Article
Biochemistry & Molecular Biology
Jordan D. Pritts, Abdulafeez A. Oluyadi, Weiliang Huang, Geoffrey D. Shimberg, Maureen A. Kane, Angela Wilks, Sarah L. J. Michel
Summary: CPSF30 is a zinc finger protein that regulates pre-mRNA processing by recognizing AU hexamers and U-rich motifs. Variations within these sequences can impact polyadenylation efficiency or be linked to diseases. The presence of adenine and uracil residues in flanking regions promotes higher-affinity CPSF30/RNA binding.
Article
Microbiology
Michael J. Holmes, Leah R. Padgett, Matheus S. Bastos, William J. Sullivan
Summary: Toxoplasma gondii utilizes m6A methylation to modify its mRNA transcripts, which is essential for parasite replication and proper mRNA 3'-end formation. The m6A epitranscriptome machinery identified in Toxoplasma may provide new targets for anti-parasitic drug therapies.
Article
Plant Sciences
Taotao Wang, Wenbin Ye, Jiaxiang Zhang, Han Li, Weike Zeng, Sheng Zhu, Guoli Ji, Xiaohui Wu, Liuyin Ma
Summary: High-salt stress induces global alternative polyadenylation (APA) dynamics in Spartina alterniflora, leading to 3'UTR lengthening of transcripts and increased protein synthesis. These alternative 3'UTRs are mainly enriched in salt stress-related ion transporters, such as SaHKT1. Regulatory AU-rich elements in alternative 3'UTRs enhance the protein level of SaHKT1, and the biogenesis of 3'UTR lengthening in SaHKT1 is controlled by SaCPSF30. Over-expression of SaHKT1 with an alternative 3'UTR in rice protoplasts promotes the mRNA accumulation of salt-tolerance genes.
Review
Cell Biology
Prakash Dharmalingam, Rajasekaran Mahalingam, Hari Krishna Yalamanchili, Tingting Weng, Harry Karmouty-Quintana, Ashrith Guha, Rajarajan A. Thandavarayan
Summary: Research has shown that alternative cleavage and polyadenylation (APA) play a crucial role in the pathogenesis of various human diseases, leading to dysfunctional gene regulation and abnormal cell proliferation. While the functions of the core APA machinery and its role in disease conditions remain largely unknown, the mechanism of APA has become a hot topic in disease research.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ana Fiszbein, Michael McGurk, Ezequiel Calvo-Roitberg, GyeungYun Kim, Christopher B. Burge, Athma A. Pai
Summary: Messenger RNA isoform differences are mainly driven by alternative first, internal, and last exons. A recent study identified hybrid exons, which are enriched in long genes and genes involved in RNA splicing, and showed their usage varies considerably across human tissues. The HIT pipeline was developed to classify exons and reveal the common occurrence of hybrid exons in the human transcriptome.
Article
Cell Biology
Ananthanarayanan Kumar, Conny W. H. Yu, Juan B. Rodriguez-Molina, Xiao-Han Li, Stefan M. V. Freund, Lori A. Passmore
Summary: The translation provided describes a detailed study of the essential subunit Fip1 in the CPF/CPSF multiprotein complex, revealing the importance of its dynamics in coordinating cleavage and polyadenylation processes at the 3' end.
