Article
Agronomy
Deshui Yu, Renchun Fan, Ling Zhang, Pengya Xue, Libing Liao, Meizhen Hu, Yanjun Cheng, Jine Li, Ting Qi, Shaojuan Jing, Qiuyun Wang, Arvind Bhatt, Qian-Hua Shen
Summary: Plants have a sophisticated immune system that detects pathogen infection and activates immune responses. HvWRKY2 acts as a repressor in barley disease resistance to the powdery mildew fungus. However, the molecular features of HvWRKY2 in its DNA-binding and repressor functions, as well as its target genes, are unknown.
Review
Biochemistry & Molecular Biology
Stefano Amatori, Mirco Fanelli
Summary: Epigenomic aberrations in cancer cells play a role in cancer initiation and progression. Formalin fixation and paraffin embedding (FFPE) is widely used to preserve tissue integrity, and new chromatin immunoprecipitation (ChIP) techniques allow analysis of histone post-translational modifications and transcription factor distribution in FFPE tissues. However, the variability in fixation and storage conditions of clinical specimens can affect the success of ChIP studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Thierry Delaveau, Antonin Thiebaut, Medine Benchouaia, Jawad Merhej, Frederic Devaux
Summary: This study revealed the interactions among CBC, Hap4 and Yap5 in Candida glabrata, showing that Yap5 regulation requires specific promoter sequences, and there is competition between Hap4 and Yap5 at the promoter of iron tolerance genes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Priyanka Barman, Amala Kaja, Pritam Chakraborty, Sukesh R. Bhaumik
Summary: Proteins are expressed through transcription, mRNA processing, export and translation, and their interactions with other proteins, DNAs or RNAs play a crucial role in maintaining cellular functions. Studying protein interactions in living cells is important for understanding their mechanisms-of-action in real time. One state-of-the-art approach is formaldehyde crosslinking-based immuno- or chemi-precipitation, which is widely used for analyzing protein-protein and protein-nucleic acid interactions in cellular analysis.
Article
Virology
Gary Z. Wang, Stephen P. Goff
Summary: This study reveals the essential role of p12 protein in tethering viral DNA to host chromatin to allow loading of histones onto the viral DNA. Mutants lacking tethering activity fail to acquire histones, retain capsid and nucleocapsid proteins, and are poorly transcribed, defining a new requirement for a viral protein in chromatinization of viral DNA.
JOURNAL OF VIROLOGY
(2021)
Article
Clinical Neurology
Dulika Sumathipala, Petter Stromme, Zohreh Fattahi, Torben Luders, Ying Sheng, Kimia Kahrizi, Ingunn Holm Einarsen, Jennifer L. Sloan, Hossein Najmabadi, Lambert van den Heuvel, Ron A. Wevers, Sergio Guerrero-Castillo, Lars Morkrid, Vassili Valayannopoulos, Paul Hoff Backe, Charles P. Venditti, Clara D. van Karnebeek, Hilde Nilsen, Eirik Frengen, Doriana Misceo
Summary: Mutations in the ZBTB11 gene are associated with intellectual disability. The study found that patients with ZBTB11 mutations showed atrophy in multiple brain regions and had malonic and methylmalonic aciduria as disease markers. In vitro experiments indicated that ZBTB11 regulates mitochondrial functions and RNA processing.
Article
Biochemistry & Molecular Biology
Meghan V. Petrie, Yiwei He, Yan Gan, Andrew Zachary Ostrow, Oscar M. Aparicio
Summary: Chromatin ImmunoPrecipitation (ChIP) is a widely used method for studying protein-DNA interactions, but it suffers from false-positive signal enrichment. We developed a new approach to control for non-specific enrichment in ChIP by co-expressing a non-genome-binding protein with the experimental target protein and using the shared epitope tags. This method improves data quality by normalizing the experimental data with the ChIP signal of the non-specific protein, and has been successfully validated with known binding sites of multiple proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Niamat Khan, Sidra Shahid, Abdul R. Asif
Summary: Chromatin is a dynamic structure consisting of DNA and proteins, playing key roles in DNA packaging, gene expression regulation, and DNA protection. Studying chromatin-associated proteins can enhance our understanding of disease pathophysiology and aid in designing new drugs.
