Article
Genetics & Heredity
Jack R. Bateman, Justine E. Johnson
Summary: In Drosophila, pairing of maternal and paternal homologs allows for trans-interactions between enhancers and promoters, known as transvection. This study investigates the parameters that govern promoter competition in transvection. The results show that the linear spacing between an enhancer and promoter can influence promoter competition, with larger distances leading to decreased activation. Additionally, increasing the spacing between the enhancer and promoter enhances transvection, resulting in increased activation of a promoter on a paired homolog.
Article
Multidisciplinary Sciences
Ye Hyun Hwang, Bruce Eliot Hayward, Marwa Zafarullah, Jay Kumar, Blythe Durbin Johnson, Peter Holmans, Karen Usdin, Flora Tassone
Summary: This study evaluated somatic mosaicism in a large cohort of female premutation carriers and found that 94% displayed evidence of somatic instability. The extent of somatic expansion was directly related to the number of CGG repeats in the originally inherited allele and inversely related to the number of AGG interruptions. Furthermore, expansions were progressive and positively correlated with age.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Elin Enervald, Lynn Marie Powell, Lora Boteva, Rossana Foti, Nerea Blanes Ruiz, Gozde Kibar, Agnieszka Piszczek, Fatima Cavaleri, Martin Vingron, Andrea Cerase, Sara B. C. Buonomo
Summary: In the process of X chromosome choice in mice, RIF1 and KAP1 play fundamental roles, with the mutual exclusion between Tsix and RIF1, as well as between RIF1 and KAP1, establishing a self-sustaining loop that transforms the initial stochastic event into a stably inherited asymmetric X-chromosome state.
Article
Developmental Biology
Saya Ichihara, Koji Nagao, Takehisa Sakaguchi, Chikashi Obuse, Takashi Sado
Summary: Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 plays an important role in this process by facilitating the formation of H3K9me3-enriched blocks on the Xi, which in combination with H3K27me3, leads to robust heterochromatin formation. Deficiency of SmcHD1 results in the loss of H3K9me3, causing aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.
Article
Microbiology
Timothy Notton, Joshua J. Glazier, Victoria R. Saykally, Cassandra E. Thompson, Leor S. Weinberger
Summary: The method introduced comprehensively maps viral cis and trans elements at single-nucleotide resolution through high-throughput random deletion, identifying essential elements in HIV and Zika virus. It provides a versatile framework for generating viral deletion mutants, aiding in the discovery of replication mechanisms and development of novel antiviral therapeutics for emerging viral infections.
Article
Multidisciplinary Sciences
Jaime Alvarez-Benayas, Nikolaos Trasanidis, Alexia Katsarou, Kanagaraju Ponnusamy, Aristeidis Chaidos, Philippa C. May, Xiaolin Xiao, Marco Bua, Maria Atta, Irene A. G. Roberts, Holger W. Auner, Evdoxia Hatjiharissi, Maria Papaioannou, Valentina S. Caputo, Ian M. Sudbery, Anastasios Karadimitris
Summary: Multiple myeloma is a genetically heterogeneous cancer driven by overexpression of specific oncogenes. By analyzing chromatin accessibility and transcriptome profiles, researchers have identified distinct genetic subgroups within multiple myeloma and uncovered unique gene regulatory networks that contribute to the disease. This study highlights the importance of understanding the transcriptional landscape in driving multiple myeloma progression and identifying potential therapeutic targets.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Sarah Lauren Svensson, Cynthia Mira Sharma
Summary: Bacterial small RNAs (sRNAs) play important roles as post-transcriptional regulators in stress responses and virulence. RNase III is involved in processing a pair of cis-encoded sRNAs in Campylobacter jejuni, where CJnc190 and CJnc180 interact with each other and impact the regulation of the colonization factor PtmG.
Article
Biochemistry & Molecular Biology
Marko Rodewald, J. Mikko Rautiainen, Helmar Goerls, Raija Oilunkaniemi, Wolfgang Weigand, Risto S. Laitinen
Summary: A new platinum complex was synthesized and its crystal structure was analyzed. It was found that the ligand undergoes isomerization and forms a dynamic equilibrium during the dissolution process. Two other platinum complexes were also successfully synthesized and their structures were characterized. The bonding and formation of these complexes were further discussed through theoretical calculations.
Article
Multidisciplinary Sciences
Ami Shah, Madison Ratkowski, Alessandro Rosa, Paul Feinstein, Thomas Bozza
Summary: The study reveals that TAAR gene expression requires two cooperative cis-acting enhancers, deletion of either one or both elements can affect the expression of TAAR genes, and the similarity exists in the expression mechanisms between ORs and TAARs.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Tannia Uribe-Calvillo, Laetitia P. Maestroni, Marie-Claude Marsolier, Basheer P. Khadaroo, Christine Arbiol, Jonathan P. Schott, Bertrand Llorente
Summary: Break-induced replication (BIR) is a highly mutagenic DNA repair pathway that is most efficient near chromosome ends. The efficiency of ectopic BIR is affected by the length of DNA to replicate and is characterized by repeated cycles of strand invasion, elongation, and dissociation. The processivity of ectopic BIR is dependent on the length of DNA already synthesized. Additionally, the Srs2 helicase promotes ectopic BIR in diploid cells but only in telomere proximal sites in haploid cells.
Article
Genetics & Heredity
Shuang Liu, Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu, Daifeng Wang, Mark Gerstein
Summary: This study investigates the transcriptional regulatory structure of the human brain, revealing the coordination of both cis- and trans-regulatory variants. By analyzing large datasets, the researchers identified candidate trans-eQTLs that influence the expression of target genes and found overlap with known cis-eQTLs. Through colocalization and mediation analyses, they identified mediators in trans-regulation and linked trans-eQTLs to schizophrenia risk genes. The findings demonstrate the importance of trans-regulatory mechanisms in understanding psychiatric disorders.
