Below you will find scientific publications authored by our members or those enabled by our platform services.
2021
Sanchez-Ferras, Oraly; Pacis, Alain; Sotiropoulou, Maria; Zhang, Yuhong; Wang, Yu Chang; Bourgey, Mathieu; Bourque, Guillaume; Ragoussis, Jiannis; Bouchard, Maxime
A coordinated progression of progenitor cell states initiates urinary tract development Journal Article
In: Nature Communications, vol. 12, no. 1, pp. 2627, 2021, ISSN: 2041-1723, (Number: 1 Publisher: Nature Publishing Group).
Abstract | Links | BibTeX | Tags: C3G, genomics, RNA-seq
@article{sanchez-ferras_coordinated_2021,
title = {A coordinated progression of progenitor cell states initiates urinary tract development},
author = {Oraly Sanchez-Ferras and Alain Pacis and Maria Sotiropoulou and Yuhong Zhang and Yu Chang Wang and Mathieu Bourgey and Guillaume Bourque and Jiannis Ragoussis and Maxime Bouchard},
url = {https://www.nature.com/articles/s41467-021-22931-5},
doi = {10.1038/s41467-021-22931-5},
issn = {2041-1723},
year = {2021},
date = {2021-01-01},
urldate = {2021-05-12},
journal = {Nature Communications},
volume = {12},
number = {1},
pages = {2627},
abstract = {The kidney and upper urinary tract develop through reciprocal interactions between the ureteric bud and the surrounding mesenchyme. Ureteric bud branching forms the arborized collecting duct system of the kidney, while ureteric tips promote nephron formation from dedicated progenitor cells. While nephron progenitor cells are relatively well characterized, the origin of ureteric bud progenitors has received little attention so far. It is well established that the ureteric bud is induced from the nephric duct, an epithelial duct derived from the intermediate mesoderm of the embryo. However, the cell state transitions underlying the progression from intermediate mesoderm to nephric duct and ureteric bud remain unknown. Here we show that nephric duct morphogenesis results from the coordinated organization of four major progenitor cell populations. Using single cell RNA-seq and Cluster RNA-seq, we show that these progenitors emerge in time and space according to a stereotypical pattern. We identify the transcription factors Tfap2a/b and Gata3 as critical coordinators of this progenitor cell progression. This study provides a better understanding of the cellular origin of the renal collecting duct system and associated urinary tract developmental diseases, which may inform guided differentiation of functional kidney tissue.},
note = {Number: 1
Publisher: Nature Publishing Group},
keywords = {C3G, genomics, RNA-seq},
pubstate = {published},
tppubtype = {article}
}
The kidney and upper urinary tract develop through reciprocal interactions between the ureteric bud and the surrounding mesenchyme. Ureteric bud branching forms the arborized collecting duct system of the kidney, while ureteric tips promote nephron formation from dedicated progenitor cells. While nephron progenitor cells are relatively well characterized, the origin of ureteric bud progenitors has received little attention so far. It is well established that the ureteric bud is induced from the nephric duct, an epithelial duct derived from the intermediate mesoderm of the embryo. However, the cell state transitions underlying the progression from intermediate mesoderm to nephric duct and ureteric bud remain unknown. Here we show that nephric duct morphogenesis results from the coordinated organization of four major progenitor cell populations. Using single cell RNA-seq and Cluster RNA-seq, we show that these progenitors emerge in time and space according to a stereotypical pattern. We identify the transcription factors Tfap2a/b and Gata3 as critical coordinators of this progenitor cell progression. This study provides a better understanding of the cellular origin of the renal collecting duct system and associated urinary tract developmental diseases, which may inform guided differentiation of functional kidney tissue.
2018
Venuto, David; Bourque, Guillaume
Identifying co-opted transposable elements using comparative epigenomics Journal Article
In: Development, Growth & Differentiation, vol. 60, no. 1, pp. 53-62, 2018.
