Publications
73 results found
Lovell D, Pawlowsky-Glahn V, Egozcue JJ, et al., 2015, Proportionality: A Valid Alternative to Correlation for Relative Data, Plos Computational Biology, Vol: 11, ISSN: 1553-7358
Clément-Ziza M, Marsellach FX, Codlin S, et al., 2014, Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast., Molecular Systems Biology, Vol: 10, Pages: 764-764, ISSN: 1744-4292
Our current understanding of how natural genetic variation affects gene expression beyond well-annotated coding genes is still limited. The use of deep sequencing technologies for the study of expression quantitative trait loci (eQTLs) has the potential to close this gap. Here, we generated the first recombinant strain library for fission yeast and conducted an RNA-seq-based QTL study of the coding, non-coding, and antisense transcriptomes. We show that the frequency of distal effects (trans-eQTLs) greatly exceeds the number of local effects (cis-eQTLs) and that non-coding RNAs are as likely to be affected by eQTLs as protein-coding RNAs. We identified a genetic variation of swc5 that modifies the levels of 871 RNAs, with effects on both sense and antisense transcription, and show that this effect most likely goes through a compromised deposition of the histone variant H2A.Z. The strains, methods, and datasets generated here provide a rich resource for future studies.
Lemay J-F, Larochelle M, Marguerat S, et al., 2014, The RNA exosome promotes transcription termination of backtracked RNA polymerase II, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 21, Pages: 919-926, ISSN: 1545-9993
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- Citations: 68
Bitton DA, Rallis C, Jeffares DC, et al., 2014, LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq, GENOME RESEARCH, Vol: 24, Pages: 1169-1179, ISSN: 1088-9051
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- Citations: 45
Marguerat S, Lawler K, Brazma A, et al., 2014, Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress, RNA Biology, Vol: 11, Pages: 702-714, ISSN: 1547-6286
The cooperation of transcriptional and post-transcriptional levels of control to shape gene regulation is only partially understood. Here we show that a combination of two simple and non-invasive genomic techniques, coupled with kinetic mathematical modeling, affords insight into the intricate dynamics of RNA regulation in response to oxidative stress in the fission yeast Schizosaccharomyces pombe. This study reveals a dominant role of transcriptional regulation in response to stress, but also points to the first minutes after stress induction as a critical time when the coordinated control of mRNA turnover can support the control of transcription for rapid gene regulation. In addition, we uncover specialized gene expression strategies associated with distinct functional gene groups, such as simultaneous transcriptional repression and mRNA destabilization for genes encoding ribosomal proteins, delayed mRNA destabilization with varying contribution of transcription for ribosome biogenesis genes, dominant roles of mRNA stabilization for genes functioning in protein degradation, and adjustment of both transcription and mRNA turnover during the adaptation to stress. We also show that genes regulated independently of the bZIP transcription factor Atf1p are predominantly controlled by mRNA turnover, and identify putative cis-regulatory sequences that are associated with different gene expression strategies during the stress response. This study highlights the intricate and multi-faceted interplay between transcription and RNA turnover during the dynamic regulatory response to stress.
Blaikley EJ, Tinline-Purvis H, Kasparek TR, et al., 2014, The DNA damage checkpoint pathway promotes extensive resection and nucleotide synthesis to facilitate homologous recombination repair and genome stability in fission yeast., Nucleic Acids Research, Vol: 42, Pages: 5644-5656, ISSN: 1362-4962
DNA double-strand breaks (DSBs) can cause chromosomal rearrangements and extensive loss of heterozygosity (LOH), hallmarks of cancer cells. Yet, how such events are normally suppressed is unclear. Here we identify roles for the DNA damage checkpoint pathway in facilitating homologous recombination (HR) repair and suppressing extensive LOH and chromosomal rearrangements in response to a DSB. Accordingly, deletion of Rad3(ATR), Rad26ATRIP, Crb2(53BP1) or Cdc25 overexpression leads to reduced HR and increased break-induced chromosome loss and rearrangements. We find the DNA damage checkpoint pathway facilitates HR, in part, by promoting break-induced Cdt2-dependent nucleotide synthesis. We also identify additional roles for Rad17, the 9-1-1 complex and Chk1 activation in facilitating break-induced extensive resection and chromosome loss, thereby suppressing extensive LOH. Loss of Rad17 or the 9-1-1 complex results in a striking increase in break-induced isochromosome formation and very low levels of chromosome loss, suggesting the 9-1-1 complex acts as a nuclease processivity factor to facilitate extensive resection. Further, our data suggest redundant roles for Rad3ATR and Exo1 in facilitating extensive resection. We propose that the DNA damage checkpoint pathway coordinates resection and nucleotide synthesis, thereby promoting efficient HR repair and genome stability.
