Article
Biochemistry & Molecular Biology
Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Ido Sagi, Gary LeRoy, Ming M. Zheng, J. Owen Andrews, Alicia Zamudio, Charalampos Lazaris, Nancy M. Hannett, Tong Ihn Lee, Phillip A. Sharp, Ibrahim I. Cisse, Arup K. Chakraborty, Richard A. Young
Summary: This study discusses the mechanisms of feedback control in regulating biological processes, especially in transcription regulation. Research indicates that RNA in transcription initiation promotes condensate formation, while RNA produced during elongation stimulates condensate dissolution. Therefore, transcriptional regulation involves a feedback mechanism where transcribed RNA both stimulates and arrests the process.
Article
Cell Biology
Yu Zhang, Wanyu Wang, Jiali Min, Suosi Liu, Qianrong Wang, Yu Wang, Yang Xiao, Xia Li, Zhiguang Zhou, Shanshan Liu
Summary: The expression of ZNF451 is upregulated in triple-negative breast cancer (TNBC) and is associated with a poor prognosis. ZNF451 enhances TNBC progression by interacting with and enhancing the activity of the transcriptional activator SLUG. Disturbing the ZNF451-SLUG interaction can suppress TNBC progression by reducing CCL5 expression and counteracting the migration and activation of tumor-associated macrophages.
Article
Multidisciplinary Sciences
Renjie Wu, Bangyan Zhou, Wei Wang, Feng Li
Summary: This study categorizes the states of single eukaryotic genes, identifies 6 essential transcriptional events, and reveals how transcriptional bursting is modulated by various regulators. The results provide insights into transcriptional sensitivity, burst profiles, intrinsic transcriptional noise, and gene induction requirements.
Review
Oncology
Shinsuke Ito, Nando Dulal Das, Takashi Umehara, Haruhiko Koseki
Summary: The review focuses on emerging views of chromatin conformations associated with enhancer-promoter interactions and the factors that establish or maintain such interactions, which may regulate gene expression. It also discusses various mechanisms that regulate eukaryotic gene expression, including the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins.
Article
Biochemical Research Methods
Stephanie C. Amack, Savio S. Ferreira, Mauricio S. Antunes
Summary: Synthetic biology uses genetically encoded devices and circuits to implement complex functions in living cells and organisms. Transcriptional promoters play a key regulatory role in genetic circuits, and the CaMV 35S promoter is widely used in plant biotechnology to direct gene expression. It can determine developmental, spatial, and tissue-specific patterns of gene expression in plants.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Plant Sciences
Syed Sarfaraz Hussain, Manzar Abbas, Sammar Abbas, Mingke Wei, Ahmed H. El-Sappah, Yuhan Sun, Yun Li, Arthur J. Ragauskas, Quanzi Li
Summary: Alternative splicing in plants regulates gene expression through differential transcriptional modifications, allowing adaptation to environmental stresses and different growth stages. It causes the retention of introns in messenger RNA, leading to the translation of differentially expressed proteins. Additionally, alternative splicing remodels transcription factors at the post-transcriptional level, activating or repressing transcription.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Johannes N. Wibisana, Takehiko Inaba, Hisaaki Shinohara, Noriko Yumoto, Tetsutaro Hayashi, Mana Umeda, Masashi Ebisawa, Itoshi Nikaido, Yasushi Sako, Mariko Okada
Summary: The NF-kappa B transcription factor plays a crucial role in cell fate determination and is involved in the activation of super-enhancers. This study investigates the characteristics of NF-kappa B-mediated super-enhancer activity and suggests that NF-kappa B super-enhancers play an important role in the transcriptional regulation of B cells possibly through liquid condensate formation consisting of macromolecular interactions.