Abstract | Links | BibTeX | Tags: comparative epigenomics, epigenetics, functional genome, genomics, transposable elements
@article{https://doi.org/10.1111/dgd.12423,
title = {Identifying co-opted transposable elements using comparative epigenomics},
author = {David Venuto and Guillaume Bourque},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/dgd.12423},
doi = {https://doi.org/10.1111/dgd.12423},
year = {2018},
date = {2018-01-01},
journal = {Development, Growth & Differentiation},
volume = {60},
number = {1},
pages = {53-62},
abstract = {The human genome gives rise to different epigenomic landscapes that define each cell type and can be deregulated in disease. Recent efforts by ENCODE, the NIH Roadmap and the International Human Epigenome Consortium (IHEC) have made significant advances towards assembling reference epigenomic maps of various tissues. Notably, these projects have found that approximately 80% of human DNA was biochemically active in at least one epigenomic assay while only approximately 10% of the sequence displayed signs of purifying selection. Given that transposable elements (TEs) make up at least 50% of the human genome and can be actively transcribed or act as regulatory elements either for their own purposes or be co-opted for the benefit of their host; we are interested in exploring their overall contribution to the “functional” genome. Traditional methods used to identify functional DNA have relied on comparative genomics, conservation analysis and low throughput validation assays. To discover co-opted TEs, and distinguish them from noisy genomic elements, we argue that comparative epigenomic methods will also be important.},
keywords = {comparative epigenomics, epigenetics, functional genome, genomics, transposable elements},
pubstate = {published},
tppubtype = {article}
}
The human genome gives rise to different epigenomic landscapes that define each cell type and can be deregulated in disease. Recent efforts by ENCODE, the NIH Roadmap and the International Human Epigenome Consortium (IHEC) have made significant advances towards assembling reference epigenomic maps of various tissues. Notably, these projects have found that approximately 80% of human DNA was biochemically active in at least one epigenomic assay while only approximately 10% of the sequence displayed signs of purifying selection. Given that transposable elements (TEs) make up at least 50% of the human genome and can be actively transcribed or act as regulatory elements either for their own purposes or be co-opted for the benefit of their host; we are interested in exploring their overall contribution to the “functional” genome. Traditional methods used to identify functional DNA have relied on comparative genomics, conservation analysis and low throughput validation assays. To discover co-opted TEs, and distinguish them from noisy genomic elements, we argue that comparative epigenomic methods will also be important.
Monlong, Jean; Girard, Simon L; Meloche, Caroline; Cadieux-Dion, Maxime; Andrade, Danielle M; Lafreniere, Ron G; Gravel, Micheline; Spiegelman, Dan; Dionne-Laporte, Alexandre; Boelman, Cyrus; Hamdan, Fadi F; Michaud, Jacques L; Rouleau, Guy; Minassian, Berge A; Bourque, Guillaume; Cossette, Patrick
Global characterization of copy number variants in epilepsy patients from whole genome sequencing Journal Article
In: PLOS Genetics, vol. 14, no. 4, pp. e1007285, 2018, ISSN: 1553-7404, (Publisher: Public Library of Science).
Abstract | Links | BibTeX | Tags: Catalogs, Epilepsy, Eyelids, Genetic linkage, Genetic polymorphism, genomics, Monozygotic twins, Twins
@article{monlong_global_2018,
title = {Global characterization of copy number variants in epilepsy patients from whole genome sequencing},
author = {Jean Monlong and Simon L Girard and Caroline Meloche and Maxime Cadieux-Dion and Danielle M Andrade and Ron G Lafreniere and Micheline Gravel and Dan Spiegelman and Alexandre Dionne-Laporte and Cyrus Boelman and Fadi F Hamdan and Jacques L Michaud and Guy Rouleau and Berge A Minassian and Guillaume Bourque and Patrick Cossette},
url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007285},
doi = {10.1371/journal.pgen.1007285},
issn = {1553-7404},
year = {2018},
date = {2018-01-01},
urldate = {2021-05-19},
journal = {PLOS Genetics},
volume = {14},
number = {4},
pages = {e1007285},
abstract = {Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.},
note = {Publisher: Public Library of Science},
keywords = {Catalogs, Epilepsy, Eyelids, Genetic linkage, Genetic polymorphism, genomics, Monozygotic twins, Twins},
pubstate = {published},
tppubtype = {article}
}
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.
Brochu, Julien; Vlachos-Breton, Émilie; Sutherland, Sarah; Martel, Makisha; Drolet, Marc
Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli Journal Article
In: PLOS Genetics, vol. 14, no. 9, pp. e1007668, 2018, ISSN: 1553-7404, (Publisher: Public Library of Science).
