Article
Multidisciplinary Sciences
Dakota L. Jones, Grey F. Hallstroem, Xi Jiang, Ryan C. Locke, Mary Kate Evans, Edward D. Bonnevie, Anjana Srikumar, Thomas P. Leahy, Madhura P. Nijsure, Joel D. Boerckel, Robert L. Mauck, Nathaniel A. Dyment
Summary: Cells integrate mechanical cues to maintain tissue function and homeostasis, but the underlying mechanisms are not well understood. This study shows that loss of tensile cues changes nuclear morphology, positioning, and gene expression, resulting in weakening of tendons.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Dermatology
Ramile Dilshat, Hong Nhung Vu, Eirikur Steingrimsson
Summary: Melanocytes originate in the neural crest, migrate and proliferate before differentiating into pigment-producing cells, determining color and protecting against UV radiation; their lineage is regulated by transcription factors and signaling pathways, with epigenetic modifiers and replacement histones playing key roles in this process.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Immunology
Juliette Roels, Jolien Van Hulle, Marieke Lavaert, Anna Kuchmiy, Steven Strubbe, Tom Putteman, Bart Vandekerckhove, Georges Leclercq, Filip Van Nieuwerburgh, Lena Boehme, Tom Taghon
Summary: This study investigates the regulatory dynamics of E and ID protein encoding genes during pediatric human T cell development and uncovers novel insights through cross-species and cross-developmental comparisons.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Cell Biology
Angeliki Ntorla, Joseph Robert Burgoyne
Summary: Histone crotonylation is a newly identified epigenetic modification that regulates gene expression and is functionally distinct from histone acetylation, potentially regulating cellular metabolic status through competition for modification sites. It plays diverse functional roles within the cell, including signal-dependent gene activation, spermatogenesis, and tissue injury.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biology
Samuel N. Bogan, Marie E. Strader, Gretchen E. Hofmann
Summary: This study investigates the effects of DNA methylation on gene expression and splicing in the larvae of the purple sea urchin. It finds that differential gene body methylation has stronger effects on gene expression among genes with poorly accessible transcriptional start sites, and the baseline transcript abundance influences the direction of this effect. Considering the interactions between methylation and chromatin accessibility, the transcriptional responses to maternal conditioning are significantly increased, suggesting that the relationship between methylation and gene regulation is partially explained by chromatin state.
Article
Developmental Biology
Howard Cedar, Ofra Sabag, Yitzhak Reizel
Summary: DNA methylation plays a crucial role in gene regulation during development. The establishment of methylation patterns in the early embryo maintains a genome-wide network of gene regulatory elements by organizing an inaccessible chromatin structure. Programmed demethylation in each cell type allows for the maintenance of select elements in an open structure, enabling interaction with a wide range of transcription factors to regulate cell identity defining gene expression profiles.
Review
Cell Biology
Arianna Mangiavacchi, Gabriele Morelli, Valerio Orlando
Summary: Non-coding DNA makes up about 98.5% of the human genome and has been re-evaluated to reveal its importance in cell regulation through the presence of non-coding RNAs (ncRNAs). This review focuses on the relationship between chromatin-interacting RNAs, such as long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), circular RNA (circRNA), and the epigenome, highlighting their role in regulating gene expression and their impact on human diseases, particularly cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bhavana Kayyar, Anjhana C. Ravikkumar, Utsa Bhaduri, M. R. S. Rao
Summary: Sox8 is a crucial transcription factor that plays an important role in sex maintenance and fertility of adult mice. It is regulated by the lncRNA Mrhl in a p68-dependent manner under the control of the Wnt signaling pathway. The downregulation of Mrhl leads to the meiotic commitment of the spermatogonial cells through Sox8 dependence. The involvement of architectural proteins CTCF and cohesin in mediating a chromatin loop, as well as the interaction between lncRNA Mrhl and the Sox8 locus through a DNA:DNA:RNA triplex, are important for the regulation of Sox8 expression.
