Article
Plant Sciences
Abhinandan Mani Tripathi, Rajneesh Singh, Ashwani Kumar Verma, Akanksha Singh, Parneeta Mishra, Varun Dwivedi, Shiv Narayan, Vivek Hari Sundar Gandhivel, Pramod Arvind Shirke, Padubidri V. V. Shivaprasad, Sribash Roy
Summary: This study demonstrates the cascade silencing caused by miR158 deletion in Himalayan Arabidopsis thaliana, leading to the failure of gene expression involved in stomatal opening and transpiration regulation.
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
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
Plant Sciences
Linlin Luo, Xiaoyu Yang, Mingxi Guo, Ting Lan, Yu Yu, Beixin Mo, Xuemei Chen, Lei Gao, Lin Liu
Summary: This study systematically characterized TAS3 siRNAs in rice and identified target genes for both tasiR-ARFs and non-tasiR-ARF siRNAs. Experimental confirmation of siRNA-target interactions revealed the regulatory role of ribosomes in these interactions, particularly in rice polysome samples. Overall, the study sheds light on TAS3 genes in plants and expands knowledge about rice TAS3 siRNA-target interactions.
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.
Article
Biochemistry & Molecular Biology
Hari Priya Parameshwaran, Kesavan Babu, Christine Tran, Kevin Guan, Aleique Allen, Venkatesan Kathiresan, Peter Z. Qin, Rakhi Rajan
Summary: The study on the BH variant of Cas12a from Francisella novicida reveals the role of the bridge helix in substrate selectivity, affecting both RNA-guided DNA cleavage in cis-activity and trans-single-stranded DNA cleavage activity. This highlights the conservation of the bridge helix in target discrimination among Cas nucleases.
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
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.
Review
Chemistry, Medicinal
Song Zhang, Zhujun Cheng, Yanan Wang, Tianyu Han
Summary: The progress of miRNA drugs in clinical trials is slow due to the characteristic of targeting multiple genes, leading to inevitable adverse effects.
DRUG DESIGN DEVELOPMENT AND THERAPY
(2021)
Review
Plant Sciences
Junpeng Zhan, Blake C. Meyers
Summary: Plant cells accumulate small RNA molecules that regulate plant development, genome stability, and environmental responses. These small RNAs fall into three major classes-microRNAs, heterochromatic small interfering RNAs, and secondary small interfering RNAs-plus several other less well-characterized categories, and their biogenesis mechanisms, targets, modes of action, and functions have been extensively studied in Arabidopsis and other plant species, contributing to a better understanding of plant small RNA biology.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
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)
Review
Biochemistry & Molecular Biology
David Zapletal, Karel Kubicek, Petr Svoboda, Richard Stefl
Summary: RNase III Dicer plays important biological roles in eukaryotes by generating small RNAs for sequence-specific regulations. RNA interference (RNAi) and microRNA (miRNA) pathways are the major Dicer-dependent mechanisms, which produce distinct types of small RNAs. Structural analyses of animal and plant Dicers have revealed the contributions of different domains to substrate recognition and cleavage, highlighting the ancestral role of siRNA generation and the derived features of miRNA biogenesis. The functional divergence is mainly attributed to a RIG-I-like helicase domain, while the dsRNA-binding domain showcases the impressive functional versatility in Dicer-mediated small RNA biogenesis.
Article
Biochemistry & Molecular Biology
Yao Xiao, TingYu M. Liu, Ian J. MacRae
Summary: Argonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) to regulate gene expression. The functional distinction between AGOs in plants and animals depends on a minor structural difference in the PIWI domain. Swapping a 9-amino acid loop in the PIWI domain can alter the targeting properties and silencing efficiency of AGO proteins.
Article
Oncology
Ana Maria Salinas-Montalvo, Aroon Supramaniam, Nigel A. J. McMillan, Adi Idris
Summary: This review discusses novel RNA-based therapies for HPV-driven cancers, including gene therapy and short-interfering RNA, and explores the potential of microRNAs, long non-coding RNAs, and mRNA vaccines as future treatment modalities. Some of these technologies have been approved for clinical use in other diseases but not for HPV cancers.