Article
Multidisciplinary Sciences
Gilles Maussion, Rhalena A. Thomas, Iveta Demirova, Gracia Gu, Eddie Cai, Carol X-Q Chen, Narges Abdian, Theodore J. P. Strauss, Sabah Kelai, Angela Nauleau-Javaudin, Lenore K. Beitel, Nicolas Ramoz, Philip Gorwood, Thomas M. Durcan
Summary: This article introduces the open-source Python software Auto-qPCR for automated processing of qPCR data, saving time and improving the systematic approach to data analysis. The software supports multiple data processing modes, simplifying the complex data analysis workflow.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
William K. M. Lai, Luca Mariani, Gerson Rothschild, Edwin R. Smith, Bryan J. Venters, Thomas R. Blanda, Prashant K. Kuntala, Kylie Bocklund, Joshua Mairose, Sarah N. Dweikat, Katelyn Mistretta, Matthew J. Rossi, Daniela James, James T. Anderson, Sabrina K. Phanor, Wanwei Zhang, Zibo Zhao, Avani P. Shah, Katherine Novitzky, Eileen McAnarney, Michael-C Keogh, Ali Shilatifard, Uttiya Basu, Martha L. Bulyk, B. Franklin Pugh
Summary: This study generated over a thousand renewable monoclonal antibodies against human presumptive chromatin proteins, with about 5% of antibodies showing high-confidence target enrichment and 34% producing distinct ChIP-exo data. The remaining 61% may require broader surveys of cell types or assay optimizations for further consideration.
Article
Biochemistry & Molecular Biology
Shinnosuke Ueda, Hiroyuki Mizuta, Toshiki Uji
Summary: A ChIP method with modifications has been developed in the red macroalga Neopyropia yezoensis, enabling the identification of histone marks in generation-specific genes. The results show that the acetylation of histone H3 remains relatively high even in generation-repressed gene expression.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jing Yang, Leilei Qi, Huai-Chin Chiang, Bin Yuan, Rong Li, Yanfen Hu
Summary: BRCA1 is a tumor suppressor frequently mutated in familial breast and ovarian cancer patients. Many commercial antibodies targeting BRCA1 are poorly characterized, leading to unreliable data. By rigorously validating several commercially available anti-BRCA1 antibodies, researchers identified specific antibodies with high performance, aiming to improve understanding of BRCA1 functions and combat challenges associated with antibody specificity and reproducibility.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Mai Nhu Uyen Le, Yichong Ning, Jianlin Zhou
Summary: The tumor suppressor gene p53 acts as a transcription factor and is commonly mutated in human cancers, especially triple negative breast cancer (TNBC). Mutations in the TP53 gene mainly occur in exons 5-8, resulting in changes in the DNA-binding domain of the p53 protein. A chromatin immunoprecipitation followed by DNA microarray (ChIP-chip) experiment was performed to identify target genes and binding motifs of the mutated p53 protein.
Article
Biochemistry & Molecular Biology
Ha T. H. Vu, Yudi Zhang, Geetu Tuteja, Karin S. Dorman
Summary: The ATAC-seq assay uses a Tn5 transposase to identify chromatin accessible regions by cutting and ligating adapters to DNA fragments, followed by amplification and sequencing. Traditional peak calling methods suffer from elevated false positive rates, while supervised deep learning methods require high quality labeled data. In this study, a novel peak caller called replicative contrastive learner (RCL) is proposed, which uses unsupervised contrastive learning to extract shared signals from multiple replicates. RCL consistently outperformed other methods on ATAC-seq data.
Article
Biotechnology & Applied Microbiology
Ariel Caride, Jin Sung Jang, Geng-Xian Shi, Sam Lenz, Jian Zhong, Kwan Hyun Kim, Mariet Allen, Keith D. Robertson, Gianrico Farrugia, Tamas Ordog, Nilufer Ertekin-Taner, Jeong-Heon Lee
Summary: Chromatin immunoprecipitation (ChIP) is a commonly used antibody-based method in chromatin biology and epigenetics. This study introduces a simple and quick method to quantify chromatin inputs and optimize antibody amounts for ChIP reactions, resulting in improved assay outcomes.
