Article
Biotechnology & Applied Microbiology
Devender Arora, Jong-Eun Park, Dajeong Lim, Bong-Hwan Choi, In-Cheol Cho, Krishnamoorthy Srikanth, Jaebum Kim, Woncheoul Park
Summary: This study identified 16 CpG islands in liver and backfat tissues, which play important regulatory roles in differentiation processes. Differential methylation regions (DMRs) and differentially expressed genes (DEGs) on these islands indicated the differences between the two tissues. Motif analysis and gene ontology studies revealed the critical roles of these differentially methylated genes in lipid metabolism, reproductive performance, and immunity pathways.
Article
Oncology
Yingxin Han, Liyan Ji, Yanfang Guan, Mengya Ma, Pansong Li, Yinge Xue, Yinxin Zhang, Wanqiu Huang, Yuhua Gong, Li Jiang, Xipeng Wang, Hong Xie, Boping Zhou, Jiayin Wang, Junwen Wang, Jinghua Han, Yuliang Deng, Xin Yi, Fei Gao, Jian Huang
Summary: Cervical cancer is the second leading cause of cancer death among women globally. Epigenetic dysregulation through DNA methylation and hydroxymethylation plays a crucial role in tumorigenesis. This study found genome-wide hypo-methylation and hypo-hydroxymethylation in CC, along with local hyper-methylation and hyper-hydroxymethylation. Additionally, novel differentially methylated/hydroxymethylated-associated genes were identified as potential epigenetic biomarkers for CC prognosis.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Genetics & Heredity
Siti Aisyah Faten Mohamed Sa'dom, Sweta Raikundalia, Shaharum Shamsuddin, Wei Cun See Too, Ling Ling Few
Summary: The study revealed that DNA methylation of CpG4C region in the promoter of ck alpha gene can promote the binding of repressive transcription factors, leading to downregulation of CK alpha expression.
Article
Biochemistry & Molecular Biology
Lei Zhao, Xiaohong Wu, Junnian Zheng, Dong Dong
Summary: In this study, an efficient workflow LCM-mu WGBS was introduced to profile the DNA methylome of circulating tumor cells from lung cancer patients. A unique DNA methylation signature of CTCs distinct from primary lung cancer tissues was identified, with promoter hypermethylation of epithelial genes as a hallmark of stable epithelial-mesenchymal transition. Furthermore, CTCs may exhibit a stemness-related feature during dissemination and metastasis, providing potential noninvasive CTC DNA methylation biomarkers for clinical diagnosis.
Review
Biochemistry & Molecular Biology
Chihiro Iwaya, Akiko Suzuki, Junichi Iwata
Summary: Cleft lip and palate is a common congenital birth defect with varied causes. Recent studies suggest that non-coding RNAs, specifically microRNAs, may play a role in the development of cleft lip and palate. This review examines the potential of microRNAs as causative mechanisms in humans and mice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Taiko Kim To, Chikae Yamasaki, Shoko Oda, Sayaka Tominaga, Akie Kobayashi, Yoshiaki Tarutani, Tetsuji Kakutani
Summary: In plant genomes, both mCG and H3K9me2/mCH play important roles in silencing TEs. The establishment of mCH is dependent on the presence of mCG, and the efficiency of mCH targeting depends on the relative levels of mCG in the genome. The study also proposes a model where local positive feedback and global negative feedback regulate DNA methylation patterning.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Hala Al Adhami, Anais Flore Bardet, Michael Dumas, Elouan Cleroux, Sylvain Guibert, Patricia Fauque, Herve Acloque, Michael Weber
Summary: This study investigates the distribution and function of DNA methylation in different vertebrate species, revealing both conservation and divergence in methylation patterns and functions. The study shows that the chicken genome has lower levels of methylation compared to other species and other species exhibit a higher frequency of CpG-rich DNA methylation compared to mice. The study also demonstrates the conservation of DNA methylation in silencing germline genes and endogenous retroviruses in vertebrates.
