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Multidisciplinary Sciences
Agnieszka Tudek, Pawel S. Krawczyk, Seweryn Mroczek, Rafal Tomecki, Matti Turtola, Katarzyna Matylla-Kulinska, Torben Heick Jensen, Andrzej Dziembowski
Summary: RNA polyadenosine tails, crucial for mRNA stability and translation, vary in length depending on mutations in yeast exonuclease, deadenylase, and poly(A) polymerase. The study demonstrates the impact of poly(A) tails on mRNA and ncRNA functions, highlighting their responses to growth conditions.
NATURE COMMUNICATIONS
(2021)
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.
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Biochemistry & Molecular Biology
Dylan J. Kiltschewskij, Paul F. Harrison, Chantel Fitzsimmons, Traude H. Beilharz, Murray J. Cairns
Summary: Differentiation of neural progenitor cells into mature neuronal phenotypes relies on extensive temporospatial coordination of mRNA expression. Cleavage and polyadenylation of mRNA has regulatory capacity through the alteration of mRNA stability and modulation of miRNA function. Our findings suggest poly(A) tail length and APA function as part of a rich post-transcriptional regulatory matrix during neuronal differentiation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Xinhong Liu, Ziwei Guo, Jing Han, Bo Peng, Bin Zhang, Haitao Li, Xiaoyu Hu, Charles J. David, Mo Chen
Summary: The PAF1 complex plays a crucial role in the termination of enhancer RNAs and promoter upstream transcripts, facilitating timely cleavage and transcription termination. PAF1C also recruits Integrator complex to coding genes and dissociates from Integrator after processive elongation.
Article
Biochemistry & Molecular Biology
Lina Hamouche, Leonora Poljak, Agamemnon J. Carpousis
Summary: Rifampicin treatment causes a decrease in cell size and total RNA content in E. coli, primarily due to a decrease in 23S and 16S rRNA levels. While rRNA degradation is not complete, growth can be reinitiated after removal of rifampicin. Analysis of mutant strains suggests RNase E, PNPase, and RNase R are involved in rifampicin-induced rRNA degradation, potentially impacting mRNA degradation rates as well.
Article
Multidisciplinary Sciences
Xavier Contreras, David Depierre, Charbel Akkawi, Marina Srbic, Marion Helsmoortel, Maguelone Nogaret, Matthieu LeHars, Kader Salifou, Alexandre Heurteau, Olivier Cuvier, Rosemary Kiernan
Summary: Pervasive transcription of the human genome generates an abundance of RNAs that are processed and degraded by the nuclear RNA exosome. This study identifies additional subunits of PAXT and reveals the association of PAP gamma with PAXT, providing insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
NATURE COMMUNICATIONS
(2023)
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)
Review
Biochemistry & Molecular Biology
Federica A. Falchi, Roberto Pizzoccheri, Federica Briani
Summary: This paper reviews the structure, RNA binding, and catalytic activity of hPNPase, as well as its functions in different cell compartments. The article emphasizes the gaps in our understanding of the physiological role of this ancient protein in human cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Nan Wu, Yumeng Zhang, Shanshan Zhang, Youhua Yuan, Shuang Liu, Tao Xu, Peng Cui, Wenhong Zhang, Ying Zhang
Summary: This study reveals that polynucleotide phosphorylase (PNPase) in Escherichia coli controls persistence by negatively regulating the crp operon. The findings provide novel targets for the development of drugs against persisters for more effective treatment.
MICROBIOLOGY SPECTRUM
(2023)
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
Multidisciplinary Sciences
Idalio J. Viegas, Juan Pereira de Macedo, Lucia Serra, Mariana De Niz, Adriana Temporao, Sara Silva Pereira, Aashiq H. Mirza, Ed Bergstrom, Joao A. Rodrigues, Francisco Aresta-Branco, Samie R. Jaffrey, Luisa M. Figueiredo
Summary: RNA modifications play an important role in gene expression regulation. In Trypanosoma brucei, the m(6)A modification is enriched in transcripts encoding variant surface glycoproteins (VSGs), particularly in the poly(A) tail of actively expressed VSG transcripts. Removal of a 16-mer motif in the 3' untranslated region of VSG genes leads to a loss of m(6)A in the poly(A) tail, resulting in rapid deadenylation and mRNA degradation. This study identifies the first RNA modification in the poly(A) tail of any eukaryote, shedding light on a post-transcriptional mechanism of gene regulation.