Review
Biochemistry & Molecular Biology
Helen Ray-Jones, Mikhail Spivakov
Summary: Transcriptional enhancers play a key role in regulating gene expression in metazoa, particularly in initiating and maintaining gene expression programmes. Understanding how enhancers control their target genes in the right place and time is a crucial question in functional genomics, and modern approaches are beginning to unravel the complexity of enhancer-promoter relationships.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Dina V. Antonova, Marina V. Zinovyeva, Liya G. Kondratyeva, Alexander V. Sass, Irina V. Alekseenko, Victor V. Pleshkan
Summary: This study identified unique transcriptional characteristics of the CXCL12 and FAP genes in model CAFs, but none of the promoters showed selective activity in these fibroblasts. Promoters of CTGF, IGFBP2, JAG1, and SPARC genes can provide higher transgene expression in fibroblasts than in cancer cells, but nonspecific viral promoters have similar features. The patterns of promoter activity observed in human cell lines were similar to those in mouse models in vivo and in vitro.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Infectious Diseases
Shang Lu, Dan Li, Leilei Wang, Yingmin Bi, Minghua Wang, Fan Yang
Summary: This study identified the mcr-1 gene in 15 clinical isolates of Enterobacteriaceae, with promoter variations associated with expression of the mcr-1 gene and ultimately the levels of colistin resistance.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2021)
Article
Engineering, Environmental
Shiva Tabatabaee, Alireza Iranbakhsh, Mansoore Shamili, Zahra Oraghi Ardebili
Summary: The study revealed that the application of copper nanoparticles had concentration-dependent effects on the physiological and molecular responses of pepper seedlings, with higher concentrations leading to decreased growth parameters and increased oxidative stress.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Jason A. Watts, Christopher Grunseich, Yesenia Rodriguez, Yaojuan Liu, Dongjun Li, Joshua T. Burdick, Alan Bruzel, Robert J. Crouch, Robert W. Mahley, Samuel H. Wilson, Vivian G. Cheung
Summary: RNA can regulate cellular processes through modifications and folding, and dysregulation of RNA sequence and structure can contribute to diseases. In this study, a new mechanism was uncovered, where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. Additionally, a noncoding RNA called AANCR was found to regulate the expression of APOE, and its folding and modification were associated with different cell types and stress conditions. Furthermore, DNA sequence variations in AANCR were significantly linked to APOE expression and Alzheimer's Disease, highlighting the potential role of AANCR as a modifier of the disease.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Cindy Y. Kok, Lauren M. MacLean, Renuka Rao, Shinya Tsurusaki, Eddy Kizana
Summary: The study aimed to identify a gene that can be delivered to the heart to protect against cancer therapy-induced cardiotoxicity. By replacing the CMV promoter with the cardiac-specific NCX1 promoter, a lentiviral vector capable of inducing the expression of cardioprotective gene Bcl-2 was successfully produced.
Article
Chemistry, Medicinal
Naresh Bhuma, Karam Chand, Mans Andreasson, James Mason, Rabindra Nath Das, Ankit Kumar Patel, Daniel Ohlund, Erik Chorell
Summary: G-quadruplex (G4) DNA structures play important roles in DNA replication and transcription, especially in the regulation of oncogenes. This study focuses on developing low molecular weight G4 ligands using synthetic organic chemistry. The compounds are evaluated for their selectivity and ability to bind and stabilize G4 DNA, and the binding interactions are analyzed in relation to the compounds' structural conformations and electrostatic potentials. The top candidates are further tested in a 3D co-culture model of pancreatic cancer, demonstrating their potential as highly active and selective G4 ligands with therapeutic advantages.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Iftekhar A. Showpnil, Julia Selich-Anderson, Cenny Taslim, Megann A. Boone, Jesse C. Crow, Emily R. Theisen, Stephen L. Lessnick
Summary: This study investigates the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma cells. The findings suggest that EWS/FLI is involved in the establishment of TAD boundaries, compartment activation, enhancer-promoter looping, and gene activation. EWS/FLI co-localizes with cohesin and promotes chromatin loops and TAD boundaries. Moreover, transcriptional heterogeneity in different Ewing sarcoma cell lines is related to local chromatin features.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Medicine, Research & Experimental
Seungyeon Kim, Songmi Kim, Seyoung Mun, Yongsik Kwak, Kwang-Sun Suh, Song-Yi Choi, Kyudong Han
Summary: In this study, genetic variants associated with ovarian granulosa cell tumor (OGCT) were identified through whole-exome sequencing. Several genes associated with ovarian cancer, including MUC3A, were found. MUC3A may play a significant role in the development of OGCT and could be a potential biomarker for diagnosis.
BOSNIAN JOURNAL OF BASIC MEDICAL SCIENCES
(2022)
Article
Microbiology
Jinuk Jeong, Seyoung Mun, Yunseok Oh, Chun-Sung Cho, Kyeongeui Yun, Yongju Ahn, Won-Hyong Chung, Mi Young Lim, Kyung Eun Lee, Tae Soon Hwang, Kyudong Han
Summary: This study utilized next-generation sequencing and quantitative real-time PCR to analyze and quantify gut microbiota, demonstrating that qRT-PCR can be used as a complementary method to address the limitations of NGS and provide important applications in the microbial industry.
