Article
Biology
Matthew T. Parker, Katarzyna Knop, Vasiliki Zacharaki, Anna Sherwood, Daniel Tome, Xuhong Yu, Pascal Gp Martin, Jim Beynon, Scott D. Michaels, Geoffrey J. Barton, Gordon G. Simpson
Summary: Genes involved in disease resistance, such as the nucleotide-binding, leucine-rich repeat (NLR) genes in plant genomes, play crucial roles but can also have negative impacts. Research shows that the RNA-binding protein FPA controls NLR transcript processing and gene annotation, revealing a co-transcriptional layer of NLR regulation with implications for plant immune responses.
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
Biochemistry & Molecular Biology
Yu Jin, Maxim Ivanov, Anna Nelson Dittrich, Andrew D. L. Nelson, Sebastian Marquardt
Summary: This study identified a long noncoding RNA (FLAIL) in Arabidopsis that is associated with flowering. FLAIL directly interacts with target genes and affects their expression through RNA-DNA interactions and alternative splicing. The findings suggest that lncRNAs can regulate gene expression and organismal development as accessory components of the spliceosome.
Article
Multidisciplinary Sciences
Buki Kwon, Mervin M. Fansler, Neil D. Patel, Jihye Lee, Weirui Ma, Christine Mayr
Summary: Multi-UTR genes express their alternative 3' UTR isoforms in a cell type-specific manner. Transcriptional enhancers, along with transcription factors, regulate the expression of these isoforms by influencing the cleavage activity of polyadenylation sites.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Hee Tae Lee, Hyo-Young Park, Keh Chien Lee, Jeong Hwan Lee, Jeong-Kook Kim
Summary: We investigated the transcriptomic changes in shoot apices during floral transition in Arabidopsis mutants of splicing factors AtU2AF65a and AtU2AF65b. AtU2AF65a mutants showed delayed flowering, while AtU2AF65b mutants exhibited accelerated flowering. RNA-seq analysis revealed that AtU2AF65a mutants had more differentially expressed genes compared to AtU2AF65b mutants. The gene FLOWERING LOCUS C (FLC), a major floral repressor, was significantly up- or down-regulated in the mutants. Additionally, the expression and alternative splicing patterns of several FLC upstream regulators were altered in the mutants. Our findings suggest that AtU2AF65a and AtU2AF65b splicing factors modulate FLC expression by affecting the expression or AS patterns of FLC upstream regulators, leading to different flowering phenotypes.
Article
Cell Biology
Joseph S. Bowness, Tatyana B. Nesterova, Guifeng Wei, Lisa Rodermund, Mafalda Almeida, Heather Coker, Emma J. Carter, Artun Kadaster, Neil Brockdorff
Summary: X chromosome inactivation is mediated by Xist and involves chromatin modification and gene silencing. The RNA binding protein SPEN plays a central role in Xist-mediated gene silencing and also contributes to the correct localization of Xist RNA. SPEN and the Polycomb pathway function in parallel to establish gene silencing, while differentiation-dependent recruitment of SmcHD1 is necessary for silencing X-linked genes.
Article
Biochemistry & Molecular Biology
Xiaoxiao Yang, Yang Tong, Gerui Liu, Jiapei Yuan, Yang Yang
Summary: Alternative polyadenylation (APA) is recognized as a crucial step in post-transcriptional regulation of eukaryotic genes, with tissue- and cell-type-specific occurrences. However, there is currently no database incorporating cell-type level information on APA. Single-cell RNA-seq technology enables analysis of APA at the cell-type level, and the scAPAatlas provides a comprehensive resource for exploring APA across different cell types and interpreting potential biological functions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Alexandre Segelle, Yaiza Nunez-Alvarez, Andrew J. Oldfield, Kimberly M. Webb, Philipp Voigt, Reini F. Luco
Summary: Histone modifications play a role in final splicing decisions. In this study, researchers used CRISPR epigenome editing tools and found that a single change in H3K27ac or H3K27me3 levels at the alternatively spliced exon is sufficient to induce splicing changes associated with epithelial-to-mesenchymal transition (EMT). These findings suggest that the dynamic nature of chromatin and its histone marks can rapidly and reversibly regulate alternative splicing in response to cell-extrinsic cues like EMT induction.
