Article
Genetics & Heredity
Giovanni Messina, Emanuele Celauro, Rene Massimiliano Marsano, Yuri Prozzillo, Patrizio Dimitri
Summary: Reporter genes inserted into the Drosophila genome have been used to monitor chromatin domains and it is commonly thought that these genes are silenced when inserted into heterochromatin. However, research has found that heterochromatin is genetically and molecularly heterogeneous and contains functional genes. This study provides evidence that even when integrated within or near actively transcribed loci in the pericentric regions of chromosome 2, reporter genes are strongly silenced. Some reporter genes were found to be insensitive to a known suppressor of position effect variegation (PEV), indicating different epigenetic regulators or mechanisms control different regions of heterochromatin.
Article
Multidisciplinary Sciences
Haofeng Wang, Yunjie Xiao, Xia Chen, Mengwen Zhang, Guangxin Sun, Feng Wang, Lin Wang, Hanxiao Zhang, Xiaoyu Zhang, Xin Yang, Wenling Li, Yi Wei, Deqiang Yao, Bing Zhang, Jun Li, Wen Cui, Fenghua Wang, Cheng Chen, Wei Shen, Dan Su, Fang Bai, Jinhai Huang, Sheng Ye, Lei Zhang, Xiaoyun Ji, Wei Wang, Zefang Wang, Mark Hochstrasser, Haitao Yang
Summary: This study reveals the importance of interface residues in the binding of CI factors CidA and CidB, which contributes to the diversity of cytoplasmic incompatibility. Sequence divergence in CidA and CidB proteins may explain the complex incompatibility patterns observed in mosquitoes infected with different Wolbachia strains.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Elisa Mascolo, Francesco Liguori, Lorenzo Stufera Mecarelli, Noemi Amoroso, Chiara Merigliano, Susanna Amadio, Cinzia Volonte, Roberto Contestabile, Angela Tramonti, Fiammetta Verni
Summary: In this study, silencing of Hex-A and Hex-C in Drosophila resulted in a MODY-2-like hyperglycemia phenotype. Hex-A is crucial for insulin secretion and required for Hex-C expression. Reduced levels of either Hex-A or Hex-C led to chromosome aberrations and increased production of advanced glycation end-products (AGEs) and reactive oxygen species (ROS). Treating GCK-depleted larvae with the antioxidant vitamin B6 rescued chromosome aberrations, while treatment with a B6 inhibitor enhanced genomic instability, suggesting a link between MODY-2 and genome integrity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Stefano Giustino Manzo, Lise Dauban, Bas van Steensel
Summary: This article reviews recent advances in the study of LAD-NL interactions, discussing molecular tethers and looseners of LADs, and their link to transcription regulation and genome replication. It also provides a brief summary of technological advances that may uncover new aspects of LAD biology.
CURRENT OPINION IN CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Farah J. Bughio, Keith A. Maggert
Summary: Position-effect variegation (PEV) results from the juxtaposition of euchromatic and heterochromatic components of eukaryotic genomes, silencing genes near the new euchromatin/heterochromatin junctions. Mutations in Su(var)3-9 compromise the initial establishment of PEV in early embryogenesis, while mutations in Su(var)205 lead to rapid loss of gained heterochromatin-induced gene silencing.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Microbiology
Wei Wang, Wen Cui, Haitao Yang
Summary: Wolbachia are highly successful intracellular bacteria in arthropods, manipulating host reproduction to their advantage. Although cytoplasmic incompatibility (CI) has been known for decades, the genes responsible for CI were only recently identified.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Entomology
Alexandru Marian Bologa, Ileana Stoica, Nicoleta Denisa Constantin, Alexandru Al. Ecovoiu
Summary: This study mapped the DNA transposons of a natural population of Drosophila melanogaster from Romania, using bioinformatics tools. Multiple insertions affecting genes with potential adaptive roles were identified, including a focus on the P-element and transposons in heterochromatic regions. The research contributes to understanding the dynamics and roles of DNA transposons in the D. melanogaster genome.
Article
Genetics & Heredity
Luisa Vernizzi, Christian F. Lehner
Summary: The pairing of homologous chromosomes during prophase I of meiosis I is a complex process that involves mechanisms to avoid or eliminate entanglements between non-homologous chromosomes. In Drosophila spermatocytes, non-homologous associations are disrupted by chromosome territory formation, while special conjunction proteins maintain linkages between homologous chromosomes. The mechanism and location of these alternative homolog conjunction proteins within bivalents are still poorly understood.
Article
Cell Biology
Paula Santabarbara-Ruiz, Pierre Leopold
Summary: The study showed that tumor-induced steroid sink promotes catabolic alterations in healthy tissues, and Oatp33Eb is specifically induced in cachectic tumors, where its overexpression causes cachexia.