Schlackow M, Marguerat S, Proudfoot NJ, et al., 2013, Genome-wide analysis of poly(A) site selection in <i>Schizosaccharomyces pombe</i>, RNA, Vol: 19, Pages: 1617-1631, ISSN: 1355-8382
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- Citations: 26
DeGennaro CM, Alver BH, Marguerat S, et al., 2013, Spt6 Regulates Intragenic and Antisense Transcription, Nucleosome Positioning, and Histone Modifications Genome-Wide in Fission Yeast, MOLECULAR AND CELLULAR BIOLOGY, Vol: 33, Pages: 4779-4792, ISSN: 0270-7306
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- Citations: 71
Marguerat S, Baehler J, 2012, Coordinating cell size, TRENDS IN GENETICS, Vol: 28, Pages: 560-565, ISSN: 0168-9525
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- Citations: 131
Marguerat S, Schmidt A, Codlin S, et al., 2012, Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells, CELL, Vol: 151, Pages: 671-683, ISSN: 0092-8674
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- Citations: 379
Atkinson SR, Marguerat S, Baehler J, 2012, Exploring long non-coding RNAs through sequencing, SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY, Vol: 23, Pages: 200-205, ISSN: 1084-9521
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- Citations: 80
Lemieux C, Marguerat S, Lafontaine J, et al., 2011, A Pre-mRNA Degradation Pathway that Selectively Targets Intron-Containing Genes Requires the Nuclear Poly(A)-Binding Protein, MOLECULAR CELL, Vol: 44, Pages: 108-119, ISSN: 1097-2765
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- Citations: 81
Kiely CM, Marguerat S, Garcia JF, et al., 2011, Spt6 Is Required for Heterochromatic Silencing in the Fission Yeast <i>Schizosaccharomyces pombe</i>, MOLECULAR AND CELLULAR BIOLOGY, Vol: 31, Pages: 4193-4204, ISSN: 0270-7306
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- Citations: 27
Wilhelm BT, Marguerat S, Aligianni S, et al., 2011, Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast., Genome Biology, Vol: 12, Pages: R82-R82, ISSN: 1474-760X
BACKGROUND: The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenylation. These processes are thought to be integrated, both spatially and temporally, but it is unclear how these connections manifest at a global level with respect to chromatin patterns and transcription kinetics. We sought to clarify the relationships between chromatin, transcription and splicing using multiple genome-wide approaches in fission yeast. RESULTS: To investigate these functional interdependencies, we determined Pol II occupancy across all genes using high-density tiling arrays. We also performed ChIP-chip on the same array platform to globally map histone H3 and its H3K36me3 modification, complemented by formaldehyde-assisted isolation of regulatory elements (FAIRE). Surprisingly, Pol II occupancy was higher in introns than in exons, and this difference was inversely correlated with gene expression levels at a global level. Moreover, introns showed distinct distributions of histone H3, H3K36me3 and FAIRE signals, similar to those at promoters and terminators. These distinct transcription and chromatin patterns of intronic regions were most pronounced in poorly expressed genes. CONCLUSIONS: Our findings suggest that Pol II accumulates at the 3' ends of introns, leading to substantial transcriptional delays in weakly transcribed genes. We propose that the global relationship between transcription, chromatin remodeling, and splicing may reflect differences in local nuclear environments, with highly expressed genes being associated with abundant processing factors that promote effective intron splicing and transcriptional elongation.
