Article
Biochemistry & Molecular Biology
Jamie R. H. Taka, Yunyuan Sun, David C. Goldstone
Summary: The transcription of endogenous retroviral elements is controlled by KRAB-ZFPs and Trim28 during development. The specific interactions between Trim28 and the KRAB domain were identified, and models were provided to explain this interaction. This study sheds light on the regulation of transcriptional silencing events.
Article
Biochemistry & Molecular Biology
Eun Kyoung Do, Hye Ji Moon, Kyung Taek Kang, Jung Won Yoon, Ye Seul Kim, Jeong Kon Seo, Jae Ho Kim
Summary: The study revealed that Kap1 regulates the pluripotency of ESCs and somatic cell reprogramming by inhibiting Itch-mediated ubiquitination of Oct4, increasing Oct4 stability. This finding may offer new insights for the treatment of stem cell and cell reprogramming-related diseases.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Biochemistry & Molecular Biology
Yao-Jen Chang, Steven Lin, Zhi-Fu Kang, Bin-Jon Shen, Wen-Hai Tsai, Wen-Ching Chen, Hsin-Pin Lu, Yu-Lun Su, Shu-Jen Chou, Shu-Yu Lin, Sheng-Wei Lin, Yin-Jung Huang, Hsin-Hui Wang, Ching-Jin Chang
Summary: TRIM28/KAP1/TIF1β is an important epigenetic modifier, and its activity is regulated by posttranslational modifications such as phosphorylation, sumoylation, and acetylation. In this study, the acetylation-mimic mutant TRIM28-K304Q was created using CRISPR-Cas9 technology, which showed altered interaction with KRAB-ZNFs and different gene expression profiles compared to wild-type cells. These findings suggest that acetylation of K304 in TRIM28 acts as a switch to regulate its interaction with KRAB-ZNFs and alters gene regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Patrycja Czerwinska, Andrzej Adam Mackiewicz
Summary: This study investigates the involvement of TRIM28-interacting KRAB-ZNFs in kidney cancer progression, revealing a negative association with cancer stemness and attenuated immune response, while also identifying the prognostic role of several KRAB-ZNFs. The study utilizes bioinformatic tools and transcriptomic data to analyze the correlation between KRAB-ZNFs expression, genomic alterations, tumor dedifferentiation, and antitumor immune response in kidney cancer. The results provide a new understanding of the role of selected KRAB-ZNF proteins in kidney cancer development and offer potential insights for better understanding the molecular basis of KIRC.
Article
Medicine, Research & Experimental
Lei Bao, Ashwani Kumar, Ming Zhu, Yan Peng, Chao Xing, Jennifer E. Wang, Yingfei Wang, Weibo Luo
Summary: SAP30 is an important protein in breast cancer, and its upregulation is associated with unfavorable prognosis. Research has shown that SAP30 promotes tumor growth and metastasis through mechanisms other than canonical gene silencing. Additionally, SAP30 enhances cell motility, angiogenesis, and lymphangiogenesis by interacting with other proteins, thereby driving breast cancer progression.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Review
Immunology
Keyera Randolph, Usman Hyder, Ivan D'Orso
Summary: This article provides an up-to-date review of the various functions of KAP1 in different contexts, including its repression of endogenous retroviruses, its role as both an activator and repressor of HIV-1 transcription, its regulation of DNA and RNA viruses, and its control of cellular responses and immune functions. Despite the extensive research on KAP1's positive and negative regulation of viral and cellular transcriptional programs, our understanding of its mechanisms remains limited.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Cell Biology
Hsuan-Yeh Pan, Mallika Valapala
Summary: The study identified the role of ZKSCAN3 in regulating lysosomal function and autophagy in RPE cells. Knockdown of ZKSCAN3 resulted in increased autophagy flux and number of functional lysosomes. The inhibition of P38 MAPK retained ZKSCAN3 in the nucleus in nutrient-deprived cells.