DEVELOPMENTAL CELL
(2021)
Article
Developmental Biology
Saya Ichihara, Koji Nagao, Takehisa Sakaguchi, Chikashi Obuse, Takashi Sado
Summary: Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 plays an important role in this process by facilitating the formation of H3K9me3-enriched blocks on the Xi, which in combination with H3K27me3, leads to robust heterochromatin formation. Deficiency of SmcHD1 results in the loss of H3K9me3, causing aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.
Article
Multidisciplinary Sciences
Henrik Lindehell, Alexander Glotov, Eshagh Dorafshan, Yuri B. Schwartz, Jan Larsson
Summary: This study investigated the role of H3K36 methylation and associated methyltransferases in balancing transcriptional output in two chromosome-specific systems in Drosophila. The findings suggest that Set2, NSD, and Ash1 play important roles in maintaining transcriptional balance on the male X chromosome and chromosome 4.
Article
Cell Biology
Rene Massimiliano Marsano, Patrizio Dimitri
Summary: Transposable elements (TEs) are abundant components of constitutive heterochromatin and their accumulation in the genome may be influenced by reduced recombination and lack of functional genes. However, recent studies suggest that constitutive heterochromatin contains active genes and the accumulation of TEs may play a role in centromere and telomere structure.
Article
Cell Biology
Peiwei Chen, Alexei A. Kotov, Baira K. Godneeva, Sergei S. Bazylev, Ludmila Olenina, Alexei A. Aravin
Summary: Small noncoding piRNAs guide repression of complementary targets in Metazoa. Previous studies in fruit fly ovaries have shown the function of the piRNA pathway in transposon silencing and genome defense. In fruit fly testes, piRNA programs exhibit sexual dimorphism and are used differently between sexes to combat sex-specific transposon landscapes.
GENES & DEVELOPMENT
(2021)
Article
Cell Biology
Tatyana D. Kolesnikova, Mikhail S. Klenov, Alina R. Nokhova, Sergey A. Lavrov, Galina V. Pokholkova, Veit Schubert, Svetlana V. Maltseva, Kevin R. Cook, Michael J. Dixon, Igor F. Zhimulev
Summary: This study used a Rif1 mutation to analyze heterochromatin in Drosophila melanogaster and discovered a new inversion. Using nanopore sequencing and FISH, the breakpoints of the inversion in both euchromatin and heterochromatin were identified. This research provides new insights into the X chromosome heterochromatin structure, nucleolar organization, and nucleolar dominance phenomenon.
Article
Biochemical Research Methods
Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla
Summary: Beacon v2 is an API specification that defines a standard for federated discovery of genomic and phenotypic data. B2RI is a set of open-source software tools that allow quick setup of a local Beacon instance.
Article
Multidisciplinary Sciences
Rene Daer, Cassandra M. Barrett, Ernesto Luna Melendez, Jiaqi Wu, Stefan J. Tekel, Jimmy Xu, Brady Dennison, Ryan Muller, Karmella A. Haynes
Article
Biochemical Research Methods
Yating Liu, Luke Sargent, Wilson Leung, Sarah C. R. Elgin, Jeremy Goecks
Article
Biotechnology & Applied Microbiology
Stefan J. Tekel, Christina L. Smith, Brianna Lopez, Amber Mani, Christopher Connot, Xylaan Livingstone, Karmella A. Haynes
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2019)
Editorial Material
Biochemistry & Molecular Biology
Natecia L. Baskin, Karmella A. Haynes
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2019)
Article
Genetics & Heredity
Sidney H. Wang, Sarah C. R. Elgin
EPIGENETICS & CHROMATIN
(2019)
Article
Biochemistry & Molecular Biology
Cassandra M. Barrett, Reilly McCracken, Jacob Elmer, Karmella A. Haynes
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Editorial Material
Biochemistry & Molecular Biology
Kelly R. Stevens, Kristyn S. Masters, P. I. Imoukhuede, Karmella A. Haynes, Lori A. Setton, Elizabeth Cosgriff-Hernandez, Muyinatu A. Lediju Bell, Padmini Rangamani, Shelly E. Sakiyama-Elbert, Stacey D. Finley, Rebecca K. Willits, Abigail N. Koppes, Naomi C. Chesler, Karen L. Christman, Josephine B. Allen, Joyce Y. Wong, Hana El-Samad, Tejal A. Desai, Omolola Eniola-Adefeso
Summary: The racial funding disparity by NIH is identified as a significant barrier to success for Black faculty members, prompting a collective effort to address and dismantle it.