Helmlinger D, Marguerat S, Villen J, et al., 2011, Tra1 has specific regulatory roles, rather than global functions, within the SAGA co-activator complex, EMBO JOURNAL, Vol: 30, Pages: 2843-2852, ISSN: 0261-4189
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- Citations: 51
Reddy BD, Wang Y, Niu L, et al., 2011, Elimination of a specific histone H3K14 acetyltransferase complex bypasses the RNAi pathway to regulate pericentric heterochromatin functions, GENES & DEVELOPMENT, Vol: 25, Pages: 214-219, ISSN: 0890-9369
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- Citations: 44
Zhurinsky J, Leonhard K, Watt S, et al., 2010, A Coordinated Global Control over Cellular Transcription, CURRENT BIOLOGY, Vol: 20, Pages: 2010-2015, ISSN: 0960-9822
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- Citations: 88
Kaufmann I, White E, Azad A, et al., 2010, Transcriptional Activation of the General Amino Acid Permease Gene <i>per1</i> by the Histone Deacetylase Clr6 Is Regulated by Oca2 Kinase, MOLECULAR AND CELLULAR BIOLOGY, Vol: 30, Pages: 3396-3410, ISSN: 0270-7306
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- Citations: 6
Wilhelm BT, Marguerat S, Goodhead I, et al., 2010, Defining transcribed regions using RNA-seq, NATURE PROTOCOLS, Vol: 5, Pages: 255-266, ISSN: 1754-2189
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- Citations: 56
Tinline-Purvis H, Savory AP, Cullen JK, et al., 2009, Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast, EMBO JOURNAL, Vol: 28, Pages: 3400-3412, ISSN: 0261-4189
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- Citations: 36
Marguerat S, Bähler J, 2009, RNA-seq: from technology to biology., Cellular and Molecular Life Sciences, Vol: 67, Pages: 569-579, ISSN: 1420-9071
Next-generation sequencing technologies are now being exploited not only to analyse static genomes, but also dynamic transcriptomes in an approach termed RNA-seq. Although these powerful and rapidly evolving technologies have only been available for a couple of years, they are already making substantial contributions to our understanding of genome expression and regulation. Here, we briefly describe technical issues accompanying RNA-seq data generation and analysis, highlighting differences to array-based approaches. We then review recent biological insight gained from applying RNA-seq and related approaches to deeply sample transcriptomes in different cell types or physiological conditions. These approaches are providing fascinating information about transcriptional and post-transcriptional gene regulation, and they are also giving unique insight into the richness of transcript structures and processing on a global scale and at unprecedented resolution.
Croucher NJ, Fookes MC, Perkins TT, et al., 2009, A simple method for directional transcriptome sequencing using Illumina technology., Nucleic Acids Research, Vol: 37, Pages: e148-e148, ISSN: 1362-4962
High-throughput sequencing of cDNA has been used to study eukaryotic transcription on a genome-wide scale to single base pair resolution. In order to compensate for the high ribonuclease activity in bacterial cells, we have devised an equivalent technique optimized for studying complete prokaryotic transcriptomes that minimizes the manipulation of the RNA sample. This new approach uses Illumina technology to sequence single-stranded (ss) cDNA, generating information on both the direction and level of transcription throughout the genome. The protocol, and associated data analysis programs, are freely available from http://www.sanger.ac.uk/Projects/Pathogens/Transcriptome/. We have successfully applied this method to the bacterial pathogens Salmonella bongori and Streptococcus pneumoniae and the yeast Schizosaccharomyces pombe. This method enables experimental validation of genetic features predicted in silico and allows the easy identification of novel transcripts throughout the genome. We also show that there is a high correlation between the level of gene expression calculated from ss-cDNA and double-stranded-cDNA sequencing, indicting that ss-cDNA sequencing is both robust and appropriate for use in quantitative studies of transcription. Hence, this simple method should prove a useful tool in aiding genome annotation and gene expression studies in both prokaryotes and eukaryotes.
