Review
Virology
Philipp Niklas Ostermann, Anastasia Ritchie, Johannes Ptok, Heiner Schaal
Summary: The study of HIV-1 gene expression has revealed a new form of nuclear export regulation, known as intrinsic RNA code. These findings provide important insights into understanding viral replication mechanisms.
JOURNAL OF VIROLOGY
(2021)
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Article
Biochemistry & Molecular Biology
Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz
Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Article
Plant Sciences
Kosuke Moriwaki, Shuichi Yanagisawa, Koh Iba, Juntaro Negi
Summary: In this study, two crucial cis-acting elements, 5'-CACGAGA-3 'and 5'-CACATGTTTCCC-3', were found to be essential for the guard cell-specific expression of SCAP1 and HT1. The findings reveal a novel transcriptional regulatory mechanism that synchronously promotes the expression of multiple genes required for stomatal maturation and function.
Article
Oncology
Ali S. Ropri, Rebecca S. DeVaux, Jonah Eng, Sridar Chittur, Jason Herschkowitz
Summary: Increased breast cancer screening has led to a rise in DCIS diagnosis, emphasizing the need to identify factors influencing DCIS progression to IDC. SE-lncRNAs, which can regulate nearby gene expression, represent novel therapeutic targets. Integrative analysis and cross-referencing with databases revealed differential expression of SE-lncRNAs and alterations in super-enhancers associated with breast cancer progression.
BREAST CANCER RESEARCH
(2021)
Article
Genetics & Heredity
Hiroki Hosoi, Akiko Niibori-Nambu, Giselle Sek Suan Nah, Avinash Govind Bahirvani, Michelle Meng Huang Mok, Takaomi Sanda, Alan Prem Kumar, Daniel G. Tenen, Yoshiaki Ito, Takashi Sonoki, Motomi Osato
Summary: The study demonstrates the crucial role of super-enhancers for the expression of RUNX3 and MYC in EBV-positive malignant B cells. The deletion of super-enhancers resulted in the downregulation of both genes, leading to suppressed cell proliferation and colony formation. These findings suggest that seR3s could be a potential therapeutic target for EBV-related tumors.
Article
Biotechnology & Applied Microbiology
Oguz Ulas Yaman, Beste Avci, Pinar Calik
Summary: Designing promoter architectures in yeast relies on genomic and functional annotations. This study introduces a curated pipeline for predicting cis-acting DNA sequences/sites (cADSs) in Saccharomyces cerevisiae. Using this pipeline and a scanning algorithm, the researchers were able to predict master transcription factors (TFs) and cADSs in Pichia pastoris, a yeast lacking extensive functional annotation studies. The methodology presented in this study provides a valuable tool for understanding gene regulation in yeasts.
BIOCHEMICAL ENGINEERING JOURNAL
(2022)
Article
Cell Biology
Eric D. Thomas, Andrew E. Timms, Sarah Giles, Sarah Harkins-Perry, Pin Lyu, Thanh Hoang, Jiang Qian, Victoria E. Jackson, Melanie Bahlo, Seth Blackshaw, Martin Friedlander, Kevin Eade, Timothy J. Cherry
Summary: Cis-regulatory elements (CREs) are crucial for the development and disease-states of human cell types, including the retina. This study used single-nucleus assay and sequencing techniques to characterize human retinal CREs in developing and adult retina as well as retinal organoids. The results provide insights into the dynamic nature of cell-specific CREs and their potential target genes, and confirm the function of a disease-associated CRE in neurogenesis and gene regulation.
DEVELOPMENTAL CELL
(2022)
Article
Plant Sciences
Eun-Deok Kim, Michael W. Dorrity, Bridget A. Fitzgerald, Hyemin Seo, Krishna Mohan Sepuru, Christine Queitsch, Nobutaka Mitsuda, Soon-Ki Han, Keiko U. Torii
Summary: This study presents an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, revealing the regulatory relationships between chromatin architecture, transcription factors, and cell-fate specification. The findings shed light on the mechanism by which specific heterotypic TF complexes recruit chromatin modifiers via key co-cis regulatory elements to facilitate cell-fate commitment.
Article
Multidisciplinary Sciences
Shuo Liu, Jiaqi Liu, Xue Yang, Minghong Jiang, Qingqing Wang, Lianfeng Zhang, Yuanwu Ma, Zhongyang Shen, Zhigang Tian, Xuetao Cao
Summary: Chemokine production by epithelial cells is crucial for neutrophil recruitment during viral infection, with the regulation being key to controlling inflammation. A newly discovered lncRNA named lnc-Cxcl2 selectively inhibits the expression of Cxcl2 in mouse lung epithelial cells but not in macrophages. This study highlights the importance of understanding the functional interactions of lncRNAs and RNA-binding proteins in regulating chemokine expression and inflammation during viral infections.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Bin Li, Yan Lu, Ming-Chao Zhong, Jin Qian, Rui Li, Dominique Davidson, Zhenghai Tang, Kaiwen Zhu, Jeremy Argenty, Anne Gonzalez de Peredo, Bernard Malissen, Romain Roncagalli, Andre Veillette
Summary: CD2 is essential for T cell activation on T cells, while its ligand CD48 is also required on T cells. During cytotoxicity, both CD48 on T cells and APCs are necessary. Fluorescence resonance energy transfer studies suggest cis interactions of CD2 with its ligands on T cells contribute to TCR signaling and T cell activation.
SCIENCE IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Greg L. Stewart, Adam P. Sage, Katey S. S. Enfield, Erin A. Marshall, David E. Cohn, Wan L. Lam
Summary: This study identified a cis-acting lncRNA, HMGA1-lnc, as significantly downregulated in lung adenocarcinoma and showed its negative regulatory effect on the oncogene HMGA1. In vitro experiments demonstrated that inhibition of HMGA1-lnc led to a significant increase in HMGA1 gene expression, suggesting the potential of HMGA1-lnc as a therapeutic target for HMGA1-driven tumors.
FRONTIERS IN GENETICS
(2021)
Article
Forestry
Yan-Min Wang, Yi-Ming Zhang, Xin Zhang, Xin Zhao, Yu Zhang, Chao Wang, Yu-Cheng Wang, Liu-Qiang Wang
Summary: PsnICE1 is a key gene in Xiaohei poplar that plays a positive role in cold tolerance by regulating the expression of cold stress-responsive genes. Its overexpression enhances tolerance to cold stress, while silencing of PsnICE1 results in reduced cold tolerance. PsnICE1 binds to specific elements to regulate stress-related genes involved in ROS scavenging, making it a potential candidate for improving plant cold tolerance through molecular breeding.
Article
Agronomy
Long Zhang, Yanzhou Qi, Mingming Wu, Lei Zhao, Zhichao Zhao, Cailin Lei, Yuanyuan Hao, Xiaowen Yu, Yinglun Sun, Xin Zhang, Xiuping Guo, Yulong Ren, Jianmin Wan
Summary: This study identified the P-type PPR protein PPR5 in rice as crucial for mitochondrial function and endosperm development, by controlling the cis-splicing of mitochondrial nad4 intron 3. Loss of PPR5 function resulted in decreased ATP production, upregulation of alternative oxidases expression, and abnormal mitochondrial morphology, impacting starch and protein content in the endosperm.
Article
Biochemistry & Molecular Biology
Yu Yamamoto, Osamu Miura, Takashi Ohyama
Summary: The study reveals that cruciform structures present in the Pou5f1 enhancer in mice play a crucial role in maintaining the integrity of ES cells and regulating the transcription of key genes involved in pluripotency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
