Article
Biochemistry & Molecular Biology
Nikolas Eggers, Peter B. Becker
Summary: Using a unique experimental system, this study explored the principles of DNA shape recognition and factor cooperativity in chromatin. By reconstituting chromatin on Drosophila genomes, the researchers identified the physiological binding profile of MSL2 through interaction with other factors and competition with non-functional sites. The results revealed novel aspects of target selection in a complex chromatin environment.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Computer Science, Artificial Intelligence
Shushan Toneyan, Ziqi Tang, Peter K. Koo
Summary: This study introduces a unified evaluation framework and uses it to compare different binary and quantitative models for predicting chromatin accessibility data. The results show that quantitative modeling improves the generalizability and interpretability of the models, and a robustness metric is introduced to enhance model selection and variant effect predictions.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Chemistry, Multidisciplinary
Shengxi Chen, Xun Ji, Larisa M. Dedkova, Sidney M. Hecht
Summary: The NF-kappa B family of transcriptional activators is responsible for the expression of key genes controlling cell development and survival. The study found that site-specific phosphorylation of the p50 subunit can significantly increase CD40 expression, providing a potential target for cancer or viral immunotherapy.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Hyeonjin Park, Tun Naw Sut, Bo Kyeong Yoon, Vladimir P. Zhdanov, Jin Woong Kim, Nam-Joon Cho, Joshua A. Jackman
Summary: The size of ligand-modified lipid vesicles has a significant impact on their membrane bending properties, with a pronounced transition between 60 and 180 nm in diameter. These findings enhance our understanding of how nanoparticle size affects multivalent-induced shape deformation and can guide the design of biomimetic nanoparticles with tailored nanomechanical properties.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Jessica M. Halow, Rachel Byron, Megan S. Hogan, Raquel Ordonez, Mark Groudine, M. A. Bender, John A. Stamatoyannopoulos, Matthew T. Maurano
Summary: The study investigates the genetic effects on DNA accessibility in vivo across multiple cell and tissue types using highly diverged hybrid mice, providing a foundation for quantitatively predicting the cell-type specific effects of non-coding variation on TF activity.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sangwoo Park, Giovanni B. Brandani, Taekjip Ha, Gregory D. Bowman
Summary: Chromatin remodelers use a helicase-type ATPase motor to shift DNA and exhibit a sequence-dependent bias in nucleosome positioning, which is influenced by local DNA perturbations throughout the nucleosome footprint.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Jack Ferguson, Karen Campos-Leon, Ieisha Pentland, Joanne D. Stockton, Thomas Guenther, Andrew Beggs, Adam Grundhoff, Sally Roberts, Boris Noyvert, Joanna L. Parish
Summary: The study utilizes Nanopore RNA sequencing to investigate the function of CTCF in controlling HPV transcription, demonstrating that CTCF regulates viral transcription and splicing in the HPV lifecycle. CTCF plays a key role in differentiation-dependent late promoter activation, with binding at the E2 ORF facilitating viral transcript processing, indicating its importance in the HPV life cycle.
Article
Multidisciplinary Sciences
Kee-Beom Kim, Ashish Kabra, Dong-Wook Kim, Yongming Xue, Yuanjian Huang, Pei-Chi Hou, Yunpeng Zhou, Leilani J. Miranda, Jae-Il Park, Xiaobing Shi, Timothy P. Bender, John H. Bushweller, Kwon-Sik Park
Summary: EP300, an important transcription coactivator in proliferation and differentiation, is frequently mutated in various cancer types. This study found that EP300 mutants without acetyltransferase domain accelerate tumor development in small cell lung cancer (SCLC) mouse models, while complete EP300 knockout suppresses SCLC development and proliferation. The kinase inducible domain-interacting (KIX) domain of EP300, specifically its interaction with transcription factors including MYB, was identified as the determinant of protumorigenic activity. Inhibition of KIX-mediated interactions inhibits SCLC development and cell growth.
Article
Biochemistry & Molecular Biology
Yogesh Kalakoti, Swathik Clarancia Peter, Swaraj Gawande, Durai Sundar
Summary: This article presents a deep learning framework that can identify and characterize the upstream and downstream genetic elements related to TF-DNA binding and score them. The framework offers differences analysis of DNA context features for bound and unbound sequences and provides excellent interpretability to identify and annotate potential elements modulating TF-DNA binding.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, Jianlin Cheng
Summary: DeepGRN, utilizing a combination of single attention module and pairwise attention module, can accurately predict transcription factor binding sites and outperforms other methods in the ENCODE-DREAM challenge dataset. The attention weights learned by the model are correlated with informative inputs, providing possible explanations for the predictive improvements in DeepGRN.