Aligianni S, Lackner DH, Klier S, et al., 2009, The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback, PLOS GENETICS, Vol: 5, ISSN: 1553-7404
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- Citations: 38
Lopez-Maury L, Marguerat S, Baehler J, 2009, Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation (vol 9, pg 583, 2008), NATURE REVIEWS GENETICS, Vol: 10, ISSN: 1471-0056
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- Citations: 8
Helmlinger D, Marguerat S, Villen J, et al., 2008, The <i>S</i>. <i>pombe</i> SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8, GENES & DEVELOPMENT, Vol: 22, Pages: 3184-3195, ISSN: 0890-9369
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- Citations: 73
Marguerat S, Wilhelm BT, Bähler J, 2008, Next-generation sequencing: applications beyond genomes., Biochemical Society Transactions, Vol: 36, Pages: 1091-1096, ISSN: 1470-8752
The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.
Lopez-Maury L, Marguerat S, Baehler J, 2008, Tuning gene expression to changing environments:: from rapid responses to evolutionary adaptation, NATURE REVIEWS GENETICS, Vol: 9, Pages: 583-593, ISSN: 1471-0056
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- Citations: 671
Monahan BJ, Villén J, Marguerat S, et al., 2008, Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast., Nature Structural & Molecular Biology, Vol: 15, Pages: 873-880, ISSN: 1545-9993
SWI/SNF chromatin-remodeling complexes have crucial roles in transcription and other chromatin-related processes. The analysis of the two members of this class in Saccharomyces cerevisiae, SWI/SNF and RSC, has heavily contributed to our understanding of these complexes. To understand the in vivo functions of SWI/SNF and RSC in an evolutionarily distant organism, we have characterized these complexes in Schizosaccharomyces pombe. Although core components are conserved between the two yeasts, the compositions of S. pombe SWI/SNF and RSC differ from their S. cerevisiae counterparts and in some ways are more similar to metazoan complexes. Furthermore, several of the conserved proteins, including actin-like proteins, are markedly different between the two yeasts with respect to their requirement for viability. Finally, phenotypic and microarray analyses identified widespread requirements for SWI/SNF and RSC on transcription including strong evidence that SWI/SNF directly represses iron-transport genes.
Wilhelm BT, Marguerat S, Watt S, et al., 2008, Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution, NATURE, Vol: 453, Pages: 1239-U39, ISSN: 0028-0836
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- Citations: 753
Watt S, Mata J, López-Maury L, et al., 2008, urg1: a uracil-regulatable promoter system for fission yeast with short induction and repression times., PLOS One, Vol: 3, Pages: e1428-e1428, ISSN: 1932-6203
BACKGROUND: The fission yeast Schizosaccharomyces pombe is a popular genetic model organism with powerful experimental tools. The thiamine-regulatable nmt1 promoter and derivatives, which take >15 hours for full induction, are most commonly used for controlled expression of ectopic genes. Given the short cell cycle of fission yeast, however, a promoter system that can be rapidly regulated, similar to the GAL system for budding yeast, would provide a key advantage for many experiments. METHODOLOGY/PRINCIPAL FINDINGS: We used S. pombe microarrays to identify three neighbouring genes (urg1, urg2, and urg3) whose transcript levels rapidly and strongly increased in response to uracil, a condition which otherwise had little effect on global gene expression. We cloned the promoter of urg1 (uracil-regulatable gene) to create several PCR-based gene targeting modules for replacing native promoters with the urg1 promoter (Purg1) in the normal chromosomal locations of genes of interest. The kanMX6 and natMX6 markers allow selection under urg1 induced and repressed conditions, respectively. Some modules also allow N-terminal tagging of gene products placed under urg1 control. Using pom1 as a proof-of-principle, we observed a maximal increase of Purg1-pom1 transcripts after uracil addition within less than 30 minutes, and a similarly rapid decrease after uracil removal. The induced and repressed transcriptional states remained stable over 24-hour periods. RT-PCR comparisons showed that both induced and repressed Purg1-pom1 transcript levels were lower than corresponding P3nmt1-pom1 levels (wild-type nmt1 promoter) but higher than P81nmt1-pom1 levels (weak nmt1 derivative). CONCLUSIONS/SIGNIFICANCE: We exploited the urg1 promoter system to rapidly induce pom1 expression at defined cell-cycle stages, showing that ectopic pom1 expression leads to cell branching in G2-phase but much less so in G1-phase. The high temporal resolution provided by the urg1 promoter should facilitate e
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