Article
Biochemistry & Molecular Biology
Katarina Wang, Marah Maayah, Joann B. Sweasy, Khadijeh S. Alnajjar
Summary: 8-Oxoguanine glycosylase (OGG1) is a base excision repair enzyme responsible for recognition and removal of oxidized DNA modifications. Its function is sensitive to oxidants, with cysteine residues playing a crucial role in its structure and function, falling into four functional categories.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Matthew Dyer, Quy Xiao Xuan Lin, Sofiia Shapoval, Denis Thieffry, Touati Benoukraf
Summary: MethMotif is a publicly available database that provides a comprehensive repository of transcription factor-binding profiles with DNA methylation patterns. The latest release includes over 700 position weight matrices, segregated based on their cofactors and DNA methylation status. The database also offers precomputed GO annotations for human TFs and TF-co-TF complexes, allowing for a comprehensive analysis of TF functions in their context with cofactors. Furthermore, MethMotif has been expanded to include data for two additional species, increasing its applicability and value to the scientific community.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Luqian Zheng, Jingjing Liu, Lijie Niu, Mohammad Kamran, Ally W. H. Yang, Arttu Jolma, Qi Dai, Timothy R. Hughes, Dinshaw J. Patel, Long Zhang, Supriya G. Prasanth, Yang Yu, Aiming Ren, Eric C. Lai
Summary: In this study, the researchers investigated how BEN factors identify their targets in humans by characterizing several mammalian BEN domain factors. They provided structural insights into sequence-specific DNA binding by these BEN proteins. The findings expand the understanding of BEN factors' DNA recognition activities and shed light on the mechanism of sequence-specific DNA binding by mammalian BEN proteins.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Paola Pellanda, Mattia Dalsass, Marco Filipuzzi, Alessia Loffreda, Alessandro Verrecchia, Virginia Castillo Cano, Hugo Thabussot, Mirko Doni, Marco J. Morelli, Laura Soucek, Theresia Kress, Davide Mazza, Marina Mapelli, Marie-Eve Beaulieu, Bruno Amati, Arianna Sabo
Summary: Eukaryotic transcription factors have both specific DNA sequence motif recognition and non-specific DNA-binding activity. Non-specific DNA binding is essential for engaging with genomic regulatory regions, while sequence recognition contributes to transcriptional activation by stabilizing Myc onto DNA and unexpectedly promoting its transcriptional activity. The seemingly pervasive genome interaction profiles detected by ChIP-seq actually encompass diverse DNA-binding modes driving defined, sequence-dependent transcriptional responses.
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Migle Tomkuvien, Markus Meier, Diana Ikasalaite, Julia Wildenauer, Visvaldas Kairys, Saulius Klimasauskas, Laura Manelyt
Summary: Methylation of cytosine is an important epigenetic mark that can alter DNA and chromatin structure. This study investigates how larger chemical variations in DNA affect chromatin structure and nucleosome formation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yuko Hasegawa, Kevin Struhl
Summary: The transcription factor SP1 exhibits varying binding dynamics at different target sites in the human genome, potentially influenced by factors such as location and cobinding factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Yizhao Luan, Zehua Tang, Yao He, Zhi Xie
Summary: In this study, evidence was provided showing that coevolving residues in TF domains contribute to DNA binding specificity. It was demonstrated that the coevolving residues are more likely to coevolve with other TF subclass-determining sites and mutation of these coevolving residues could significantly reduce the stability of the TF-DNA complex. Overall, this study expands our understanding of the interaction among coevolving residues in TFs and their importance in transcriptional regulation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Genetics & Heredity
Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J. Najm, Yuanyuan Zhang, Molly M. Moore, Vivian Hecht, Noam Shoresh, Bradley E. Bernstein
Summary: The use of targeted nanopore sequencing allowed researchers to analyze chromatin accessibility and DNA methylation on contiguous DNA molecules, leading to the identification of gene regulatory elements such as promoters, enhancers, insulators, and transcription factor binding sites. They also inferred relationships among dynamic elements within immune loci and determined the order of remodeling events during T cell stimulation. Additionally, they phased primary sequences and regulatory elements across the H19/IGF2 locus, revealing primate-specific features and a mechanism that overrides IGF2 imprinting in human cells.
Article
Biochemical Research Methods
Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello
Summary: GRAFIMO is a command-line tool for scanning known TF DNA motifs in VGs, extending the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG, recovering additional potential binding sites than scanning only the reference genome.
PLOS COMPUTATIONAL BIOLOGY
(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
Plant Sciences
Renan Pardal, Ben Scheres, Renze Heidstra
Summary: Plant development relies on asymmetric cell division and fate segregation, which are crucial for cellular diversity. Mutations in the SCZ gene in Arabidopsis result in fate segregation defects in the roots, leading to the presence of an additional endodermis layer, root hairs growing from subepidermal tissue, and abnormal expression of tissue identity markers. The SCZ protein, a class B HEAT-SHOCK TRANSCRIPTION FACTOR, is found to act as a nonmotile transcriptional repressor, with its DNA-binding domain playing a major role in developmental function. This study demonstrates the evolution of HSF family members in acquiring functions beyond stress response.
Article
Biochemistry & Molecular Biology
Zeynep Kalender Atak, Ibrahim Ihsan Taskiran, Jonas Demeulemeester, Christopher Flerin, David Mauduit, Liesbeth Minnoye, Gert Hulselmans, Valerie Christiaens, Ghanem-Elias Ghanem, Jasper Wouters, Stein Aerts
Summary: This study introduces a deep learning model called DeepMEL2 that outperforms conventional motif-based scoring models in capturing regulatory programs in melanoma cells. It identifies hundreds to thousands of allele-specific chromatin accessibility variants in melanoma genomes, with some attributed to changes in transcription factor binding sites.