Article
Cell & Tissue Engineering
Joong-Hyun Shim, JongHyun Kim, Jiyou Han, Su Yeon An, Yu Jin Jang, Jeongsang Son, Dong-Hun Woo, Suel-Kee Kim, Jong-Hoon Kim
CELL TRANSPLANTATION
(2015)
Article
Biochemistry & Molecular Biology
Andrey N. Kuzmichev, Suel-Kee Kim, Ana C. D'Alessio, Josh G. Chenoweth, Ina M. Wittko, Loraine Campanati, Ronald D. McKay
Article
Biochemistry & Molecular Biology
Jung-Eun Gil, Dong-Hun Woo, Joong-Hyun Shim, Sung-Eun Kim, Hyun-Ju You, Sung-Hye Park, Sun Ha Paek, Suel-Kee Kim, Jong-Hoon Kim
Article
Gastroenterology & Hepatology
Dong-Hun Woo, Suel-Kee Kim, Hee-Joung Lim, Jeonghoon Heo, Hyung Soon Park, Gum-Yong Kang, Sung-Eun Kim, Hyun-Ju You, Daniel J. Hoeppner, Youngchul Kim, Heechung Kwon, Tae Hyun Choi, Joo Hee Lee, Su Hee Hong, Kang Won Song, Eun-Kyung Ahn, Josh G. Chenoweth, Paul J. Tesar, Ronald D. G. McKay, Jong-Hoon Kim
Article
Biochemistry & Molecular Biology
Hee-Joung Lim, Jiyou Han, Dong-Hun Woo, Sung-Eun Kim, Suel-Kee Kim, Hee-Gyoo Kang, Jong-Hoon Kim
MOLECULES AND CELLS
(2011)
Article
Cell & Tissue Engineering
Joong Yull Park, Suel-Kee Kim, Dong-Hun Woo, Eun-Joong Lee, Jong-Hoon Kim, Sang-Hoon Lee
Article
Engineering, Biomedical
Jong Hyun Kim, Bo Gi Park, Suel-Kee Kim, Dong-Hyun Lee, Gyung Gyu Lee, Doek-Ho Kim, Byung-Ok Choi, Kyu Back Lee, Jong-Hoon Kim
ACTA BIOMATERIALIA
(2019)
Article
Multidisciplinary Sciences
Ji Yeon Kim, Hye Young Lim, Sang Eon Shin, Hyo Kyeong Cha, Jeong-Han Seo, Suel-Kee Kim, Seong Hwan Park, Gi Hoon Son
Article
Multidisciplinary Sciences
Emily E. Burke, Joshua G. Chenoweth, Joo Heon Shin, Leonardo Collado-Torres, Suel-Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni, Richard E. Straub, Daniel J. Hoeppner, Huei-Ying Chen, Alana Sellers, Kamel Shibbani, Gregory R. Hamersky, Marcelo Diaz Bustamante, BaDoi N. Phan, William S. Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J. Price, Anandita Rajpurohit, Stephen A. Semick, Roland W. Burli, James C. Barrow, Daniel J. Hiler, Stephanie C. Page, Keri Martinowich, Thomas M. Hyde, Joel E. Kleinman, Karen F. Berman, Jose A. Apud, Alan J. Cross, Nicholas J. Brandon, Daniel R. Weinberger, Brady J. Maher, Ronald D. G. McKay, Andrew E. Jaffe
NATURE COMMUNICATIONS
(2020)
Article
Cell Biology
Nicola Micali, Suel-Kee Kim, Marcelo Diaz-Bustamante, Genevieve Stein-O'Brien, Seungmae Seo, Joo-Heon Shin, Brian G. Rash, Shaojie Ma, Yanhong Wang, Nicolas A. Olivares, Jon Arellano, Kristen R. Maynard, Elana J. Fertig, Alan J. Cross, Roland W. Burli, Nicholas J. Brandon, Daniel R. Weinberger, Joshua G. Chenoweth, Daniel J. Hoeppner, Nenad Sestan, Pasko Rakic, Carlo Colantuoni, Ronald D. McKay
Article
Neurosciences
Phan Q. Duy, Stefan C. Weise, Claudia Marini, Xiao-Jun Li, Dan Liang, Peter J. Dahl, Shaojie Ma, Ana Spajic, Weilai Dong, Jane Juusola, Emre Kiziltug, Adam J. Kundishora, Sunil Koundal, Maysam Z. Pedram, Lucia A. Torres-Fernandez, Kristian Haendler, Elena De Domenico, Matthias Becker, Thomas Ulas, Stefan A. Juranek, Elisa Cuevas, Le Thi Hao, Bettina Jux, Andre M. M. Sousa, Fuchen Liu, Suel-Kee Kim, Mingfeng Li, Yiying Yang, Yutaka Takeo, Alvaro Duque, Carol Nelson-Williams, Yonghyun Ha, Kartiga Selvaganesan, Stephanie