Editorial Material
Biochemistry & Molecular Biology
Karmella Haynes, Christopher Yau, Andrea Bild, Ashley Laughney, Leonardo Morsut, Xia Yang, Judith Zaugg, Patrick Hsu, Vera Pancaldi, Srividya Iyer-Biswas
Article
Oncology
Cara E. Shields, Sindhu Potlapalli, Selma M. Cuya-Smith, Sarah K. Chappell, Dongdong Chen, Daniel Martinez, Jennifer Pogoriler, Komal S. Rathi, Shiv A. Patel, Kristianne M. Oristian, Corinne M. Linardic, John M. Maris, Karmella A. Haynes, Robert W. Schnepp
Summary: Rhabdomyosarcoma (RMS) is an aggressive pediatric soft tissue sarcoma with two main subtypes, alveolar rhabdomyosarcoma (ARMS) and embryonal rhabdomyosarcoma. There are no targeted therapies for ARMS, but recent studies have shown a potential cooperation between epigenetic proteins and PAX3-FOXO1 fusion, suggesting epigenetic proteins as targets in ARMS. In this study, BMI1 was identified as a potential therapeutic vulnerability in ARMS, with inhibition activating the Hippo pathway and reducing tumor growth.
MOLECULAR ONCOLOGY
(2021)
Article
Chemistry, Physical
Allen P. Liu, Eric A. Appel, Paul D. Ashby, Brendon M. Baker, Elisa Franco, Luo Gu, Karmella Haynes, Neel S. Joshi, April M. Kloxin, Paul H. J. Kouwer, Jeetain Mittal, Leonardo Morsut, Vincent Noireaux, Sapun Parekh, Rebecca Schulman, Sindy K. Y. Tang, Megan T. Valentine, Sebastian L. Vega, Wilfried Weber, Nicholas Stephanopoulos, Ovijit Chaudhuri
Summary: Recent advancements in synthetic biology and biomaterials have provided exciting tools for creating new materials and extending the application of synthetic biology. Despite their transformative potential, these fields have mostly progressed separately. This Perspective reviews recent key advances and presents a roadmap for collaboration between the two communities, emphasizing the near-term applications in developing hierarchically structured biomaterials.
Review
Biochemistry & Molecular Biology
Kierra A. Franklin, Cara E. Shields, Karmella A. Haynes
Summary: This article discusses the regulation of gene expression by chromatin and its associated proteins and enzymes. Recent studies have shown that reader-effectors play a key role in driving chromatin-mediated processes, although our understanding of these proteins is still limited. By integrating proteomics, epigenomics, and synthetic biology, further insights into the activity of reader-effectors can be gained.
TRENDS IN BIOCHEMICAL SCIENCES
(2022)
Article
Engineering, Biomedical
Cara E. Shields, Robert W. Schnepp, Karmella A. Haynes
Summary: This study aimed to investigate the role of BMI1 as a therapeutic target in FP-RMS and identify gene expression changes associated with the inhibition of BMI1. The results showed that inhibition of BMI1 led to downregulation of cell cycle progression, DNA damage response, and cholesterol biosynthesis pathways in FP-RMS cell lines. It also identified potential kinases that are upregulated in response to BMI1 inhibition. These findings suggest that targeting BMI1 could be an effective therapy for FP-RMS.
REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Rae Hunter, Kathleen J. Imbach, Chengjing Zhou, Jodi Dougan, Jamie A. G. Hamilton, Kevin Z. Chen, Priscilla Do, Ashley Townsel, Greg Gibson, Erik C. Dreaden, Edmund K. Waller, Karmella A. Haynes, Curtis J. Henry, Christopher C. Porter
Summary: This study identified immune suppression mechanisms in B-cell acute lymphoblastic leukemia (B-ALL) and explored strategies to overcome them. Differential cytokine expression and genes associated with immune exhaustion were observed in B-ALL patients with measurable residual disease. Leukemia cells were found to suppress T-cell function, and a compromised tumor immune microenvironment was observed in a mouse model of B-ALL. However, treatment with recombinant IL-12 (rIL-12) restored the immune microenvironment, increased the number of T-cells and dendritic cells, and reduced the expression of exhaustion-related genes. Additionally, combining IL-12 and blinatumomab treatments enhanced the cytolytic capacity of T-cells. These findings suggest that rIL-12 treatment could be therapeutically beneficial in B-ALL.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Miyoung Lee, Delaney K. K. Geitgey, Jamie A. G. Hamilton, Jeremy M. M. Boss, Christopher D. D. Scharer, Jennifer M. M. Spangle, Karmella A. A. Haynes, Curtis J. J. Henry
Summary: The relationship between obesity and T-ALL development is inverse, with obesity inducing cell death in T-ALL cells through epigenetic modifications. Epigenetic modifying drugs may be a potential treatment option for T-ALL.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Engineering, Biomedical
Rene Daer, Fatima Hamna, Cassandra M. Barrett, Karmella A. Haynes
APL BIOENGINEERING
(2020)