Article
Biochemistry & Molecular Biology
Weiwei Jin, Qizhao Zhu, Yanbo Yang, Wenqian Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Debing Yu, Jing Gong
Summary: APA is a crucial post-transcriptional regulatory mechanism that impacts various biological processes in different species. A study systematically characterized APA profiles in 18 species using RNA sequencing data and developed a user-friendly database for further research and exploration.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Junliang Wang, Wei Chen, Wenjun Yue, Wenhong Hou, Feng Rao, Hanbing Zhong, Yuanming Qi, Ni Hong, Ting Ni, Wenfei Jin
Summary: This study developed a single-cell polyadenylation sequencing method to investigate the landscape of alternative polyadenylation (APA) at the single-cell level. The results showed that genes with multiple polyA sites in bulk data tend to use only one site in each single cell. Cell cycle genes were found to have high variation in polyA site usages. Furthermore, polyA site usage switch played an important role in cell cycle regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Joana Wilton, Filipa Lopes de Mendonca, Isabel Pereira-Castro, Michael Tellier, Takayuki Nojima, Angela M. Costa, Jaime Freitas, Shona Murphy, Maria Jose Oliveira, Nicholas J. Proudfoot, Alexandra Moreira
Summary: In this study, new 3'UTR-APA and IPA mRNA isoforms were found during pro-inflammatory polarization of primary human macrophages and CRC co-culture, which may be used as diagnostic or therapeutic tools in the future.
FRONTIERS IN IMMUNOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Andrea Cerase, J. Mauro Calabrese, Gian Gaetano Tartaglia
Summary: This study reveals the molecular mechanisms through which the long non-coding RNA Xist silences genes on the entire X chromosome. By forming dimeric foci, Xist seeds the formation of large protein assemblies that contain various proteins, including SPEN, CIZ1, CELF, PTBP1, and components of Polycomb repressive complexes 1 and 2. These protein assemblies extend spatially beyond each Xist focus, explaining how this long non-coding RNA triggers silencing across the entire chromosome.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemical Research Methods
Krzysztof J. Szkop, David S. Moss, Irene Nobeli
Summary: The study introduces a new beta-regression-based method flexiMAP for discovering differential alternative polyadenylation events in RNA-seq data. Results show that flexiMAP exhibits a good balance between specificity and sensitivity, and allows modeling of multiple confounding variables, improving the results of RNA-seq data analysis.
Article
Multidisciplinary Sciences
Teresa Robert-Finestra, Beatrice F. Tan, Hegias Mira-Bontenbal, Erika Timmers, Cristina Gontan, Sarra Merzouk, Benedetto Daniele Giaimo, Francois Dossin, Wilfred F. J. van IJcken, John W. M. Martens, Tilman Borggrefe, Edith Heard, Joost Gribnau
Summary: The study demonstrates that SPEN plays a crucial role in the initiation of X chromosome inactivation by mediating the silencing of Tsix by Xist.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Xiaohui Wu, Tao Liu, Congting Ye, Wenbin Ye, Guoli Ji
Summary: APA plays a crucial role in transcriptome diversity and gene expression regulation. The newly developed tool scAPAtrap can accurately identify poly(A) sites at the whole genome level in individual cells, even for sites with low read coverage, without relying on priori genome annotation. Compared to existing methods, scAPAtrap shows higher accuracy and sensitivity in identifying poly(A) sites, making it a valuable tool for exploring APA dynamics and heterogeneous APA isoform expression at the single-cell level.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Celine Duc, Matthias Benoit, Samuel Le Goff, Lauriane Simon, Axel Poulet, Sylviane Cotterell, Christophe Tatout, Aline V. Probst
Article
Cell Biology
