Article
Biochemistry & Molecular Biology
Joshua A. R. Brown, Jieying Hazel Cui, Maggie Y. M. Ling, Ellia X. C. Gao, LeAnn J. Howe, Sheila S. Teves, James Davie
Summary: The 43rd Asilomar Chromatin, Chromosomes, and Epigenetics Conference was held online, allowing researchers at different career stages to share promising new findings. The conference covered modern chromatin research in various model systems and explored the fundamental principles of nuclear organization and transcription regulation, as well as key mechanisms underlying human disease.
BIOCHEMISTRY AND CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Joshua A. R. Brown, Jieying Hazel Cui, Maggie Y. M. Ling, Ellia X. C. Gao, LeAnn J. Howe, Sheila S. Teves
Summary: The 43rd Asilomar Chromatin, Chromosomes, and Epigenetics Conference provided a platform for researchers at various career stages to share promising new findings in the field of chromatin research. The conference covered a wide range of topics, including nuclear organization, transcription regulation, and mechanisms underlying human diseases.
BIOCHEMISTRY AND CELL BIOLOGY
(2022)
Review
Multidisciplinary Sciences
Jason H. Brickner
Summary: This article discusses the mechanisms by which histone modifications can be inherited and relates them to the phenomenon of epigenetic transcriptional memory. Recent studies have found that the histone H3 lysine 4 dimethylation associated with this memory plays a critical role in sustaining memory and can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism involves a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1(-) COMPASS. This is the first example of chromatin-mediated inheritance of a mark that promotes transcription.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Multidisciplinary Sciences
Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A. Doudna
Summary: The fusion of PRDM9 and Cas9 in CRISPR-Cas genome editing can increase the efficiency of homology-directed repair (HDR) and avoid off-target editing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Lucia Ramos-Alonso, Petter Holland, Stephanie Le Gras, Xu Zhao, Bernard Jost, Magnar Bjoras, Yves Barral, Jorrit M. Enserink, Pierre Chymkowitch
Summary: Mitotic entry is associated with a series of cellular changes in chromosomes and transcription factors, leading to downregulation of transcription. However, the influence of mitotic condensation on transcription during interphase is unknown. In this study, we found that failure to condense a specific chromosome during mitosis resulted in aberrant transcription in the subsequent interphase, leading to high expression levels of genes in cis and the activation of inducible transcriptional programs in trans. These findings reveal an unexpected role of mitosis and mitotic chromosome condensation in maintaining transcriptional homeostasis during interphase.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Oncology
Kosuke Yamaguchi, Xiaoying Chen, Asami Oji, Ichiro Hiratani, Pierre-Antoine Defossez
Summary: Chromatin changes in cancer have significant implications for gene expression, genome stability, and cancer progression, making them important for diagnosis and treatment.
Review
Immunology
J. Peter Svensson
Summary: HIV-1 integrates as a provirus in the host genome, forming a reservoir of infected cells similar to oncogenes. Both HIV-1 provirus and oncogenes require expression to cause disease. Successful cure for HIV-1 and cancer involves eliminating cells with potential to regenerate the disease, and epigenetic drugs used against cancer have been applied in HIV-1 field to modulate the proviral chromatin state.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
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
Biochemistry & Molecular Biology
Zhengtao Xiao, Jason W. Locasale
Summary: Chromatin and associated epigenetic marks provide important platforms for gene regulation in response to metabolic changes associated with environmental exposures. Studies have shown that fluctuations of key metabolites can influence chromatin modifications, but their effects on chromatin structure are largely unknown.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Agata Izabela Kalita, Eric Marois, Magdalena Kozielska, Franz J. Weissing, Etienne Jaouen, Martin M. Moeckel, Frank Ruehle, Falk Butter, M. Felicia Basilicata, Claudia Isabelle Keller Valsecchi
Summary: The discovery of the sex chromosome activation (SOA) gene as a master regulator of dosage compensation (DC) in Anopheles mosquitoes sheds light on the evolutionary steps leading to the establishment of a chromosome-specific fine-tuning mechanism. The male isoform of the SOA gene encodes a DNA-binding protein that binds the promoters of active X chromosomal genes and expressing it induces DC in female cells. Male mosquitoes lacking SOA or female mosquitoes expressing the male isoform exhibit X chromosome misregulation and developmental delay.