M. Robert, Amrita K. Singh, Garrett Allington, Charuta G. Furey, Andrew T. Timberlake, Benjamin C. Reeves, Hannah Smith, Ashley Dunbar, Tyrone DeSpenza, June Goto, Arnaud Marlier, Andres Moreno-De-Luca, Xin Yu, William E. Butler, Bob S. Carter, Evelyn M. R. Lake, R. Todd Constable, Pasko Rakic, Haifan Lin, Engin Deniz, Helene Benveniste, Nikhil S. Malvankar, Juvianee Estrada-Veras, Christopher A. Walsh, Seth L. Alper, Joachim L. Schultze, Katrin Paeschke, Angelika Doetzlhofer, F. Gregory Wulczyn, Sheng Chih Jin, Richard P. Lifton, Nenad Sestan, Waldemar Kolanus, Kristopher T. Kahle
Summary: This study reveals a neuroprogenitor-based genetic subtype of human hydrocephalus with defective neurogenesis and altered brain-fluid biomechanics. By analyzing genomic and transcriptomic data of 483 patients with congenital hydrocephalus, the study identifies a group of risk genes that converge in embryonic neuroepithelial stem cells. Mutations in these genes lead to premature neuroepithelial cell differentiation and reduced neurogenesis, resulting in the development of hydrocephalus. This research highlights the importance of precisely regulated neuroepithelial cell fate for normal brain-CSF biomechanics and provides insights into the genetic mechanisms behind hydrocephalus.
NATURE NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
David Andrijevic, Zvonimir Vrselja, Taras Lysyy, Shupei Zhang, Mario Skarica, Ana Spajic, David Dellal, Stephanie L. Thorn, Robert B. Duckrow, Shaojie Ma, Phan Q. Duy, Atagun U. Isiktas, Dan Liang, Mingfeng Li, Suel-Kee Kim, Stefano G. Daniele, Khadija Banu, Sudhir Perincheri, Madhav C. Menon, Anita Huttner, Kevin N. Sheth, Kevin T. Gobeske, Gregory T. Tietjen, Hitten P. Zaveri, Stephen R. Latham, Albert J. Sinusas, Nenad Sestan
Summary: Researchers have developed a technology called OrganEx that can maintain tissue integrity, reduce cell death, and restore molecular and cellular processes in multiple vital organs in a pig's whole body. Single-nucleus transcriptomic analysis revealed gene expression patterns specific to organ and cell type, reflecting specific molecular and cellular repair processes. This study reveals the underappreciated potential for cellular recovery after prolonged whole-body warm ischemia in large mammals.
Article
Multidisciplinary Sciences
Nicola Micali, Shaojie Ma, Mingfeng Li, Suel-Kee Kim, Xoel Mato-Blanco, Suvimal Kumar Sindhu, Jon I. Arellano, Tianliuyun Gao, Mikihito Shibata, Kevin T. Gobeske, Alvaro Duque, Gabriel Santpere, Nenad Sestan, Pasko Rakic
Summary: This study provides a detailed analysis of early telencephalic development in primates, revealing the molecular programs of early organizing centers and their interaction with neural stem cells (NSCs). The study also identifies regional transcriptomic variations and highlights the potential role of genes associated with neuropsychiatric disorders and brain cancer risk in early telencephalic development and NSC progression.
Article
Cell & Tissue Engineering
Hyun-Ju You, Jiyou Han, Dong-Hun Woo, Su Yeon An, Jong Hyun Kim, Yu Jin Jang, Jeong Sang Son, Suel-Kee Kim, Jong-Hoon Kim
TISSUE ENGINEERING AND REGENERATIVE MEDICINE
(2011)