Article
Biochemistry & Molecular Biology
Marc Kenneth M. Cajili, Eloise Prieto
Summary: This study investigated the role of archaeal architectural proteins Alba and Cren7 in chromatin folding and dynamics. The results showed that Alba can mediate the formation of folded DNA structures to regulate chromatin compaction, while Cren7 affects the formation of Alba-mediated higher-order chromatin structures.
Article
Biochemical Research Methods
Ke Yan, Jiawei Feng, Jing Huang, Hao Wu
Summary: Nucleic acid-binding proteins are important for regulating gene expression and transcriptional control. This study proposes a new method, iDRPro-SC, to accurately predict the type of nucleic acid-binding proteins based on sequence information. By considering internal differences and using ensemble learning, iDRPro-SC achieved better prediction performance than existing methods.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Soumen Pal, Ajit Gupta, Rajender Parsad
Summary: DNA-binding proteins (DBPs) are crucial in cellular processes, but existing computational techniques for identifying them have limited accuracy in plant species. This study developed a comprehensive computational model for predicting plant specific DBPs, using shallow learning methods that outperformed deep learning algorithms. The support vector machine achieved the highest accuracy, with 94.0% AUC-ROC and 93.5% AUC-PR. The developed approach showed higher accuracy compared to existing tools, making it more efficient and reliable for predicting DBPs in plants. A prediction server, PIDBPred, and source code are publicly accessible for convenience.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Soumen Pal, Ajit Gupta, Rajender Parsad
Summary: This study developed a computational model for predicting plant-specific DNA-binding proteins. The model achieved high accuracy using shallow learning methods, outperforming existing tools.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Wayne O. Hemphill, Calvin K. Voong, Regan Fenske, James A. Goodrich, Thomas R. Cech
Summary: We have demonstrated that the polycomb repressive complex 2 chromatin-modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. This direct transfer mechanism has been observed in several well-characterized nucleic acid-binding proteins, indicating its prevalence. The ability of proteins to conduct a one-dimensional search for their target sites through direct transfer may have important implications for understanding gene regulation and protein-ligand interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng, Yunjie Zhao
Summary: RNA-protein complexes play vital roles in various cellular processes. The authors develop a deep-learning-based method called DRPScore to identify native-like structures of RNA-protein complexes. DRPScore outperforms existing methods and shows significant improvements in accuracy, especially for unbound cases.
NATURE COMMUNICATIONS
(2023)
Review
Chemistry, Medicinal
Bidhan C. Dhar, Nathalie Steimberg, Giovanna Mazzoleni
Summary: The discovery of versatile engineered nucleic acid-binding proteins has revolutionized the field of gene editing, with CRISPR technology bringing about innovations in diagnostic platforms, and the transmission of adaptive immunity by CRISPR and Cas proteins driving advances in molecular biology.
Article
Biochemistry & Molecular Biology
Alyssa Kramer Morrow, John Weston Hughes, Jahnavi Singh, Anthony Douglas Joseph, Nir Yosef
Summary: Epitome is a deep neural network that achieves state-of-the-art accuracy in predicting transcription factor binding sites by learning chromatin accessibility similarities between reference cell types and a query cellular context, and copying over signals from reference cell types when chromatin profiles are similar. It can further improve predictions as more epigenetic signals are collected.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Shuanghong Yan, Liying Wang, Yuqin Wang, Zhenyuan Cao, Shanyu Zhang, Xiaoyu Du, Pingping Fan, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: This study demonstrates a barcode system based on self-assembly of synthetic nucleic acids and direct nanopore decoding. Each barcode is composed of multiple information nodes, which can be scanned and decoded sequentially. This system can be applied to detect various antibody proteins or cancer-related microRNAs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Cell Biology
Kathryn M. Stevens, Tobias Warnecke