Article
Biochemistry & Molecular Biology
Wonseok Shin, Cherl-Joon Lee, Yong-Moon Lee, Young-Bong Choi, Seyoung Mun, Kyudong Han
Summary: This study compared and evaluated the diagnostic capability of two COVID-19 test kits. The results showed that the test results of the two kits on 301 specimens perfectly matched the pre-diagnosis results of the medical institution. The measurement results of diagnostic sensitivity and specificity were both 1, indicating high diagnostic capability. The Cohen's Kappa coefficient value was 1, indicating almost perfect concordance between the two kits. The dilutional linearity tests showed that both kits had very high detection reliability.
Review
Green & Sustainable Science & Technology
Kornsorn Srikulnath, Nattakan Ariyaraphong, Worapong Singchat, Thitipong Panthum, Artem Lisachov, Syed Farhan Ahmad, Kyudong Han, Narongrit Muangmai, Prateep Duengkae
Summary: Mitochondrial displacement loop (mt D-loop) sequence analyses have improved assessments of genetic diversity and population dynamics of endangered species facing climate change and habitat loss. Tracking population haplotypes of these species using mitochondrial-based markers has advanced conservation genomics and biodiversity research. Studies on Asian elephants have used mt D-loop sequences to assess genetic diversity and population-scale hypotheses, shedding light on evolutionary processes and facilitating conservation efforts.
Article
Biochemistry & Molecular Biology
Wonseok Shin, Jeongseok Yun, Kyudong Han, Dong-Guk Park
Summary: By studying the genetic characteristics of primary colorectal cancer and synchronous peritoneal metastatic lesions, we propose an appropriate peritoneal metastasis treatment policy. It was found that mutations on the KMT2C and THBS1 genes were commonly found in both primary colorectal cancer and peritoneal metastasis. The PDE4DIP gene was mutated in all cases except for one peritoneal metastasis sample. Analysis using the mutation database confirmed that the gene mutations of primary colorectal cancer and the peritoneal metastasis derived from it showed the same tendency.
Article
Biochemistry & Molecular Biology
Jihee Kim, Young In Lee, Seyoung Mun, Jinuk Jeong, Dong-Geol Lee, Misun Kim, HyungWoo Jo, Sieun Lee, Kyudong Han, Ju Hee Lee
Summary: The study investigated the effect of topical application of Epidermidibacterium Keratini (EPI-7) ferment filtrate on skin aging through a randomized split-face clinical study. The results showed significant improvements in skin barrier function, elasticity, and dermal density with the use of the EPI-7 ferment filtrate. The study also revealed that EPI-7 ferment filtrate increased the abundance of certain beneficial skin microbes and showed potential effects on skin microbiome diversity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Wongsathit Wongloet, Worapong Singchat, Aingorn Chaiyes, Hina Ali, Surachai Piangporntip, Nattakan Ariyaraphong, Trifan Budi, Worawit Thienpreecha, Wannapa Wannakan, Autchariyapron Mungmee, Kittipong Jaisamut, Thanyapat Thong, Thitipong Panthum, Syed Farhan Ahmad, Artem Lisachov, Warong Suksavate, Narongrit Muangmai, Rattanaphon Chuenka, Mitsuo Nunome, Wiyada Chamchumroon, Kyudong Han, Aniroot Nuangmek, Yoichi Matsuda, Prateep Duengkae, Kornsorn Srikulnath
Summary: This study investigated the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed in North Thailand. The breed was found to have high levels of genetic diversity and a unique DNA fingerprint. Genetic introgression from red junglefowl and indigenous breeds was identified, supporting the hypothesis of its crossbreeding origin. These findings contribute to our understanding of the genetic blueprint and potential for improving domestic chickens using this breed.
Article
Microbiology
Yunseok Oh, Seyoung Mun, Young-Bong Choi, HyungWoo Jo, Dong-Geol Lee, Kyudong Han
Summary: Functional cosmetics industries are focusing on screening skin microbiome and isolating beneficial materials from key microorganisms. Epidermidibacterium keratini EPI-7(T) was found to produce a new compound, 1,1'-biuracil, with anti-aging effects on human skin. Genomic analysis of E. keratini EPI-7(T) was conducted to provide up-to-date information and explore its potential in functional cosmetics. Comparative genomic analysis revealed that E. keratini EPI-7(T) has more metabolite-related genes compared to other strains, and annotation identified vital genes for biosynthesis of amino acids and other substances. The study aims to provide genetic information for further strain development and biotechnology utilization of E. keratini EPI-7(T).
