Article
Biochemistry & Molecular Biology
Kumari Kavita, Aixia Zhang, Chin-Hsien Tai, Nadim Majdalani, Gisela Storz, Susan Gottesman
Summary: Hfq, a bacterial RNA chaperone, plays a crucial role in stabilizing small regulatory RNAs and facilitating their interactions with target mRNAs. Deletion of the C-terminal domain in Hfq leads to defects in the accumulation and function of various sRNAs, particularly those that bind to the distal face. The region between amino acids 66-72 is essential for this defect, while the CTD region beyond amino acid 72 is important for functions associated with the Hfq rim.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Dahong Chen, Catherine E. McManus, Behram Radmanesh, Leah H. Matzat, Elissa P. Lei
Summary: The study suggests that the Drosophila chromatin insulator antagonist Shep represses gene expression during neuronal maturation by preventing E-P looping. Through chromatin conformation capture and reporter assays, two enhancer regions were identified to increase in looping frequency with the brat promoter specifically in pupal brains after Shep depletion, indicating temporal regulation of chromatin looping and enhancer accessibility during neuronal maturation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
David H. Tse, Nicole A. Becker, Robert T. Young, Wilma K. Olson, Justin P. Peters, Tanya L. Schwab, Karl J. Clark, L. James Maher
Summary: Architectural proteins can alter the shape of DNA, either relieving strain in tightly-bent structures or facilitating DNA looping. The study designed and tested artificial architectural proteins based on TALE proteins or fused with HMGB domain, showing evidence of stiffening DNA to inhibit looping or enhancing looping by bending DNA without introducing twisting flexibility. These findings provide insight into manipulating DNA geometry with functional consequences, offering potential applications in tuning the stability of small DNA loops in eukaryotes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Bo Zhao, Yanpeng Xi, Junghyun Kim, Sibum Sung
Summary: The study explored a group of linker histone-like proteins named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators to promote the floral transition and repress FLC gene expression. These family members preferentially bind to the 5' and 3' ends of gene bodies, and the loss of this binding increases FLC expression by stabilizing the FLC 5' to 3' gene looping. This study provides insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.
Article
Immunology
Yi Zhong, Sarah K. Walker, Yuri Pritykin, Christina S. Leslie, Alexander Y. Rudensky, Joris van der Veeken
Summary: Zhong et al. studied the transcriptional regulation of T cell gene expression upon viral challenge using B6/Cast F1 hybrid mice. They found that members of Ets, Runx, and TCF/Lef transcription factor families play key roles in maintaining or increasing chromatin accessibility during T cell activation. Some highly induced immune response genes exhibit a noncanonical TF recruitment pattern.
Article
Biochemistry & Molecular Biology
Chelsea L. Blankenchip, Justin Nguyen, Rebecca K. Lau, Qiaozhen Ye, Yajie Gu, Kevin D. Corbett
Summary: Bacteria utilize diverse immune systems to defend against viruses, with the transcription factor CapW associated with regulating the CBASS bacterial immune system response. CapW represses CBASS gene expression in uninfected cells and its activation is not necessary for strong anti-phage activity, suggesting it may play a role in response to signals other than phage infection. CapW is part of a family of universal defense signaling proteins, similar to the BrxR transcription factor associated with the BREX anti-phage system.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Fredy Kurniawan, Neha Chetlangia, Mohammad Kamran, Christophe E. Redon, Lorinc Pongor, Qinyu Sun, Yo-Chuen Lin, Vijay Mohan, Oways Shaqildi, Darya Asoudegi, Qinyu Hao, Abid Khan, Mirit Aladjem, Kannanganattu Prasanth, Supriya G. Prasanth
Summary: BEND3, a quadruple BEN domain-containing protein, is highly expressed in pluripotent cells and plays a crucial role in regulating chromatin function and transcription repression, thereby contributing to normal development and preventing differentiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Kangwen Xu, Long Lin, Danyu Shen, Shan-Ho Chou, Guoliang Qian
Summary: The review summarizes the mechanisms through which Clp, a CRP-like protein, initiates a mobile-attack strategy in Lysobacter enzymogenes against fungal pathogens, including binding to DNA in a unique pattern, interacting directly with small molecules or responding to them, and specific interactions with proteins adopting distinct structures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Immunology
Fangwei Leng, Wenxiang Zhang, Ricardo N. Ramirez, Juliette Leon, Yi Zhong, Lifei Hou, Koichi Yuki, Joris van der Veeken, Alexander Y. Rudensky, Christophe Benoist, Sun Hur
Summary: It has been discovered that FoxP3 can exist in two different dimerization forms, head-to-head dimerization and swap dimerization, with the former being associated with functional specificity and the latter being associated with functional impairment.
Article
Biochemistry & Molecular Biology
Nan Hao, Adrienne E. Sullivan, Keith E. Shearwin, Ian B. Dodd
Summary: The study developed a quantitative in vivo assay for DNA-looping proteins in Escherichia coli, using basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, inserting two binding sites for the candidate looping protein into a pair of operators for the E. coli LacI repressor.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Hadeel Khamis, Sergei Rudnizky, Philippa Melamed, Ariel Kaplan
Summary: This study introduces a novel single-molecule assay utilizing DNA hairpin thermal fluctuations to detect the binding and dissociation of individual transcription factors. The research demonstrates that both binding and dissociation processes are modulated by the core motif and surrounding sequences, while CpG methylation can also impact dissociation kinetics. These findings highlight how variations in sequence and methylation patterns synergistically extend a protein's binding properties.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Xingcheng Lin, Rachel Leicher, Shixin Liu, Bin Zhang
Summary: This study utilized various techniques to elucidate the structure of Polycomb repressive complex 2 (PRC2) and its interactions with DNA, confirming that PRC2 binds to DNA in multiple ways, forming a loop-like configuration.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Zhihao Wang, Hongliang Wang, Nancy Mulvenna, Maximo Sanz-Hernandez, Peipei Zhang, Yanqing Li, Jia Ma, Yawen Wang, Steve Matthews, Sivaramesh Wigneshweraraj, Bing Liu
Summary: Proteins mimic DNA to occupy DNA binding sites, preventing further access. The phage protein Gp44 employs this strategy to inhibit host RNA polymerase, leading to bacterial growth inhibition. This non-specific strategy may have potential applications in developing genetically engineered phages for phage therapy targeting a range of bacterial hosts.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Cell Biology
Yu Zhang, Wanyu Wang, Jiali Min, Suosi Liu, Qianrong Wang, Yu Wang, Yang Xiao, Xia Li, Zhiguang Zhou, Shanshan Liu
Summary: The expression of ZNF451 is upregulated in triple-negative breast cancer (TNBC) and is associated with a poor prognosis. ZNF451 enhances TNBC progression by interacting with and enhancing the activity of the transcriptional activator SLUG. Disturbing the ZNF451-SLUG interaction can suppress TNBC progression by reducing CCL5 expression and counteracting the migration and activation of tumor-associated macrophages.
Article
Biochemistry & Molecular Biology
Rebecca K. Lau, Eray Enustun, Yajie Gu, Justin Nguyen, Kevin D. Corbett
Summary: Bacteria have evolved diverse immune systems to protect themselves from phage infection. Researchers have discovered a transcriptional regulator module associated with hundreds of CBASS immune systems and demonstrated its role in driving the expression of the CBASS system in response to DNA damage. This finding highlights a mechanism by which bacterial immune systems can sense and respond to cellular stress.