Summary: Exchanging core histones in the nucleosome for paralogous variants can have important functional ramifications. Many of these variants and their physiological roles have been extensively studied in model eukaryotes, but our knowledge of histone biology in archaea, including histone variants, remains limited. Recent findings provide glimpses into the unknown world of archaeal histone biology, offering insights into chromatin organization and shedding light on the evolution of histone-based chromatin in eukaryotes.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hu Zhao, Zhuo Tu, Yinmeng Liu, Zhanxiang Zong, Jiacheng Li, Hao Liu, Feng Xiong, Jinling Zhan, Xuehai Hu, Weibo Xie
Summary: Characterizing regulatory effects of genomic variants in plants is a challenge. PlantDeepSEA is a deep learning-based web service designed to predict the regulatory effects of genomic variants in multiple tissues of six plant species. The tool includes two main functions, Variant Effector and Sequence Profiler, which can help discover high-impact sites in sequences.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Sophia Groh, Anna Viktoria Milton, Lisa Marinelli, Cara Sickinger, Angela Russo, Heike Bollig, Gustavo Pereira de Almeida, Andreas Schmidt, Ignasi Forne, Axel Imhof, Gunnar Schotta
Summary: Endogenous retroviruses (ERVs) make up a significant portion of mammalian genomes, and Morc3 has been identified as a key regulator of ERV silencing. Through interactions with the H3.3 chaperone Daxx, Morc3 plays a critical role in incorporating histone H3.3 into ERV regions.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
S. Mayo-Perez, Y. Gama-Martinez, S. Davila, N. Rivera, I. Hernandez-Lucas
Summary: This review focuses on the distribution, abundance, evolution, structural organization, transcriptional regulation, and fundamental roles of LysR-type transcriptional regulators (LTTRs) in bacteria, archaea, and algae. It also discusses their involvement in free life, pathogenesis, and bacteria-plant interaction, providing a current understanding of LTTR biology.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Fu-Yu Hung, Yuan-Hsin Shih, Pei-Yu Lin, Yun-Ru Feng, Chenlong Li, Keqiang Wu
Summary: WRKY63 acts as a dual regulator by directly activating FLC under non-vernalization conditions and indirectly repressing FLC during vernalization through inducing COOLAIR and COLDAIR. WRKY63 also activates the expression of COOLAIR and COLDAIR by binding to their promoters. The binding of WRKY63 is associated with increased vernalization-induced gene expression and decreased H3K27me3 levels, indicating its importance in vernalization-induced transcriptional regulation.
Article
Multidisciplinary Sciences
Chunlei Jiao, Sahil Sharma, Gaurav Dugar, Natalia L. Peeck, Thorsten Bischler, Franziska Wimmer, Yanying Yu, Lars Barquist, Christoph Schoen, Oliver Kurzai, Cynthia M. Sharma, Chase L. Beisel
Summary: The study found that tracrRNA hybridizing with cellular RNAs can lead to the formation of new crRNAs capable of guiding DNA targeting by Cas9. Reprogrammed tracrRNAs linking the presence of RNA of interest to DNA targeting were used in the LEOPARD diagnostic platform, allowing simultaneous detection of RNAs from different viruses in one test.
Article
Biochemical Research Methods
Jacquelyn Cafasso, Babu A. Manjasetty, Elizabeth A. Karr, Kathleen Sandman, Mark R. Chance, John N. Reeve
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2010)
Article
Microbiology
Elizabeth A. Karr, Kathleen Sandman, Rudi Lurz, John N. Reeve
JOURNAL OF BACTERIOLOGY
(2008)
Article
Biochemistry & Molecular Biology
Katrin Weidenbach, Jens Gloeer, Claudia Ehlers, Kathleen Sandman, John N. Reeve, Ruth A. Schmitz
MOLECULAR MICROBIOLOGY
(2008)
Article
Education, Scientific Disciplines
Kathleen Sandman, Christopher Ecker
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION
(2014)
Article
Microbiology
L'ubomira Cubonova, Kathleen Sandman, Elizabeth A. Karr, Andrew J. Cochran, John N. Reeve
JOURNAL OF BACTERIOLOGY
(2007)
Review
Microbiology
Kathleen Sandman, John N. Reeve
CURRENT OPINION IN MICROBIOLOGY
(2006)
Review
Microbiology
K Sandman, JN Reeve
CURRENT OPINION IN MICROBIOLOGY
(2005)
Article
Microbiology
L Cubonová, K Sandman, SJ Hallam, EF DeLong, JN Reeve
JOURNAL OF BACTERIOLOGY
(2005)
Article
Biochemistry & Molecular Biology
JN Reeve, KA Bailey, WT Li, F Marc, K Sandman, DJ Soares
BIOCHEMICAL SOCIETY TRANSACTIONS
(2004)
Article
Biochemistry & Molecular Biology
F Marc, K Sandman, R Lurz, JN Reeve
JOURNAL OF BIOLOGICAL CHEMISTRY
(2002)
Article
Biochemistry & Molecular Biology
KA Bailey, F Marc, K Sandman, JN Reeve
JOURNAL OF BIOLOGICAL CHEMISTRY
(2002)
Article
Biochemistry & Molecular Biology
K Sandman, D Soares, JN Reeve
Article
Biochemistry & Molecular Biology
K Decanniere, AM Babu, K Sandman, JN Reeve, U Heinemann
JOURNAL OF MOLECULAR BIOLOGY
(2000)
Article
Astronomy & Astrophysics
BC Christner, E Mosley-Thompson, LG Thompson, V Zagorodnov, K Sandman, JN Reeve