GENES & DEVELOPMENT
(2021)
Article
Medicine, Research & Experimental
Eric Rovira, Beatriz Moreno, Nerea Razquin, Roland Hjerpe, Monika Gonzalez-Lopez, Rosa Barrio, Igor Ruiz de los Mozos, Jernej Ule, Fernando Pastor, Lorea Blazquez, Puri Fortes
Summary: This study reveals a new regulatory role of U1A in increasing gene expression by directly recruiting target transcripts. U1A not only affects key cellular processes such as cell cycle and adhesion but also shows potential as a therapeutic target for cancer treatment. The findings suggest that U1A-binding sequences should be considered in biotechnological applications.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Biochemistry & Molecular Biology
Miguel Barquin, Ian U. Kouzel, Beat Ehrmann, Michael Basler, Andreas J. Gruber
Summary: This study presents a single cell-based Terminal Exon Annotation database (scTEA-db), which provides yet unannotated terminal exons and associated transcript isoforms for studying their biological role in cell identity and function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Jia Jia Chan, Bin Zhang, Xiao Hong Chew, Adil Salhi, Zhi Hao Kwok, Chun You Lim, Ng Desi, Nagavidya Subramaniam, Angela Siemens, Tyas Kinanti, Shane Ong, Avencia Sanchez-Mejias, Phuong Thao Ly, Omer An, Raghav Sundar, Xiaonan Fan, Shi Wang, Bei En Siew, Kuok Chung Lee, Choon Seng Chong, Bettina Lieske, Wai-Kit Cheong, Yufen Goh, Wee Nih Fam, Melissa G. Ooi, Bryan T. H. Koh, Shridhar Ganpathi Iyer, Wen Huan Ling, Jianbin Chen, Boon-Koon Yoong, Rawisak Chanwat, Glenn Kunnath Bonney, Brian K. P. Goh, Weiwei Zhai, Melissa J. Fullwood, Wilson Wang, Ker-Kan Tan, Wee Joo Chng, Yock Young Dan, Jason J. Pitt, Xavier Roca, Ernesto Guccione, Leah A. Vardy, Leilei Chen, Xin Gao, Pierce K. H. Chow, Henry Yang, Yvonne Tay
Summary: This study systematically reveals the role of 3' UTR splicing in cancer, finding its widespread presence in various types of cancer and its correlation with poor prognosis. Inhibiting 3' UTR splicing can effectively reduce oncogene expression and impede tumor progression, providing new directions for RNA-based anti-cancer therapeutics.
NATURE CELL BIOLOGY
(2022)
Article
Cell Biology
Vytaute Boreikaite, Thomas S. Elliott, Jason W. Chin, Lori A. Passmore
Summary: In this study, the researchers reconstituted the 3' endonuclease activity of human CPSF and identified the protein factors required for this activity. They found that the activation and site-specific pre-mRNA cleavage by CPSF are tightly controlled. The results suggest that fidelity in mRNA processing is maintained through precise regulation of CPSF activity.
GENES & DEVELOPMENT
(2022)
Article
Biology
Masahiro Nakano, Yukihiko Sugita, Noriyuki Kodera, Sho Miyamoto, Yukiko Muramoto, Matthias Wolf, Takeshi Noda
Summary: Nakano et al. utilize high-speed AFM and cryo-EM to investigate the structure of influenza A virus vRNPs during RNA synthesis, revealing two distinct types of vRNP structures associated with newly synthesized RNAs: an intact, helical structure and a deformed structure.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alina Chakraborty, Mandy Cadix, Sebastien Relier, Nicolo Taricco, Tina Alaeitabar, Alexandre Devaux, Celine M. Labbe, Sylvain Martineau, Amelie Heneman-Masurel, Pierre Gestraud, Alberto Inga, Nicolas Servant, Stephan Vagner, Martin Dutertre
Summary: This study reveals differential regulation of intronic polyadenylation (IPA) isoform ratio across subcellular compartments during drug response, suggesting distinct patterns of IPA isoform regulation in the transcriptome and translatome, as well as between the nucleus and cytosol.
Article
Multidisciplinary Sciences
Shani Hadar, Anatoly Meller, Naseeb Saida, Reut Shalgi
Summary: Exposure to certain stresses leads to readthrough transcription, which has an important impact on cellular stress response. This study found that readthrough transcription can extend into downstream genes, and these read-in genes have common genomic characteristics, such as GC-richness and short length. Moreover, read-in genes show significant intron retention, which is not solely related to their intron length and GC content. Additionally, H3K36me3 is enriched upstream of read-in genes.
