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Gnan S, Matelot M, Weiman M, Arnaiz O, Guérin F, Sperling L, Bétermier M, Thermes C, Chen CL, Duharcourt S. GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium. Genome Res 2022; 32:699-709. [PMID: 35264448 PMCID: PMC8997360 DOI: 10.1101/gr.276125.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
Abstract
Eukaryotic genes are interrupted by introns that must be accurately spliced from mRNA precursors. With an average length of 25 nt, the more than 90,000 introns of Paramecium tetraurelia stand among the shortest introns reported in eukaryotes. The mechanisms specifying the correct recognition of these tiny introns remain poorly understood. Splicing can occur cotranscriptionally, and it has been proposed that chromatin structure might influence splice site recognition. To investigate the roles of nucleosome positioning in intron recognition, we determined the nucleosome occupancy along the P. tetraurelia genome. We show that P. tetraurelia displays a regular nucleosome array with a nucleosome repeat length of ∼151 bp, among the smallest periodicities reported. Our analysis has revealed that introns are frequently associated with inter-nucleosomal DNA, pointing to an evolutionary constraint favoring introns at the AT-rich nucleosome edge sequences. Using accurate splicing efficiency data from cells depleted for nonsense-mediated decay effectors, we show that introns located at the edge of nucleosomes display higher splicing efficiency than those at the center. However, multiple regression analysis indicates that the low GC content of introns, rather than nucleosome positioning, is associated with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.
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Affiliation(s)
- Stefano Gnan
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, 75005 France
| | - Mélody Matelot
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Marion Weiman
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Olivier Arnaiz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Frédéric Guérin
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Linda Sperling
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, 75005 France
| | - Sandra Duharcourt
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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2
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Top-down characterization of chicken core histones. J Proteomics 2018; 184:34-38. [PMID: 29935335 DOI: 10.1016/j.jprot.2018.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/07/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022]
Abstract
Core histones and their PTMs play important roles in regulating gene transcription and other DNA-related processes. The study of core histones PTMs, their cross-talk and functional roles is not only of broad biological significance but also of wide pathological and clinical relevance. Having the strength of comprehensive proteoform identification with 100% amino acid sequence coverage and combinatorial PTMs, top-down proteomics has become the state-of-the-art analytical tool for combinatorial PTM characterization of core histones. In this study, we report our top-down characterization of chicken (Gallus gallus domesticus) core histones, which have been widely used as models for chromosome re-construction among others because of easy availability and not-so-dense PTMs. With nanoRPLC-MS/MS analysis and ProteinGoggle database search, a total of 58 proteoforms were identified for the core histone families of H4, H2B, H2A, and H3.
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3
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González S, García A, Vázquez E, Serrano R, Sánchez M, Quintales L, Antequera F. Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome. Genome Res 2016; 26:1532-1543. [PMID: 27662899 PMCID: PMC5088595 DOI: 10.1101/gr.207241.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
In the yeast genome, a large proportion of nucleosomes occupy well-defined and stable positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genome remains controversial. Through quantitative analysis of nucleosome positioning, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes in three species of Schizosaccharomyces and in Saccharomyces cerevisiae. This effect is equally detected in transcribed and nontranscribed regions, suggesting the existence of sequence elements that contribute to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open the possibility of designing coding and noncoding DNA molecules capable of directing their own nucleosomal organization.
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Affiliation(s)
- Sara González
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Alicia García
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Enrique Vázquez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Rebeca Serrano
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
| | - Luis Quintales
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain.,Departamento de Informática y Automática, Universidad de Salamanca/Facultad de Ciencias, 37007 Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca, 37007 Salamanca, Spain
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4
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Beh LY, Müller MM, Muir TW, Kaplan N, Landweber LF. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res 2015; 25:1727-38. [PMID: 26330564 PMCID: PMC4617968 DOI: 10.1101/gr.188516.114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 08/20/2015] [Indexed: 12/13/2022]
Abstract
A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these “seed” nucleosomes—together with trans-acting factors—may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.
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Affiliation(s)
- Leslie Y Beh
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Manuel M Müller
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Noam Kaplan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Laura F Landweber
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA
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