Review
Biochemistry & Molecular Biology
Robert S. Piecyk, Luca Schlegel, Frank Johannes
Summary: This article explores the application of Deep Learning models in gene regulation, analyzing their model accuracy, training strategies, and data preparation steps. It finds that transfer learning combined with functionally curated interactions is the most promising approach for learning cell-type specific sequence features in the future.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Review
Plant Sciences
Xinxin Zhang, Tianzuo Wang
Summary: Over the past few decades, research on eukaryotic linear genomes, epigenomes, and now the three-dimensional chromatin organization, has revealed the importance of chromosomal architecture characteristics and chromatin domains in transcriptional activities and cellular responses. Advanced visualization techniques and 3C-based methods have provided insights into the intricate interplay between different factors shaping the 3D genome conformation in plants. The review also discusses the methods, advantages, limitations, and future implications of studying 3D genome organization in plants.
PLANT AND CELL PHYSIOLOGY
(2021)
Review
Immunology
Carolyn H. Rogers, Olga Mielczarek, Anne E. Corcoran
Summary: This article reviews the complex mechanisms of antigen receptor gene recombination in the immune system, focusing on recent advances in the study of the mouse immunoglobulin heavy chain locus. Key regulatory elements, local chromatin state at V genes, and imaging studies providing insights into the dynamic looping and contraction of the Igh locus during recombination are discussed. Additionally, higher resolution pictures of Igh locus structure using chromosome conformation capture-based technologies and the roles of transcription and architectural factors in regulating these processes are explored. Exciting recent mechanistic findings, such as Rag recombinase scanning and a new phase separation model for Igh locus compartmentalization, are also highlighted.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ezequiel Nazer
Summary: Lamins are components of the nuclear lamina and play a role in transcriptional regulation and chromatin organization. Recent studies have shown that lamins not only regulate gene transcription in regions associated with the nuclear lamina, but also interact with promoters and enhancers located inside the nucleus. Functional studies suggest that lamins play a role in transcription and chromatin interactions of key developmental gene programs. This review focuses on the emerging non-canonical functions of lamins in Drosophila and mammals as model organisms.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Review
Cell Biology
A. K. Balaji, Santam Saha, Shruti Deshpande, Darshini Poola, Kundan Sengupta
Summary: Dysregulation of chromatin remodeling and nuclear envelope proteins plays a significant role in cancer development. Recent advances in single-cell sequencing, imaging technologies, and data mining approaches enable the design of small molecules to selectively inhibit cancer cell growth and proliferation in a genome- and epigenome-specific manner.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Cell Biology
Marie Kervella, Maureen Jahier, Albano C. Meli, Antoine Muchir
Summary: Cardiomyopathy is a myocardial disorder characterized by abnormal heart muscle, which often leads to heart failure. Dilated cardiomyopathy, a common type, is significantly associated with compromised left ventricular function. Gene mutations, including those in the LMNA gene, have been identified as major causative factors. Mutated A-type lamins affect 3D genome organization and transcription activity of tissue-specific genes in Chromatin remodeling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Lorenzo Boninsegna, Asli Yildirim, Guido Polles, Sofia A. Quinodoz, Elizabeth Finn, Mitchell Guttman, Xianghong Jasmine Zhou, Frank Alber, Yuxiang Zhan
Summary: This study developed a multimodal data integration approach to predict the nuclear locations of genes and nuclear bodies, local chromatin compaction, and spatial segregation of functionally related chromatin. The results demonstrate that multimodal data integration can improve the accuracy and coverage of genome structure models, and different combinations of data sources can converge to models with similar predictive power.
Review
Immunology
Gisela Orozco
Summary: Since 2005, thousands of GWAS have been conducted to identify genetic variants associated with complex traits such as autoimmune diseases. The data from these studies has the potential to improve patient care through personalized medicine and the discovery of new drug targets. However, fully realizing the clinical translation of GWAS has been challenging due to the difficulty in interpreting the functional effects of risk variants and identifying causal variants and genes. Recent advances in genomics and epigenomics tools have helped overcome these limitations by mapping and characterizing regulatory elements and chromatin interactions, allowing for a better understanding of the biological mechanisms underlying disease.