Abstract | Links | BibTeX | Tags: DNA amplification, DNA extraction, DNA replication, genomics, K cells, Next-generation sequencing, Phenotypes, Ribonucleases
@article{brochu_topoisomerases_2018,
title = {Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli},
author = {Julien Brochu and Émilie Vlachos-Breton and Sarah Sutherland and Makisha Martel and Marc Drolet},
url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007668},
doi = {10.1371/journal.pgen.1007668},
issn = {1553-7404},
year = {2018},
date = {2018-01-01},
urldate = {2021-05-19},
journal = {PLOS Genetics},
volume = {14},
number = {9},
pages = {e1007668},
abstract = {Type 1A topoisomerases (topos) are the only ubiquitous topos. E. coli has two type 1A topos, topo I (topA) and topo III (topB). Topo I relaxes negative supercoiling in part to inhibit R-loop formation. To grow, topA mutants acquire compensatory mutations, base substitutions in gyrA or gyrB (gyrase) or amplifications of a DNA region including parC and parE (topo IV). topB mutants grow normally and topo III binds tightly to single-stranded DNA. What functions topo I and III share in vivo and how cells lacking these important enzymes can survive is unclear. Previously, a gyrB(Ts) compensatory mutation was used to construct topA topB null mutants. These mutants form very long filaments and accumulate diffuse DNA, phenotypes that appears to be related to replication from R-loops. Here, next generation sequencing and qPCR for marker frequency analysis were used to further define the functions of type 1A topos. The results reveal the presence of a RNase HI-sensitive origin of replication in the terminus (Ter) region of the chromosome that is more active in topA topB cells than in topA and rnhA (RNase HI) null cells. The S9.6 antibodies specific to DNA:RNA hybrids were used in dot-blot experiments to show the accumulation of R-loops in rnhA, topA and topA topB null cells. Moreover topA topB gyrB(Ts) strains, but not a topA gyrB(Ts) strain, were found to carry a parC parE amplification. When a topA gyrB(Ts) mutant carried a plasmid producing topo IV, topB null transductants did not have parC parE amplifications. Altogether, the data indicate that in E. coli type 1A topos are required to inhibit R-loop formation/accumulation mostly to prevent unregulated replication in Ter, and that they are essential to prevent excess negative supercoiling and its detrimental effects on cell growth and survival.},
note = {Publisher: Public Library of Science},
keywords = {DNA amplification, DNA extraction, DNA replication, genomics, K cells, Next-generation sequencing, Phenotypes, Ribonucleases},
pubstate = {published},
tppubtype = {article}
}
Type 1A topoisomerases (topos) are the only ubiquitous topos. E. coli has two type 1A topos, topo I (topA) and topo III (topB). Topo I relaxes negative supercoiling in part to inhibit R-loop formation. To grow, topA mutants acquire compensatory mutations, base substitutions in gyrA or gyrB (gyrase) or amplifications of a DNA region including parC and parE (topo IV). topB mutants grow normally and topo III binds tightly to single-stranded DNA. What functions topo I and III share in vivo and how cells lacking these important enzymes can survive is unclear. Previously, a gyrB(Ts) compensatory mutation was used to construct topA topB null mutants. These mutants form very long filaments and accumulate diffuse DNA, phenotypes that appears to be related to replication from R-loops. Here, next generation sequencing and qPCR for marker frequency analysis were used to further define the functions of type 1A topos. The results reveal the presence of a RNase HI-sensitive origin of replication in the terminus (Ter) region of the chromosome that is more active in topA topB cells than in topA and rnhA (RNase HI) null cells. The S9.6 antibodies specific to DNA:RNA hybrids were used in dot-blot experiments to show the accumulation of R-loops in rnhA, topA and topA topB null cells. Moreover topA topB gyrB(Ts) strains, but not a topA gyrB(Ts) strain, were found to carry a parC parE amplification. When a topA gyrB(Ts) mutant carried a plasmid producing topo IV, topB null transductants did not have parC parE amplifications. Altogether, the data indicate that in E. coli type 1A topos are required to inhibit R-loop formation/accumulation mostly to prevent unregulated replication in Ter, and that they are essential to prevent excess negative supercoiling and its detrimental effects on cell growth and survival.