MOLECULAR AND CELLULAR BIOLOGY
(2022)
Review
Cell Biology
Nikolas James Tsiouplis, David Wesley Bailey, Lilly Felicia Chiou, Fiona Jane Wissink, Ageliki Tsagaratou
Summary: TET proteins oxidize 5-methylcytosine to facilitate DNA demethylation and serve as novel epigenetic marks. Loss of TET function is strongly associated with cancer, especially in hematological malignancies. TET proteins govern cell fate decisions by activating cell-specific gene expression programs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ann Collier, Angela Liu, Jessica Torkelson, Jillian Pattison, Sadhana Gaddam, Hanson Zhen, Tiffany Patel, Kelly McCarthy, Hana Ghanim, Anthony E. Oro
Summary: This study identifies a protein called Gibbin as a key regulator of early epithelial morphogenesis. Gibbin interacts with multiple sequence-specific transcription factors and methyl-CpG-binding proteins to regulate the expression of mesoderm genes. The loss of Gibbin leads to increased DNA methylation at GATA3-dependent mesodermal genes, resulting in a loss of signaling between dermal and epidermal cell types.
Article
Genetics & Heredity
Alejandra Rodriguez-Ortiz, Julio Cesar Montoya-Villegas, Felipe Garcia-Vallejo, Yecid Mina-Paz
Summary: The study revealed that HMGN1 and HMGN5 genes were significantly overexpressed in the hippocampus and areas of prefrontal cortex in Down Syndrome (DS) brain, while HMGN2 and HMGN4 genes were also overexpressed in DS brain at 16 to 22 gestation weeks. These findings provide strong evidence to support DS as an epigenetics-based aneuploidy.
Review
Oncology
Siwei Deng, Yuliang Feng, Siim Pauklin
Summary: This review discusses the importance of three-dimensional chromatin structures in biological processes and diseases, as well as the key structural protein elements involved in chromatin interactions. The recent development of technologies and bioinformatics approaches for studying chromatin interactions in gene expression regulation is also summarized.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Review
Plant Sciences
M. Teresa Alejo-Vinogradova, Diego Ornelas-Ayala, Rosario Vega-Leon, Adriana Garay-Arroyo, Berenice Garcia-Ponce, Elena R. Alvarez-Buylla, Maria de la Paz Sanchez
Summary: Current understanding suggests that regulation of asymmetric cell divisions in plants involves not only key transcription factor networks, but also crucial epigenetic mechanisms. Proper epigenetic regulation and chromatin dynamics are essential for integrating signals and specifying cell lineages during asymmetric cell divisions.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Review
Genetics & Heredity
Reza Raeisossadati, Merari F. R. Ferrari, Alexandre Hiroaki Kihara, Issam AlDiri, Jeffrey M. Gross
Summary: This review highlights the importance of epigenetic regulation in the developing vertebrate retina, emphasizing its role in cell differentiation and disease development. It also suggests future studies should focus on investigating these mechanisms to develop novel treatment strategies for various retinal disorders.
EPIGENETICS & CHROMATIN
(2021)
Review
Cell Biology
Kousik Sundararajan, Aaron F. Straight
Summary: Eukaryotes segregate their chromosomes during mitosis and meiosis by attaching them to the microtubules of the spindle using centromeres, with CENP-A playing a crucial role in centromere organization. Understanding and correcting errors in CENP-A organization is important for proper chromosome segregation during cell division.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Medicine, Research & Experimental
Prachi Mishra, Wei Tang, Vasanta Putluri, Tiffany H. Dorsey, Feng Jin, Fang Wang, Donewei Zhu, Lauren Amable, Tao Deng, Shaofei Zhang, J. Keith Killian, Yonghong Wang, Tsion Z. Minas, Harry G. Yfantis, Dong H. Lee, Arun Sreekumar, Michael Bustin, Wei Liu, Nagireddy Putluri, Stefan Ambs
JOURNAL OF CLINICAL INVESTIGATION
(2018)
Article
Oncology