Axel Poulet, Celine Duc, Maxime Voisin, Sophie Desset, Sylvie Tutois, Emmanuel Vanrobays, Matthias Benoit, David E. Evans, Aline V. Probst, Christophe Tatout
JOURNAL OF CELL SCIENCE
(2017)
Article
Biochemistry & Molecular Biology
Celine Duc, Matthias Benoit, Gwenaelle Detourne, Lauriane Simon, Axel Poulet, Matthieu Jung, Alaguraj Veluchamy, David Latrasse, Samuel Le Goff, Sylviane Cotterell, Christophe Tatout, Moussa Benhamed, Aline V. Probst
Article
Plant Sciences
Matthias Benoit, Lauriane Simon, Sophie Desset, Celine Duc, Sylviane Cotterell, Axel Poulet, Samuel Le Goff, Christophe Tatout, Aline V. Probst
Article
Multidisciplinary Sciences
Konstantina Katsarou, Yun Wu, Runxuan Zhang, Nicola Bonar, Jenny Morris, Pete E. Hedley, Glenn J. Bryan, Kriton Kalantidis, Csaba Hornyik
Article
Agronomy
Ankush Prashar, Csaba Hornyik, Vanessa Young, Karen McLean, Sanjeev Kumar Sharma, M. Finlay B. Dale, Glenn J. Bryan
THEORETICAL AND APPLIED GENETICS
(2014)
Article
Plant Sciences
Nicola Bonar, Michele Liney, Runxuan Zhang, Ceri Austin, Jimmy Dessoly, Diane Davidson, Jennifer Stephens, Gordon McDougall, Mark Taylor, Glenn J. Bryan, Csaba Hornyik
FRONTIERS IN PLANT SCIENCE
(2018)
Article
Biochemical Research Methods
Kimon Froussios, Nick J. Schurch, Katarzyna Mackinnon, Marek Gierliniski, Celine Duc, Gordon G. Simpson, Geoffrey J. Barton
Article
Plant Sciences
Cristiane P. G. Calixto, Nikoleta A. Tzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. S. Brown
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Biochemistry & Molecular Biology
Guenter G. Lehretz, Sophia Sonnewald, Csaba Hornyik, Jose M. Corral, Uwe Sonnewald
Review
Biochemistry & Molecular Biology
Celine Duc, Christophe Thiriet
Summary: The review focuses on the remodeling of chromatin during DNA replication in the S-phase, including the eviction of nucleosomes and the assembly of newly synthesized histones. The recycling of parental histones and the nuclear import of histones are also discussed in relation to epigenetic inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Elodie Layat, Marie Bourcy, Sylviane Cotterell, Julia Zdzieszynska, Sophie Desset, Celine Duc, Christophe Tatout, Christophe Bailly, Aline V. Probst
Summary: Histone chaperones play a crucial role in dry seed embryo, with the loss of HIRA responsible for H3.3 deposition leading to increased chromatin accessibility and seed dormancy. HIRA also impacts seed germination efficiency and seed adaptability to unfavorable environmental conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Axel Poulet, Ellyn Rousselot, Stephane Teletchea, Celine Noirot, Yannick Jacob, Josien van Wolfswinkel, Christophe Thiriet, Celine Duc
Summary: The nucleosome is made up of histones and DNA, and histones are protected by specialized proteins called histone chaperones before they are deposited onto chromatin. In this study, the conservation of histone chaperones in Physarum polycephalum and their evolution relative to animals and plants were investigated. It was found that while histones are highly conserved in Physarum, histone chaperones differ significantly between animal and plant kingdoms. RNA sequencing revealed distinct patterns of chaperone expression during the cell cycle in Physarum. Overall, this study demonstrates the conserved role of histone chaperones in an early-branching eukaryote.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Axel Poulet, Laxmi Narayan Mishra, Stephane Teletchea, Jeffrey J. Hayes, Yannick Jacob, Christophe Thiriet, Celine Duc
Summary: Histones in Physarum polycephalum are highly conserved, shedding light on the organism's position in the eukaryotic phylogeny. Studying histones contributes to a better understanding of the evolutionary history of Mycetozoans.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Celine Duc, Marianne Yoth, Silke Jensen, Nolwenn Mouniee, Casey M. Bergman, Chantal Vaury, Emilie Brasset