BMC BIOINFORMATICS
(2021)
Article
Developmental Biology
Tina R. Lynch, Mingyu Xue, Cazza W. Czerniak, ChangHwan Lee, Judith Kimble
Summary: This study provides important insights into how DNA cis-regulatory elements impact stem cell regulation and gene expression by mutating these elements in the nematode C. elegans.
Article
Biochemistry & Molecular Biology
Wenmeng Wang, Shiyao Qiao, Guangyue Li, Jiahui Cheng, Cuicui Yang, Chen Zhong, Daniel B. Stovall, Jinming Shi, Chunbo Teng, Dangdang Li, Guangchao Sui
Summary: It has been discovered that YY1 can activate target gene expression by forming liquid-liquid phase separation condensates to assemble enhancers and super-enhancers. The histidine cluster in YY1's transactivation domain plays a crucial role in this process.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Carmen Paulmann, Ria Spallek, Oleksandra Karpiuk, Michael Heider, Isabell Schaeffer, Jana Zecha, Susan Klaeger, Michaela Walzik, Rupert Oellinger, Thomas Engleitner, Matthias Wirth, Ulrich Keller, Jan Kroenke, Martina Rudelius, Susanne Kossatz, Roland Rad, Bernhard Kuster, Florian Bassermann
Summary: This study identifies OTUD6B as a key oncogene in multiple myeloma, which stabilizes LIN28B and drives the G1/S transition. High expression of OTUD6B is associated with disease progression and adverse outcome in multiple myeloma.
Article
Plant Sciences
Robert H. Calderon, Jutta Dalton, Yu Zhang, Peter H. Quail
Summary: The study investigates the potential role of epigenetic chromatin modifications in regulating the response of plants to light signals. The results suggest that changes in chromatin modifications may buffer the rapid light-to-shade transitions in plant canopies. This research provides insights into the regulatory mechanisms underlying plant adaptation to light conditions.
Article
Multidisciplinary Sciences
Cheng Wang, Xiaoyan Dai, Shengnan Wu, Wenjing Xu, Ping Song, Kai Huang
Summary: Mitochondria-associated ER membranes (MAMs) regulated by FUNDC1 play a crucial role in angiogenesis by promoting the formation of functional blood vessels through VEGF-induced MAM formation. Targeting FUNDC1-dependent MAMs could be a potential therapeutic strategy for angiogenesis-related disorders in humans.
NATURE COMMUNICATIONS
(2021)
Review
Pediatrics
Aline Saliba, Ana Carolina Vaqueiro Figueiredo, Jose Eduardo Baroneza, Jorge Yuseff Afiune, Aline Pic-Taylor, Silviene Fabiana de Oliveira, Juliana Forte Mazzeu
JORNAL DE PEDIATRIA
(2020)
Article
Substance Abuse
Luciana Marangni Nolli, Danilo Gustavo Rodrigues de Oliveira, Stefany Sousa Alves, Marcus Vinicius von Zuben, Aline Pic-Taylor, Marcia Renata Mortari, Eloisa Dutra Caldas
Article
Pharmacology & Pharmacy
Sandra M. Mazutti da Silva, Ricardo Ferreira-Nunes, Clara R. Amore, Diegue H. N. Martins, Aline Pic-Taylor, Yris M. Fonseca-Bazzo, Damaris Silveira, Guilherme M. Gelfuso, Perola O. Magalhaes
JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY
(2020)
Article
Endocrinology & Metabolism
Camila Schoueri Colaco, Stefany Sousa Alves, Luciana Marangni Nolli, Willie Oliveira Pinheiro, Danilo Gustavo Rodrigues de Oliveira, Beatriz Werneck Lopes Santos, Aline Pic-Taylor, Marcia Renata Mortari, Eloisa Dutra Caldas
METABOLIC BRAIN DISEASE
(2020)
Letter
Genetics & Heredity
Patricia N. Moretti, Ana Carolina V. Figueiredo, Aline Saliba, Beatriz R. Versiani, Silviene F. Oliveira, Aline Pic-Taylor, Juliana F. Mazzeu
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2020)
Article
Cell Biology
Anne Clancy, Claire Heride, Adan Pinto-Fernandez, Hannah Elcocks, Andreas Kallinos, Katherine J. Kayser-Bricker, Weiping Wang, Victoria Smith, Simon Davis, Shawn Fessler, Crystal McKinnon, Marie Katz, Tim Hammonds, Neil P. Jones, Jonathan O'Connell, Bruce Follows, Steven Mischke, Justin A. Caravella, Stephanos Ioannidis, Christopher Dinsmore, Sunkyu Kim, Axel Behrens, David Komander, Benedikt M. Kessler, Sylvie Urbe, Michael J. Clague