Article
Biochemistry & Molecular Biology
Phaedra Winstanley-Zarach, Gregor Rot, Shweta Kuba, Aibek Smagul, Mandy J. J. Peffers, Simon R. R. Tew
Summary: Polyadenylation (polyA) defines the 3' boundary of a transcript's genetic information. Alternative polyadenylation (APA) transcripts can exist for a gene, causing variance in regulatory domains and potential coding sequence changes. This study analyzed the polyA site distribution in healthy and osteoarthritic knee articular chondrocytes and found modest differential use of polyadenylation sites between the two conditions, suggesting potential functional relevance in affected genes. This characterization of polyadenylation landscape contributes to understanding the role of polyA in knee osteoarthritis, distinguishing it from other pathologies such as cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Peizhe Song, Junbo Yang, Chunling Wang, Qiang Lu, Linqing Shi, Subiding Tayier, Guifang Jia
Summary: This study reveals that CPSF30-L acts as an m(6)A reader in plants, with its m(6)A-binding function playing a crucial role in the floral transition and ABA response; The m(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies and prolongs the untranslated regions of specific transcripts, leading to late flowering and ABA hypersensitivity.
Article
Microbiology
Gah-Hyun Lim, M. B. Shine, Laura de Lorenzo, Keshun Yu, Weier Cui, Duroy Navarre, Arthur G. Hunt, Jung-Youn Lee, Aardra Kachroo, Pradeep Kachroo
CELL HOST & MICROBE
(2016)
Article
Multidisciplinary Sciences
Stephen A. Bell, Chi Shen, Alishea Brown, Arthur G. Hunt
Article
Plant Sciences
Manohar Chakrabarti, Randy D. Dinkins, Arthur G. Hunt
Article
Biochemistry & Molecular Biology
Laura de Lorenzo, Reed Sorenson, Julia Bailey-Serres, Arthur G. Hunt
Article
Biotechnology & Applied Microbiology
Xiaohui Wu, Bobby Gaffney, Arthur G. Hunt, Qingshun Q. Li
Letter
Education, Scientific Disciplines
Vincent Buonaccorsi, Mark Peterson, Gina Lamendella, Jeff Newman, Nancy Trun, Tammy Tobin, Andres Aguilar, Arthur Hunt, Craig Praul, Deborah Grove, Jim Roney, Wade Roberts
CBE-LIFE SCIENCES EDUCATION
(2014)
Review
Plant Sciences
Arthur G. Hunt
CURRENT OPINION IN PLANT BIOLOGY
(2014)
Article
Biochemical Research Methods
Liuyin Ma, Pratap Kumar Pati, Man Liu, Qingshun Q. Li, Arthur G. Hunt
Article
Biochemistry & Molecular Biology
Patrick E. Thomas, Xiaohui Wu, Man Liu, Bobby Gaffney, Guoli Ji, Qingshun Q. Li, Arthur G. Hunt
Article
Multidisciplinary Sciences
Man Liu, Ruqiang Xu, Carrie Merrill, Liwei Hong, Carol Von Lanken, Arthur G. Hunt, Qingshun Q. Li
Article
Multidisciplinary Sciences
Ashley T. Stevens, Daniel K. Howe, Arthur G. Hunt
Article
Multidisciplinary Sciences
Manohar Chakrabarti, Randy D. Dinkins, Arthur G. Hunt
SCIENTIFIC REPORTS
(2018)
Article
Plant Sciences
Barbara Tellez-Robledo, Concepcion Manzano, Angela Saez, Sara Navarro-Neila, Javier Silva-Navas, Laura de Lorenzo, Mary-Paz Gonzalez-Garcia, Rene Toribio, Arthur G. Hunt, Roberto Baigorri, Ilda Casimiro, Siobhan M. Brady, M. Mar Castellano, J. Carlos del Pozo
Article
Plant Sciences
Jingyi Cao, Congting Ye, Guijie Hao, Carole Dabney-Smith, Arthur G. Hunt, Qingshun Q. Li
FRONTIERS IN PLANT SCIENCE
(2019)
Review
Biochemistry & Molecular Biology
Manohar Chakrabarti, Arthur G. Hunt