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)
Article
Multidisciplinary Sciences
Ke Xiao, Dan Xiong, Gong Chen, Jinsong Yu, Yue Li, Kening Chen, Lu Zhang, Yangyang Xu, Qian Xu, Xi Huang, Anran Gao, Kai Cao, Keji Yan, Jinxia Dai, Xueying Hu, Yijun Ruan, Zhenfang Fu, Guoliang Li, Gang Cao
Summary: This study demonstrates a genome-wide trans-species chromatin interaction between pseudorabies virus (PRV) and host cells, where the viral genome is delivered into the open and active chromatin zone by the host DNA binding protein RUNX1. This facilitates viral gene transcription by hijacking host transcription machinery, a process significantly inhibited by either a RUNX1 inhibitor or RNA interference. These findings provide insights into herpesvirus genome transcription and suggest new research directions in this area.
Article
Biochemistry & Molecular Biology
Steffen Erkelenz, Gereon Poschmann, Johannes Ptok, Lisa Mueller, Heiner Schaal
Summary: By combining transcriptomics with functional splicing reporter assays, researchers have found that GT>GC>TT are the top three dinucleotides of human 5'ss. U1 snRNP binding to functional 5'ss prevents DNA damage response components from binding to RNA, indicating a close link between spliceosome arrangement and genome stability. All tested noncanonical 5'ss have been shown to be bona-fide targets of the U2-type spliceosome, and internal GT at positions +5/+6 may be advantageous for splicing at noncanonical splice sites.
Article
Biochemistry & Molecular Biology
Franz Waibl, Klaus R. Liedl, Bernhard Rupp
Summary: Many macromolecular structure models in the PDB contain biologically relevant small molecule ligands with incorrect cis-trans stereochemistry. The errors may stem from deficiencies in stereochemical restraint files or negligence during model building. Awareness, identification, and correction of these errors are crucial to prevent inadvertent use of incorrect models.
Article
Oncology
Yufeng Zhao, Hai Zhang, Aili Yan, Juanxia Zhu, Ke Liu, Di Chen, Rong Xie, Xi Xu, Xingli Su
MOLECULAR MEDICINE REPORTS
(2018)
Article
Medicine, Research & Experimental
Yu-Feng Zhao, Feng Jiang, Xiang-Yan Liang, Lan-Lan Wei, Yan-Yan Zhao, Qiong Ma, Yun-Sheng Hu, Xing-Li Su
BIOMEDICINE & PHARMACOTHERAPY
(2018)
Article
Pharmacology & Pharmacy
Yufeng Zhao, Lei Zhang, Aili Yan, Di Chen, Rong Xie, Yingguang Liu, Xiangyan Liang, Yanyan Zhao, Lanlan Wei, Jun Yu, Xi Xu, Xingli Su
BMC PHARMACOLOGY & TOXICOLOGY
(2018)
Article
Endocrinology & Metabolism
Yu-Feng Zhao, Jianming Pei, Chen Chen
JOURNAL OF ENDOCRINOLOGY
(2008)
Article
Endocrinology & Metabolism
Li Wang, Yufeng Zhao, Baosong Gui, Rongguo Fu, Feng Ma, Jun Yu, Ping Qu, Lei Dong, Chen Chen
JOURNAL OF ENDOCRINOLOGY
(2011)
Article
Multidisciplinary Sciences
Yufeng Zhao, Li Wang, Jianhua Qiu, Dingjun Zha, Qiang Sun, Chen Chen
Article
Anatomy & Morphology
Yufeng Zhao, Dingjun Zha, Li Wang, Li Qiao, Lianjun Lu, Lin Mei, Chen Chen, Jianhua Qiu
Article
Biotechnology & Applied Microbiology
Xing-Li Su, Ying-Guang Liu, Man Shi, Yan-Yan Zhao, Xiang-Yan Liang, Li-Jun Zhang, Lan-Lan Wei, Yu-Feng Zhao
BIOMED RESEARCH INTERNATIONAL
(2020)
Article
Biochemistry & Molecular Biology
Yan-Yan Zhao, Li-Jun Zhang, Xiang-Yan Liang, Xiao-Chun Zhang, Jin-Rui Chang, Man Shi, Huan Liu, Ying Zhou, Zhuo Sun, Yu-Feng Zhao
Summary: Pyruvate activates PDEs to reduce cAMP levels and inhibits the cAMP-Epac-CREB signaling pathway, resulting in upregulation of FGF21 expression in hepatocytes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Medicinal
Xi Xu, Xiaochun Zhang, Yanyan Zhao, Xiangyan Liang, Lijun Zhang, Yu-Feng Zhao
Summary: This study showed that PQQ has protective effects against thrombin-induced cell death in astrocytes by inhibiting oxidative stress and improving mitochondrial function.
NATURAL PRODUCT COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Zhuo Sun, Jinbo Fan, Yang Wang
Summary: X-chromosome inactivation (XCI) is a mechanism in mammalian female cells to balance the expression levels of X-linked genes. Many diseases are associated with XCI, and their severity and symptoms largely depend on the status of XCI. This review discusses different types of diseases, their definitions, symptoms, and the role of XCI in their pathogenesis.
Article
Endocrinology & Metabolism
Yu-Feng Zhao, Li Wang, Soohyun Lee, Qiang Sun, Ya Tuo, Yuemin Wang, Jianming Pei, Chen Chen
Article
Endocrinology & Metabolism
Dan-Dan Feng, Yu-Feng Zhao, Zi-Qiang Luo, Damien J. Keating, Chen Chen
JOURNAL OF ENDOCRINOLOGY
(2008)