Article
Multidisciplinary Sciences
Elizabeth D. Larson, Hideyuki Komori, Tyler J. Gibson, Cyrina M. Ostgaard, Danielle C. Hamm, Jack M. Schnell, Cheng-Yu Lee, Melissa M. Harrison
Summary: The pioneer transcription factor Zelda plays a crucial role in reprogramming germ cells during early Drosophila embryo development. Research further demonstrates that Zelda promotes undifferentiated stem-cell fate in the larval brain, and its ability to define cis-regulatory regions is influenced by cell-type-specific chromatin architecture. It is proposed that Zelda regulates essential transitions in neuroblasts and embryos through a shared gene-regulatory network driven by cell-type-specific enhancers.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Rachel Waymack, Mario Gad, Zeba Wunderlich
Summary: Transgenic reporters are valuable tools for studying enhancers, but they may inhibit the expression of other genes. Competition for transcription factors is thought to be partially responsible for this inhibition of gene expression.
Review
Biochemistry & Molecular Biology
Sylvia Varland, Joel Vandekerckhove, Adrian Drazic
TRENDS IN BIOCHEMICAL SCIENCES
(2019)
Article
Biology
Jirka Peschek, Peter Walter
Article
Biotechnology & Applied Microbiology
Laura Heinisch, Katharina Zoric, Maike Krause, Herbert Schmidt
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Food Science & Technology
Maike Krause, Katharina Sessler, Anna Kaziales, Richard Grahl, Sabrina Noettger, Holger Barth, Herbert Schmidt
Article
Multidisciplinary Sciences
Grzegorz Rebowski, Malgorzata Boczkowska, Adrian Drazic, Rasmus Ree, Marianne Goris, Thomas Arnesen, Roberto Dominguez
Article
Biochemistry & Molecular Biology
Rasmus Ree, Laura Kind, Anna Kaziales, Sylvia Varland, Minglu Dai, Klaus Richter, Adrian Drazic, Thomas Arnesen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Toxicology
Katharina Sessler, Panagiotis Papatheodorou, Fanny Wondany, Maike Krause, Sabrina Noettger, Denise Bernhard, Jens Michaelis, Herbert Schmidt, Holger Barth
Summary: The study found that in the absence of SubB, SubA is internalized into the endoplasmic reticulum (ER) and cleaves the chaperone GRP78, leading to cytotoxic effects. By analyzing a SubA mutant, the C-terminal SEEL motif was identified as an ER-targeting signal.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Philipp W. N. Schmid, Nicole C. H. Lim, Carsten Peters, Katrin C. Back, Benjamin Bourgeois, Franz Pirolt, Bettina Richter, Jirka Peschek, Oliver Puk, Oana V. Amarie, Claudia Dalke, Martin Haslbeck, Sevil Weinkauf, Tobias Madl, Jochen Graw, Johannes Buchner
Summary: Analysis of lenses from different mouse strains with early-onset cataracts due to mutations in alpha-, beta-, or gamma-crystallin proteins reveals that the mutant crystallins are unstable in vitro, reduced in levels within the lens, and do not accumulate in the water-insoluble fraction. Precipitation of other crystallin proteins, including alpha-crystallins, suggests that imbalance in the lenticular proteome and altered crystallin interactions are the basis for cataract formation, rather than the aggregation propensity of the mutant crystallins.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Biochemical Research Methods
Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Adrian Drazic, Sylvia Varland
Summary: N-terminal acetylation is a common protein modification with biological and clinical significance. The NatC complex is a major NAT enzyme crucial for the proper functioning of its substrates. Yeast cells lacking NAA30 exhibit growth defects under stress conditions, highlighting the evolutionary conservation of NAA30 function.
BIOSCIENCE REPORTS
(2021)
Article
Food Science & Technology
Laura Heinisch, Maike Krause, Astrid Roth, Holger Barth, Herbert Schmidt
Summary: AB(5) protein toxins consist of an enzymatically active A-subunit and a B-subunit pentamer, with B-subunit responsible for toxin uptake into target cells. Contrary to traditional belief, some toxins like SubAB can intoxicate cells with A-subunit alone, without the need for B-subunit. The study suggests that the A-subunit of Stx2a, StxA2a, can also be toxic on its own in different cells.
Article
Biology
Weihan Li, Kelly Crotty, Diego Garrido Ruiz, Mark Voorhies, Carlos Rivera, Anita Sil, R. Dyche Mullins, Matthew P. Jacobson, Jirka Peschek, Peter Walter
Summary: The study demonstrates the functional specialization of Ire1's RNase activity, which is determined by the protomer alignment at the dimer interface, and this alteration affects the substrate specificity.
Article
Biochemistry & Molecular Biology
Adrian Drazic, Evy Timmerman, Ulrike Kajan, Michael Marie, Sylvia Varland, Francis Impens, Kris Gevaert, Thomas Arnesen
Summary: Actin is a crucial protein in the cytoskeleton of eukaryotic cells, and its dynamics are regulated by various actin-binding proteins and post-translational modifications. This study provides detailed insights into the N-terminal processing of actin and challenges the previously claimed N-terminal arginylation of beta-actin.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Janina L. Gerber, Sandra Koehler, Jirka Peschek
Summary: This review summarizes the mechanism of eukaryotic tRNA splicing and highlights the recent advances in structural research that have shaped our understanding of this process. It also emphasizes the different strategies for exon-exon ligation in fungi versus metazoans.
BIOLOGICAL CHEMISTRY
(2022)
Article
Biology
G. Elif Karagoz, Jirka Peschek, Peter Walter, Diego Acosta-Alvear