Review
Chemistry, Analytical
Shuo Yin, Aipeng Chen, Yue Ding, Jia Song, Rui Chen, Peng Zhang, Chaoyong Yang
Summary: Exosomes, small extracellular vesicles, play essential roles in various physiological and pathological processes by selectively enclosing various RNAs and mediating intercellular communications. Accurate analysis of exosomal RNAs is crucial for both research and clinical applications. This review provides an overview of exosomal RNAs and discusses the advances in detection techniques and their applications in cancer diagnosis and therapy, highlighting their potential as non-invasive biomarkers and therapeutic tools. The challenges and future prospects in exosomal RNA analysis for diagnostic and therapeutic applications are also discussed.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Mom Das, Dimitrios Zattas, John C. Zinder, Elizabeth Wasmuth, Julien Henri, Christopher D. Lima
Summary: This study demonstrates a proofreading mechanism in nuclear RNA quality control, where different activities like polyadenylation, helicase, and exoribonucleases work together to protect stable RNA and selectively target less stable RNA for degradation. Inactivation of certain activities leads to loss of substrate discrimination, resulting in degradation of both stable and unstable RNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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
Genetics & Heredity
Syed-Rehan A. Hussain, Mehmet E. Yalvac, Benedict Khoo, Sigrid Eckardt, K. John McLaughlin
Summary: Gene editing of the mitochondrial genome using CRISPR-Cas9 system faces challenges due to inefficient delivery of guide RNA and Cas9 into mitochondria. This study demonstrates successful gene editing in mitochondrial DNA by appending a targeting RNA to a stem-loop element and expressing Cas9 with a mitochondrial localization sequence. The results suggest potential therapeutic applications of CRISPR-Cas9 for mitochondrial-related diseases.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Arnon D. Lieber, Shlomit Yehudai-Resheff, Erin L. Barnhart, Julie A. Theriot, Kinneret Keren
Article
Hematology
Roni Shouval, Liran I. Shlush, Shlomit Yehudai-Resheff, Shahnaz Ali, Neta Pery, Ehud Shapiro, Maty Tzukerman, Jacob M. Rowe, Tsila Zuckerman
EXPERIMENTAL HEMATOLOGY
(2014)
Review
Microbiology
Vered Irihimovitch, Shlomit Yehudai-Resheff
FEMS MICROBIOLOGY LETTERS
(2008)
Article
Microscopy
I. Seroussi, D. Veikherman, N. Ofer, S. Yehudai-Resheff, K. Keren
JOURNAL OF MICROSCOPY
(2012)
Article
Plant Sciences
Chloe Marchive, Shlomit Yehudai-Resheff, Arnaud Germain, Zhangjun Fei, Xingshan Jiang, Joshua Judkins, Hong Wu, Alisdair R. Fernie, Aaron Fait, David B. Stern
Article
Oncology
Shlomit Yehudai-Resheff, Shira Attias-Turgeman, Rawan Sabbah, Tal Gabay, Raneem Musallam, Anna Fridman-Dror, Tsila Zuckerman
INTERNATIONAL JOURNAL OF CANCER
(2019)
Article
Biochemistry & Molecular Biology
Victoria Portnoy, Gili Palnizky, Shlomit Yehudai-Resheff, Fabian Glaser, Gadi Schuster
Article
Biochemistry & Molecular Biology
S Yehudai-Resheff, V Portnoy, S Yogev, N Adir, G Schuster
Article
Biochemistry & Molecular Biology
S Baginsky, A Shteiman-Kotler, V Liveanu, S Yehudai-Resheff, M Bellaoui, RE Settlage, J Shabanowitz, DF Hunt, G Schuster, W Gruissem
Article
Biochemistry & Molecular Biology
S Yehudai-Resheff, M Hirsh, G Schuster
MOLECULAR AND CELLULAR BIOLOGY
(2001)
Article
Biochemistry & Molecular Biology
Shlomit Yehudai-Resheff, Sara L. Zimmer, Yutaka Komine, David B. Stern
Article
Biochemistry & Molecular Biology
S Yehudai-Resheff, G Schuster
NUCLEIC ACIDS RESEARCH
(2000)
Article
Biochemistry & Molecular Biology
Damien Marchese, Florent Guislain, Tamara Pringels, Laure Bridoux
Summary: Homopolymeric amino acid repeats are common in human proteins, particularly in transcription factors and kinases. This study focuses on homopolymeric histidine repeats (polyH) and their role in regulating embryonic development. Through bioinformatic analysis, the study identifies that polyH-containing proteins interact with cysteine-rich proteins and proteins containing cysteine repeats. The study further investigates the HOXA1 protein, a transcription factor with a long polyH motif, and finds that the polyH motif is necessary for its interaction with cysteine-rich proteins. Additionally, the study discovers that metal ions are required for the HOXA1-MDFI interaction and identifies three polyH interactors that down-regulate the transcriptional activity of HOXA1.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2024)