SEMINARS IN IMMUNOPATHOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Nicholas S. Alagna, Tiera I. Thomas, Katherine L. Wilson, Karen L. Reddy
Summary: This review highlights recent studies uncovering factors that govern the organization and dynamics of lamina-associated domains (LADs) at the nuclear lamina, and their relevance to gene regulation and overall 3D genome organization.
Article
Biotechnology & Applied Microbiology
Tharvesh M. Liyakat Ali, Annael Brunet, Philippe Collas, Jonas Paulsen
Summary: The study reveals that long-range interactions of TADs are associated with key features of chromatin organization, and domains forming large TAD cliques tend to be repressive.
Review
Biochemistry & Molecular Biology
Alexandra G. Liddane, James M. Holaska
Summary: It is commonly recognized in the field that cancer cells exhibit changes in the size and shape of their nuclei, which can impact cell migration and metastasis. Nuclear structural changes are predicted to regulate cancer cell migration across various tumor types, and alterations in nuclear lamina proteins, such as emerin, may play a significant role in cancer progression and clinical outcomes. Understanding the factors driving these nuclear abnormalities and their functional consequences remains an area of ongoing research in the field of cancer biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Aura Stephenson-Gussinye, Mayra Furlan-Magaril
Summary: 3D genome organization plays a crucial role in regulating gene expression in various physiological and pathological conditions. Chromatin structure analysis has provided insights into the spatial organization of the genome, ranging from chromosome territories to chromatin loops. Recent advancements in chromosome conformation capture technologies have enabled the identification and characterization of structural variations (SVs) in pathological conditions, such as cancer. Understanding SVs in a 3D context can provide valuable information about transcriptional misregulation and its impact on disease progression. This review discusses bioinformatic tools for characterizing SVs and highlights their potential in reconstructing the 3D landscape of cancer genomes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biology
Claudia Caudai, Monica Zoppe, Anna Tonazzini, Ivan Merelli, Emanuele Salerno
Summary: The three-dimensional structure of chromatin in the cellular nucleus is crucial for physiological and pathological functions, and researchers use experimental and computational methods to study the spatial organization of DNA in cells. Different experimental techniques provide complementary information that is challenging to integrate.
Article
Biochemistry & Molecular Biology
Zilong Li, Tamar Schlick
Summary: This article presents a method called Hi-BDiSCO that generates 3D genome structures from Hi-C and Micro-C data using a mesoscale-resolution chromatin model based on the DiSCO model. By integrating reconstruction with nucleosome resolution chromatin simulations, the method is applied to different gene contexts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuka W. Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, Haruhiko Siomi
Summary: piRNAs form effector complexes with PIWI proteins for maintaining genomic integrity by repressing transposable elements. The Piwi-piRNA pathway induces stepwise changes in nuclear architecture and chromatin state at target loci for transcriptional silencing, involving nuclear lamins and histone modifications. The removal of active histone marks leads to transcriptional silencing, chromatin conformational changes, and association of specific proteins at target sites.
Article
Polymer Science
Annael Brunet, Catherine Tardin, Laurence Salome, Philippe Rousseau, Nicolas Destainville, Manoel Manghi
Article
Biochemistry & Molecular Biology
Annael Brunet, Sebastien Chevalier, Nicolas Destainville, Manoel Manghi, Philippe Rousseau, Maya Salhi, Laurence Salome, Catherine Tardin
NUCLEIC ACIDS RESEARCH
(2015)
Article
Biochemistry & Molecular Biology
Annael Brunet, Laurence Salome, Philippe Rousseau, Nicolas Destainville, Manoel Manghi, Catherine Tardin
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemical Research Methods
Manoel Manghi, Nicolas Destainville, Annael Brunet
Review
Genetics & Heredity
Philippe Collas, Tharvesh M. Liyakat Ali, Annael Brunet, Thomas Germier
FRONTIERS IN GENETICS
(2019)
Article
Genetics & Heredity
Annael Brunet, Frida Forsberg, Qiong Fan, Thomas Saether, Philippe Collas
FRONTIERS IN GENETICS
(2019)
Article
Cell Biology
Annael Brunet, Nicolas Destainville, Philippe Collas
Summary: The study utilized polymer simulations to investigate how physical parameters of chromatin affect its interactions with the nuclear lamina. It found that polymer stiffness has a greater impact on configurations at the lamina compared to stretching, leading to extended interactions and desorbed regions. The presence of an attraction potential results in persistent interaction and adsorption-desorption regimes, modulated by polymer stiffness and stretching.