Review
Cell Biology
Susanne Bacher, Johanna Meier-Soelch, Michael Kracht, M. Lienhard Schmitz
Summary: Activation of NF-kappa B results in a tailored transcriptional response to meet specific cellular needs. Regulation of induction kinetics, amplitude, and termination of gene expression by NF-kappa B involves multiple layers in the nucleus. Changes in genome folding, including in senescence or cancer cells, can lead to sustained increases in NF-kappa B activity, while NF-kappa B also plays a role in forming hierarchically organized super enhancers for coordinated expression of target genes. Identifying mechanisms for specific regulation of NF-kappa B target gene clusters could enable targeted therapeutic interventions.
Article
Biochemical Research Methods
Sarah M. Mangiameli, Haiqi Chen, Andrew S. Earl, Julie A. Dobkin, Daniel Lesman, Jason D. Buenrostro, Fei Chen
Summary: Photoselective sequencing is a new method for genomic and epigenomic profiling in morphologically distinct regions. It uses targeted illumination to selectively unblock a photocaged fragment library, enabling sequencing-based readout in microscopically identified spatial regions. The method was validated by analyzing chromatin accessibility profiles of fluorescently-labeled cell types in the mouse brain and comparing with published data. Photoselective sequencing is a flexible and generalizable platform for studying the interplay of spatial structures with genomic and epigenomic properties.
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
Biochemistry & Molecular Biology
Esteban Dodero-Rojas, Matheus F. Mello, Sumitabha Brahmachari, Antonio B. Oliveira, Vinicius G. Contessoto, Jose N. Onuchic
Summary: The folding patterns of interphase genomes in higher eukaryotes, as obtained from DNA-proximity-ligation or Hi-C experiments, are classified into compartments and subcompartments, which exhibit specific epigenomic characteristics and cell-type-specific variations. To explore the relationship between genome structure and epigenome, a maximum-entropy-based neural network model called PyMEGABASE (PYMB) is presented to predict compartment annotations solely based on local epigenome. PYMB can accurately predict compartments in different cell types and species, and its predictions are interpretable. It is also used to investigate compartment-specific gene expression and can be integrated with OpenMiChroM software for generating three-dimensional genome structures.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Maria Theresia Watzlowik, Sujaan Das, Markus Meissner, Gernot Laengst
Summary: The gene transcription regulation of the human malaria parasite Plasmodium falciparum is governed by complex epigenetic mechanisms involving chromatin structure and dynamics. The high AT-content of the parasite genome and sequence divergence of chromatin-related proteins suggest significant differences in chromatin-dependent regulation compared to other eukaryotes. Specialized chromatin remodeling enzymes play an essential role in gene regulation in P. falciparum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Physiology
Ridwan Babatunde Ibrahim, Yo-Tsen Liu, Ssu-Yu Yeh, Jin-Wu Tsai
FRONTIERS IN PHYSIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Ridwan Babatunde Ibrahim, Ssu-Yu Yeh, Kon-Ping Lin, Frans Ricardo, Tsyr-Yan Yu, Chih-Chiang Chan, Jin-Wu Tsai, Yo-Tsen Liu
CELLULAR AND MOLECULAR LIFE SCIENCES
(2020)
Article
Multidisciplinary Sciences
Ravneet Jaura, Ssu-Yu Yeh, Kaitlin N. Montanera, Alyssa Ialongo, Zobia Anwar, Yiming Lu, Kavindu Puwakdandawa, Ho Sung Rhee
Summary: This study reveals that extended intergenic regions play a role in tissue-specific gene expression, particularly in neural tissues. These intergenic regions contain more active enhancers and are associated with co-expression of neighboring neural genes. Generic neural genes expressed in multiple tissues have longer intergenic regions and contain tissue-specific enhancers.
NATURE COMMUNICATIONS
(2022)
