung metastasis of pancreatic ductal adenocarcinoma (PDAC). NLRP3 activation in TAMs enhances the lung metastasis of PDAC.
TRANSLATIONAL LUNG CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Setsuko Komatsu, Kazuki Murata, Sayuri Yakeishi, Kazuyuki Shimada, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Rumina Obi, Shoichi Akita, Ryo Fukuda
Summary: Fiber crosslinked with zinc oxide nanoparticles (NPs) was found to enhance soybean growth. Compared to the solution form of ZnO NPs, fiber crosslinked with ZnO NPs promoted soybean growth at a lower concentration. Proteomic analysis revealed that proteins involved in photosynthesis and secondary metabolism accumulated more in soybeans grown on fiber crosslinked with ZnO NPs. Additionally, the abundance of NADPH oxidoreductase, which increased in soybeans by ZnO NPs application, might be related to the growth-promoting effect of auxin with fiber crosslinked with ZnO NPs on soybean growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Ghazala Mustafa, Suzuna Miyagawa, Murtaza Hasan, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Setsuko Komatsu
Summary: Plant-mediated synthesis methods of nanoflowers (NFs) enable the synthesis of stable and economical zinc oxide (ZnO) NFs, which have a positive impact on soybean growth. Bio-synthesized (BS) NFs ZnO can enhance root length and weight, regulate hormone metabolism, improve protein folding, and promote redox metabolism through detoxification of hydrogen peroxide, compared to chemically synthesized nanowires (CS NWs) ZnO.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Medicine, General & Internal
Hikari Yoshizawa, Haruki Nishizawa, Hidehito Inagaki, Keisuke Hitachi, Akiko Ohwaki, Yoshiko Sakabe, Mayuko Ito, Kunihiro Tsuchida, Takao Sekiya, Takuma Fujii, Hiroki Kurahashi
Summary: A long non-coding RNA gene called MG828507 was found to be overexpressed in pre-eclamptic placentas, and it is located in the same genomic region as the FLT1 gene. While overexpression or knockdown of MG828507 did not affect FLT1 expression, the transcript level of MG828507 was associated with genetic variants linked to pre-eclampsia and correlated with birth weight and placental weight.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Cell Biology
Keisuke Hitachi, Masahiko Honda, Kunihiro Tsuchida
Summary: Skeletal muscle atrophy is a serious health condition that reduces muscle mass and impairs muscle function. Recent studies have shown that long non-coding RNAs (lncRNAs) play a role in regulating skeletal muscle mass and function. They can also induce muscle hypertrophy or atrophy. Although the exact functions of lncRNAs have not been fully elucidated, novel lncRNAs associated with muscle atrophy have been discovered. Targeting lncRNAs may be a potential treatment for skeletal muscle atrophy and muscle wasting disorders in humans.
Article
Biochemistry & Molecular Biology
Keisuke Hitachi, Yuri Kiyofuji, Hisateru Yamaguchi, Masashi Nakatani, Masafumi Inui, Kunihiro Tsuchida
Summary: This study investigated the effects of the loss of MyHC-IIb and MyHC-IIx on skeletal muscle function using a mouse model. The results showed that the simultaneous loss of IIb and IIx led to severe muscle hypoplasia after 2 weeks of age in mice. Increased expression of other MyHCs was observed in 3-week-old mice, but it was not sufficient to compensate for the loss of IIb and IIx. Aberrant sarcomere structure and altered expression of sarcomere components were also observed. These findings contribute to the understanding of molecular mechanisms underlying skeletal muscle wasting disorders caused by the loss of skeletal muscle MyHCs.
Editorial Material
Endocrinology & Metabolism
Akiyoshi Uezumi
Summary: Tissue-resident stem cells are essential for tissue regeneration, but accessory cells also play a role. A recent study by Sastourne-Arrey et al. uncovers a delicate mechanism of skeletal muscle regeneration, where stromal cells from adipose tissue support the process.
NATURE REVIEWS ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Masahide Harada, Daisuke Okuzaki, Akemi Yamauchi, Shiho Ishikawa, Yoshihiro Nomura, Asuka Nishimura, Yuji Motoike, Masayuki Koshikawa, Keisuke Hitachi, Kunihiro Tsuchida, Kentaro Amano, Atsuo Maekawa, Yasushi Takagi, Eiichi Watanabe, Yukio Ozaki, Hideo Izawa
Summary: This study aimed to identify cardiac-specific circulating miRNAs as biomarkers for atrial fibrillation (AF). The researchers found that miR-20b-5p and miR-330-3p can serve as cardiac-specific biomarkers for atrial remodeling progression and arrhythmia recurrence after catheter ablation in AF patients.
Article
Endocrinology & Metabolism
Shinji Ueno, Yusuke Seino, Shihomi Hidaka, Masashi Nakatani, Keisuke Hitachi, Naoya Murao, Yasuhiro Maeda, Haruki Fujisawa, Megumi Shibata, Takeshi Takayanagi, Katsumi Iizuka, Daisuke Yabe, Yoshihisa Sugimura, Kunihiro Tsuchida, Yoshitaka Hayashi, Atsushi Suzuki
Summary: This study investigated the effect of blockade of glucagon action on skeletal muscle using GCGKO mice. The results showed that blockade of glucagon action increased skeletal muscle weight and stimulated slow-to-fast transition in type II fibers, resembling the phenotype of a high-protein diet.
JOURNAL OF DIABETES INVESTIGATION
(2023)
Article
Multidisciplinary Sciences
Tadahiro Nagaoka, Tatsuya Katsuno, Kyoka Fujimura, Kunihiro Tsuchida, Masashi Kishi
Summary: Here, we provide genetic and molecular evidence of a functional interaction between Vangl2 and N-cadherin for PCP-dependent neural development. This interaction is essential for planar polarized development of neural tissues but is not significantly associated with the RhoA or JNK pathways of Wnt/PCP signaling.
SCIENTIFIC REPORTS
(2023)