Rashi Kalra, Ella Bhagyaraj, Drishti Tiwari, Ravikanth Nanduri, Anuja P. Chacko, Monika Jain, Sahil Mahajan, Neeraj Khatri, Pawan Gupta
Article
Multidisciplinary Sciences
Bing He, Tao Deng, Iris Zhu, Takashi Furusawa, Shaofei Zhang, Wei Tang, Yuri Postnikov, Stefan Ambs, Caiyi Cherry Li, Ferenc Livak, David Landsman, Michael Bustin
NATURE COMMUNICATIONS
(2018)
Article
Cell Biology
Ravikanth Nanduri, Rashi Kalra, Ella Bhagyaraj, Anuja P. Chacko, Nancy Ahuja, Drishti Tiwari, Sumit Kumar, Monika Jain, Raman Parkesh, Pawan Gupta
Article
Biochemistry & Molecular Biology
Shaofei Zhang, Tao Deng, Wei Tang, Bing He, Takashi Furusawa, Stefan Ambs, Michael Bustin
NUCLEIC ACIDS RESEARCH
(2019)
Article
Cell Biology
Ella Bhagyaraj, Nancy Ahuja, Sumit Kumar, Drishti Tiwari, Shalini Gupta, Ravikanth Nanduri, Pawan Gupta
Article
Multidisciplinary Sciences
Cristina Morales Torres, Mary Y. Wu, Sebastijan Hobor, Elanor N. Wainwright, Matthew J. Martin, Harshil Patel, William Grey, Eva Gronroos, Steven Howell, Joana Carvalho, Ambrosius P. Snijders, Michael Bustin, Dominique Bonnet, Paul D. Smith, Charles Swanton, Michael Howell, Paola Scaffidi
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Lucia Cabal-Hierro, Peter van Galen, Miguel A. Prado, Kelly J. Higby, Katsuhiro Togami, Cody T. Mowery, Joao A. Paulo, Yingtian Xie, Paloma Cejas, Takashi Furusawa, Michael Bustin, Henry W. Long, David B. Sykes, Steven P. Gygi, Daniel Finley, Bradley E. Bernstein, Andrew A. Lane
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Sumit Kumar, Ravikanth Nanduri, Ella Bhagyaraj, Rashi Kalra, Nancy Ahuja, Anuja P. Chacko, Drishti Tiwari, Kanupriya Sethi, Ankita Saini, Vemika Chandra, Monika Jain, Shalini Gupta, Deepak Bhatt, Pawan Gupta
Summary: Vitamin D3 can induce autophagy through its receptor VDR to inhibit foam cell formation in atherosclerosis, providing a potential therapeutic target for the disease.
Article
Biochemistry & Molecular Biology
Drishti Tiwari, Nancy Ahuja, Sumit Kumar, Rashi Kalra, Ravikanth Nanduri, Shalini Gupta, Asheesh Kumar Khare, Ella Bhagyaraj, Rashmi Arora, Pawan Gupta
Summary: Nr1d1 is found to play a crucial role in T helper cell polarization and inhibits the formation of Th2 cells by suppressing the transcription of GATA3 gene. Nr1d1 forms a repression complex with its companion protein on the promoter of GATA3 gene. Additionally, Nr1d1 interacts with other gene subsets to regulate metabolism, immunity, and brain functions, providing evidence for the genetic connection between asthma and other comorbid conditions.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Genetics & Heredity
Bing He, Iris Zhu, Yuri Postnikov, Takashi Furusawa, Lisa Jenkins, Ravikanth Nanduri, Michael Bustin, David Landsman
Summary: The study reveals that HMGN proteins occupy the A compartment in the 3D nucleus space and are associated with cell-type-specific long-range promoter-enhancer interactions. However, depletion of HMGN proteins in different cell types does not cause changes in higher order chromatin structure. Furthermore, the binding of HMGN proteins to chromatin is not dependent on specific protein partners, as revealed through ChIP-seq combined with mass spectrometry.
EPIGENETICS & CHROMATIN
(2022)
Article
Multidisciplinary Sciences
Ravikanth Nanduri, Takashi Furusawa, Alexei Lobanov, Bing He, Carol Xie, Kimia Dadkhah, Michael C. Kelly, Oksana Gavrilova, Frank J. Gonzalez, Michael Bustin
Summary: The lack of nucleosome binding proteins HMGN1 and HMGN2 in mice leads to changes in body weight, fat tissue mass, food intake, and differentiation rate of white preadipocytes into brown-like adipocytes, affecting energy metabolism.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Ravikanth Nanduri
Summary: Adipocytes play a critical role in energy balance maintenance, with different types of adipose tissue serving different functions. Transdifferentiation into brown-like beige adipocytes is crucial for improving metabolic health.