Summary: When a ribosome stalls during translation, it may collide with a trailing ribosome, leading to the formation of a stable di-ribosome complex. This complex requires the activity of Makorin and ZNF598 ubiquitin E3 ligases for resolution, with the protein deubiquitylase USP9X regulating the abundance of these E3 ligases. In the absence of USP9X or following its inhibition, levels of Makorins and ZNF598 decrease, impacting the ribosomal quality control pathway.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Raphael Severino Bonadio, Larissa Barbosa Nunes, Patricia Natalia S. Moretti, Juliana Forte Mazzeu, Stefano Cagnin, Aline Pic-Taylor, Silviene Fabiana de Oliveira
Summary: The study analyzed the transcriptome of mouse brains after death in different environments and how these environments influenced post-mortem RNA abundance and biological processes.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Ana Caroline G. Goncalves, Patricia N. Moretti, Mara S. Cordoba, Renata S. Oliveira, Fernanda S. C. Lopes, Silviene F. Oliveira, Aline Pic-Taylor, Luiz Claudio Castro, Juliana F. Mazzeu
Summary: This article reports a case of SHORT syndrome in an individual from Brazil, with additional clinical features compared to the common characteristics. Diagnosis was confirmed through genetic sequencing and comparison with other reported cases helps in better understanding SHORT syndrome.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2022)
Article
Dermatology
S. Braz, R. A. Benicio, G. S. S. S. Tonelli, S. N. Bao, P. N. Moretti, A. Pic-Taylor, S. F. Oliveira, A. C. Acevedo, I. M. C. Costa, J. F. Mazzeu
CLINICAL AND EXPERIMENTAL DERMATOLOGY
(2022)
Review
Genetics & Heredity
Vanessa Sodre de Souza, Gabriela Corassa Rodrigues da Cunha, Beatriz R. Versiani, Claudiner Pereira de Oliveira, Maria Teresa Alves Silva Rosa, Silviene F. de Oliveira, Patricia N. Moretti, Juliana F. Mazzeu, Aline Pic-Taylor
Summary: WAGR syndrome is a contiguous gene deletion syndrome characterized by the joint deletion of PAX6 and WT1 genes. Analysis of deleted regions and phenotypic changes can contribute to a more accurate clinical characterization of the syndrome, emphasizing its broad phenotypic spectrum.
MOLECULAR SYNDROMOLOGY
(2022)
Article
Genetics & Heredity
Anna Karolina Silva Ramos, Erica Carine Campos Caldas-Rosa, Barbara Merfort Ferreira, Beatriz Ribeiro Versiani, Patricia Natalia Moretti, Silviene Fabiana de Oliveira, Aline Pic-Taylor, Juliana F. Mazzeu
Summary: The ZDHHC9 gene mutation leads to intellectual disabilities and symptoms such as low IQ, developmental delay, facial dysmorphisms, and skeletal defects. Although there are differences in clinical manifestations among different patients, intellectual disabilities and developmental delay are reported in all cases. These mutations mainly occur in the arginine residues located in the cytoplasmic domains of the protein and may be hotspot mutations.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Biochemistry & Molecular Biology
Anne Clancy, Emma V. Rusilowicz-Jones, Iona Wallace, Kirby N. Swatek, Sylvie Urbe, Michael J. Clague
Summary: Type 1 interferon stimulation leads to up-regulation of a ubiquitin-like conjugation system. USP18, a member of the deubiquitylase family, is up-regulated and can inhibit JAK-STAT signaling. USP18's role in cell viability and growth inhibition is not solely dependent on ISGylation activity.
BIOCHEMICAL JOURNAL
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
G. C. R. Cunha, M. V. Zuben, A. Lofrano-Porto, M. Soares, P. Moretti, R. S. Bonadio, S. F. De Oliveira, J. Mazzeu, A. Pic-Taylor
EUROPEAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Genetics & Heredity
Marcela D. Hanna, Patricia N. Moretti, Claudiner P. de Oliveira, Maria T. A. Rosa, Beatriz R. Versiani, Silviene F. de Oliveira, Aline Pic-Taylor, Juliana F. Mazzeu
MOLECULAR SYNDROMOLOGY
(2019)
Article
Genetics & Heredity
Halinna Dornelles-Wawruk, Romina Soledad Heredia, Milton R. de Paula-Junior, Maria Terezinha O. Cardoso, Raphael S. Bonadio, Bianca F. dos Reis, Aline Pic-Taylor, Silviene F. de Oliveira, Juliana F. Mazzee
MOLECULAR SYNDROMOLOGY
(2019)