Review
Cell Biology
James A. Cain, Bertille Montibus, Rebecca J. Oakey
Summary: The mammalian genome is generally lacking in CG dinucleotides, except for CpG islands (CGIs) found in protected regions. CGIs serve as gene regulatory hubs, with a quarter of them located within genes. These intragenic CGIs play a crucial role in gene regulation, influencing transcription activity and transcriptome diversity within genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Dan Huang, Xiansong Wang, Yingzhi Liu, Ziheng Huang, Xiaoxu Hu, Wei Hu, Qing Li, Hung Chan, Yidan Zou, Idy H. T. Ho, Yan Wang, Alfred S. L. Cheng, Wei Kang, Ka F. To, Maggie H. T. Wang, Sunny H. Wong, Jun Yu, Tony Gin, Qingpeng Zhang, Zheng Li, Jianxiong Shen, Lin Zhang, Matthew T. Chan, Xiaodong Liu, William K. K. Wu
Summary: Tumor suppressor genes exhibit unique promoter features that optimize cancer resistance by achieving high expression in normal tissues and resisting downregulation during tumorigenesis. The CpG dinucleotide frequencies in TSG promoters are higher and positively correlated with gene expression, suggesting an evolutionary pressure on young TSGs. Higher CpG frequencies and chromatin accessibility are associated with the ability of TSGs to resist downregulation during tumorigenesis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Y. Feng, S. Cirera, E. Tasoz, Y. Liu, L. H. Olsen, B. O. Christoffersen, H. D. Pedersen, T. P. Ludvigsen, R. K. Kirk, C. Schumacher-Petersen, Y. Deng, M. Fredholm, F. Gao
Summary: The study found that Gottingen minipigs become morbidly obese on a high fat/fructose/cholesterol diet, and reversing their diet to a standard one can reverse lipid-related metabolic parameters. Differences were identified in the methylation patterning of promoters between the feeding groups, leading to dysregulation of metabolically-related genes. The potential of exploring diet-epigenome interactions for treating obesity was highlighted through this research.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Sujun Chen, Jessica Petricca, Wenbin Ye, Jiansheng Guan, Yong Zeng, Nicholas Cheng, Linsey Gong, Shu Yi Shen, Junjie T. Hua, Megan Crumbaker, Michael Fraser, Stanley Liu, Scott Bratman, Theodorus van der Kwast, Trevor Pugh, Anthony M. Joshua, Daniel D. De Carvalho, Kim N. Chi, Philip Awadalla, Guoli Ji, Felix Feng, Alexander W. Wyatt, Housheng Hansen He
Summary: The authors used cell-free DNA methylation analysis to demonstrate changes in hypermethylation in metastatic prostate cancer, and its impact on immune features and clinical outcomes. The results showed that the cell-free DNA methylome can capture variations beyond the tumor, and has a high accuracy in predicting disease types.
NATURE COMMUNICATIONS
(2022)
Article
Endocrinology & Metabolism
Pavlos Fanis, Maria Morrou, Marios Tomazou, Kyriaki Michailidou, George M. M. Spyrou, Meropi Toumba, Nicos Skordis, Vassos Neocleous, Leonidas A. A. Phylactou
Summary: Makorin RING finger protein 3 (MKRN3) is an important factor associated with Prader-Willi syndrome. It is expressed in the hypothalamus and mutations in the gene have been found in patients with central precocious puberty. The methylation status of the Mkrn3 promoter was investigated in female mice and differential methylation patterns were observed between pre-pubertal and pubertal/post-pubertal stages.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Cell Biology
Ivana Bukova, Katarzyna Izabela Szczerkowska, Michaela Prochazkova, Inken M. Beck, Jan Prochazka, Radislav Sedlacek
Summary: The study found that in the WIZ knockout mouse model, defective embryos exhibited abnormalities in multiple aspects during development, particularly in the craniofacial region, such as shorter snout, cleft palate, and cleft eyelids. These results suggest that WIZ plays an important role in craniofacial development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Daiki Oshikawa, Shintaro Inaba, Yudai Kitagawa, Kaori Tsukakoshi, Kazunori Ikebukuro
Summary: CpG methylation alters the stability and structure of the i-motif in CpG islands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Aleix Noguera-Castells, Carlos A. Garcia-Prieto, Damiana Alvarez-Errico, Manel Esteller
Summary: DNA methylation, a well-studied epigenetic mark, plays a critical role in gene regulation and is altered in cancer and other diseases. The newly developed 900K EPIC v2 microarray provides significant improvements in coverage and includes additional probes for DNA cis-regulatory regions. Validation studies demonstrate the reproducibility and versatility of this updated tool for studying the DNA methylome.