Article
Biology
Nattakan Ariyaraphong, Wongsathit Wongloet, Pish Wattanadilokchatkun, Thitipong Panthum, Worapong Singchat, Thanyapat Thong, Artem Lisachov, Syed Farhan Ahmad, Narongrit Muangmai, Kyudong Han, Prateep Duengkae, Yosapong Temsiripong, Kornsorn Srikulnath
Summary: Morphological divergence between Siamese and other crocodiles has been observed, leading to questions about potential crocodile hybrids. Genetic analysis revealed evidence of introgression between Siamese and saltwater crocodiles, highlighting the importance of identifying hybrids for conservation efforts.
Article
Genetics & Heredity
Eun Gyung Park, Du Hyeong Lee, Woo Ryung Kim, Yun Ju Lee, Woo Hyeon Bae, Jung-min Kim, Hae Jin Shin, Hongseok Ha, Joo Mi Yi, Ssang Goo Cho, Yung Hyun Choi, Sun Hee Leem, Hee Jae Cha, Sang Woo Kim, Heui Soo Kim
Summary: Although most HERVs have lost their function due to accumulated mutations, they still contribute to human biology, especially in cancer. In this study, 29 miRNAs derived from HERV sequences were identified in the human genome, and miR-4454, a HERV-H-derived miRNA, was found to be upregulated in NMIBC cells. Two target genes, DNAJB4 and SASH1, were confirmed to be negatively regulated by miR-4454 through the dual-luciferase assay. These findings suggest that the upregulation of miR-4454 derived from HERV-H promotes NMIBC progression by suppressing tumor suppressor genes.
Article
Biology
Ryan Rasoarahona, Pish Wattanadilokchatkun, Thitipong Panthum, Thanyapat Thong, Worapong Singchat, Syed Farhan Ahmad, Aingorn Chaiyes, Kyudong Han, Ekaphan Kraichak, Narongrit Muangmai, Akihiko Koga, Prateep Duengkae, Agostinho Antunes, Kornsorn Srikulnath
Summary: The research aims to enhance the ant colony optimization algorithm by integrating marker effectiveness indicators, providing cost-effective solutions for genetic assessments, breeding, and conservation efforts. The study addresses the trade-off between accuracy and cost, and provides valuable insights into real-world genetic studies.
Article
Biochemistry & Molecular Biology
Wattanawan Jaito, Thitipong Panthum, Syed Farhan Ahmad, Worapong Singchat, Narongrit Muangmai, Kyudong Han, Akihiko Koga, Prateep Duengkae, Kornsorn Srikulnath
Summary: In this study, sex-specific and linked loci were identified in the Siamese cobra through in silico chromosome mapping. These loci were mainly mapped on the Z sex chromosome, and a putative sex-determining region was found, with one specific locus homologous to the TOPBP1 gene. The findings contribute to our understanding of the genetic basis and sex-specific traits in the Siamese cobra.
Article
Biochemistry & Molecular Biology
Young Mok Heo, Dong-Geol Lee, Seyoung Mun, Minji Kim, Chaeyun Baek, Haeun Lee, Seok Kyun Yun, Seunghyun Kang, Kyudong Han
Summary: The culture filtrate of Micrococcus luteus YM-4 shows significant therapeutic potential for dermatological applications by enhancing skin barrier function, modulating immune response, and aiding in the recovery from environmental damage. It also exhibits anti-aging properties and promotes wound healing processes.
Review
Biochemistry & Molecular Biology
Du Hyeong Lee, Woo Hyeon Bae, Hongseok Ha, Eun Gyung Park, Yun Ju Lee, Woo Ryung Kim, Heui-Soo Kim
Summary: Transposable elements, including human endogenous retrovirus families, play a significant role in gene regulation and can affect human diseases. The presence of Z-DNA in LTR elements provides insights into understanding gene function and its relation to various diseases.
MOLECULES AND CELLS
(2022)
Article
Agriculture, Dairy & Animal Science
V Sampath, J. H. Park, B. D. Ha, K. Han, I. H. Kim
Summary: This study analyzed the effects of adding different concentrations of Lactobacillus plantarum to diets with different nutrient densities on the growth performance, excreta microbiota, nutrient digestibility, gas emission, and meat quality in Ross308 broilers. The results showed that adding 0.1% L. plantarum to a low-density diet significantly improved the growth performance and nutrient digestibility of the broilers, while reducing E. coli and ammonium emission.
BRAZILIAN JOURNAL OF POULTRY SCIENCE
(2022)