Review
Biochemistry & Molecular Biology
Joanna Sobocinska, Sara Molenda, Marta Machnik, Urszula Oleksiewicz
Summary: Kruppel-associated box zinc finger proteins (KRAB-ZFPs) constitute the largest family of transcriptional factors exerting co-repressor functions in mammalian cells. They play essential roles in various biological processes, including development, imprinting, retroelement silencing, and carcinogenesis. KRAB-ZFPs can act as oncogenes or tumor suppressors in various tumor types and are involved in regulating clinicopathological features, treatment response, and cancer cell phenotype through upstream and downstream molecular mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Mohammed Eslami, Amin Espah Borujeni, Hamed Eramian, Mark Weston, George Zheng, Joshua Urrutia, Carolyn Corbet, Diveena Becker, Paul Maschhoff, Katie Clowers, Alexander Cristofaro, Hamid Doost Hosseini, D. Benjamin Gordon, Yuval Dorfan, Jedediah Singer, Matthew Vaughn, Niall Gaffney, John Fonner, Joe Stubbs, Christopher A. Voigt, Enoch Yeung
Summary: The Host Response Model (HRM) combines high-throughput sequencing and machine learning to accurately predict the directionality of gene dysregulation to a combination of inducers. The use of prior knowledge of cell regulatory networks doubles the predictive performance of the HRM.
Article
Biochemistry & Molecular Biology
Jun Zhao, Wenmin Ma, Yucheng Zhong, Hao Deng, Bingyu Zhou, Yaqin Wu, Meiqiong Yang, Huan Li
Summary: This study found that inhibiting the expression of gadd7 through the CRISPR-dCas9-KRAB system can prevent apoptosis and enhance proliferation of spermatocytes, providing a new molecular intervention method for the treatment of male infertility caused by varicocele.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Genetics & Heredity
Alexandra Iouranova, Delphine Grun, Tamara Rossy, Julien Duc, Alexandre Coudray, Michael Imbeault, Jonas De Tribolet-Hardy, Priscilla Turelli, Alexandre Persat, Didier Trono
Summary: By studying genes driven by endogenous retrovirus LTRs during early human development, ZNF676 is identified as a specific repressor of a subset of these genes. The binding of this repressor correlates with the epigenetic marking of TEeRS in the germline, and is crucial for the control of genes involved in ciliogenesis/flagellogenesis.
Article
Biochemistry & Molecular Biology
Enas R. Abu-Zhayia, Laila A. Bishara, Feras E. Machour, Alma Sophia Barisaac, Bella M. Ben-Oz, Nabieh Ayoub
Summary: CDYL1 induces transcriptional silencing at DSB sites by counteracting active marks and regulating repair and silencing activity.
Article
Multidisciplinary Sciences
Abhishek Sinha, Vinson B. Fan, Aravinda-Bharathi Ramakrishnan, Nicole Engelhardt, Jennifer Kennell, Ken M. Cadigan
Summary: SOX9 promotes turnover of β-catenin independently of the destruction complex and proteasome in mammalian cell culture. This requires the activation of MAML2, which acts as a coactivator for SOX9 in antagonizing the Wnt/β-catenin pathway. This newly identified pathway provides a parallel mechanism for restricting Wnt/β-catenin signaling.
Article
Cell Biology
Yangyang Yang, Binggong Zhao, Linlin Lv, Yuxi Yang, Shujing Li, Huijian Wu
Summary: FBXL10 plays a role in promoting the migration and invasion of breast cancer cells by inhibiting E-cadherin expression and inducing EMT. It may provide a novel regulatory axis in the EMT of breast cancer.
CELL DEATH DISCOVERY
(2021)
Article
Biology
Kei Fukuda, Yoshinori Makino, Satoru Kaneko, Chikako Shimura, Yuki Okada, Kenji Ichiyanagi, Yoichi Shinkai
Summary: The Kruppel-associated box domain zinc finger proteins are associated with DNA methylation of retroelements in human primordial germ cells, and during human spermatogenesis, the hominoid-specific retroelement SINE-VNTR-Alus (SVA) may undergo transcription-directed de novo DNA methylation, leading to significant inter-individual epigenetic variation in sperm.
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)