Article
Reproductive Biology
Ratnam S. Seelan, Partha Mukhopadhyay, Dennis R. Warner, Irina A. Smolenkova, M. Michele Pisano, Robert M. Greene
REPRODUCTIVE TOXICOLOGY
(2017)
Article
Reproductive Biology
Partha Mukhopadhyay, Ratnam S. Seelan, Francine Rezzoug, Dennis R. Warner, Irina A. Smolenkova, Guy Brock, M. Michele Pisano, Robert M. Greene
REPRODUCTIVE TOXICOLOGY
(2017)
Review
Pharmacology & Pharmacy
Ratnam S. Seelan, Partha Mukhopadhyay, M. Michele Pisano, Robert M. Greene
DRUG METABOLISM REVIEWS
(2018)
Article
Biochemical Research Methods
Ratnam S. Seelan, Dennis R. Warner, Partha M. Mukhopadhyay, Sarah A. Andres, Irina A. Smolenkova, James L. Wittliff, M. Michele Pisano, Robert M. Greene
ANALYTICAL BIOCHEMISTRY
(2013)
Article
Developmental Biology
Ratnam S. Seelan, Savitri N. Appana, Partha Mukhopadhyay, Dennis R. Warner, Guy N. Brock, M. Michele Pisano, Robert M. Greene
BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY
(2013)
Article
Neurosciences
Muthusamy Thangavel, Ratnam S. Seelan, Jaganathan Lakshmanan, Robert E. Vadnal, John I. Stagner, Latha K. Parthasarathy, Manuel F. Casanova, Rifaat Shody El-Mallakh, Ranga N. Parthasarathy
JOURNAL OF NEUROSCIENCE RESEARCH
(2014)
Article
Cell Biology
R. N. Parthasarathy, J. Lakshmanan, M. Thangavel, R. S. Seelan, J. I. Stagner, A. J. Janckila, R. E. Vadnal, M. F. Casanova, L. K. Parthasarathy
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2013)
Article
Reproductive Biology
Partha Mukhopadhyay, Ratnam S. Seelan, Robert M. Greene, M. Michele Pisano
REPRODUCTIVE TOXICOLOGY
(2019)
Review
Developmental Biology
Ratnam S. Seelan, Michele Pisano, Robert M. Greene
BIRTH DEFECTS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Partha Mukhopadhyay, Robert M. Greene, M. Michele Pisano
CELL BIOCHEMISTRY AND FUNCTION
(2020)
Article
Cell Biology
R. S. Seelan, P. Mukhopadhyay, J. Philipose, R. M. Greene, M. M. Pisano
Summary: Folate receptor 1 (Folr1) deficiency may cause embryonic developmental abnormalities and affect important biological processes such as cellular proliferation, apoptosis, and migration. Under folate-deficient conditions, cranial neural crest cells and neural tube explants showed a significant reduction in directed migration, partly due to alterations in cell skeleton.
Article
Dentistry, Oral Surgery & Medicine
Partha Mukhopadhyay, Irina Smolenkova, Ratnam S. Seelan, M. Michele Pisano, Robert M. Greene
Summary: This study investigates the role of microRNA-22 (miR-22) in the development of the orofacial region in mice. The results indicate that miR-22 plays a significant role in the removal of the midline epithelial seam (MES) during palatogenesis and may contribute to the etiology of cleft palate.
CLEFT PALATE-CRANIOFACIAL JOURNAL
(2023)
Article
Cell Biology
Ratnam S. Seelan, M. Michele Pisano, Robert M. Greene
Summary: Environmental and genetic factors contribute significantly to orofacial clefting, and epigenetics plays an important role in embryogenesis. MicroRNAs are crucial in the ontogeny of the orofacial region. Several miRNAs and their target genes involved in lip and palate morphogenesis have been identified, but further validation is needed.