MYLK*FLNB and DOCK1*LAMA2 gene–gene interactions associated with rheumatoid arthritis in the focal adhesion pathway

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing

Caractérisation de la reprogrammation de l'expression des gènes chez les blés allopyloïdes

Polyploidy is a major evolutionary force, especially in angiosperms, all of which species have undergone recurrent polyploidization events during their evolution.In order to understand reprogramming of gene expression in response to polyploidy in the economically important wheat species (genera Triticum and Aegilops), I used an original model that consists in decreasing and reincreasing ploidy levels. Thus, the allotetraploid T. turgidum (BBAA) is extracted from the allohexaploid bread wheat T. aestivum (BBAADD), consisting in decreasing ploidy level. This extracted allotetraploid is crossed with the diploid species Ae. tauschii (DD) to synthesize an allohexaploid wheat, consisting in re-increasing ploidy level.The characterization of reprogramming of gene expression in response to decreasing and re-increasing ploidy levels was done here using first microarray technologies and then massive parallel mRNA sequencing (RNA-Seq), that has been rendered possible by the recent ‘draft' hexaploid wheat genome sequencing and subsequently the availability of the three homoeologs sequences (Ah, Bh, Dh) of 8605 genes. Adequate bioinformatics and statistics methods have been adopted and/or developed and used.My work reveals a partitioning of global expression of genes into that of their constituent homoeologs in different wheats allopolyploids. Most of homoeologs contribute equally to the overall gene expression and a low proportion reveals a bias towards one homoeolog, without showing a global dominance of a specific sub-genome. The partitioning and concerted expression of homoeologs is also established in wheat. Most homoeologs increase their expression when separated and reduce their expression levels when joined together in a higher ploidy level. For most genes, Ah and Bh homoeolog expression in allohexaploid wheat is equal to 2/3 of their expression level in the extracted allotetraploid wheat whereas the Dh homoeolog expression level is equal to 1/3 of that in the wheat diploid genome. This concerted change in homoeolog expression maintains the global gene expression at nearly similar levels in different ploidy levels.Results obtained in this work contribute to our understanding of global gene expression regulation and its partitioning between constituent homoeologs at different ploidy levels. Functional analysis of the different gene expression categories would reveal important gene functional categories that are regulated in response to polyploidy.La polyploïdie ou la duplication des génomes est une force majeure dans l'évolution et l'adaptation des espèces, notamment des angiospermes qui ont tous eu des évènements de polyploïdisation réccurrents au cours de leur évolution. Afin de comprendre la reprogrammation de l'expression des gènes en réponse à la polyploïdie chez les espèces économiquement importantes du blé (genres Triticum et Aegilops), j'ai utilisé un modèle original, qui consiste à caractériser les réponses à la diminution puis la ré-augmentation du niveau de ploïdie. Ainsi, le blé allotétraploïde (T. turgidum, BBAA) est extrait à partir du blé naturel allohexaploïde (T. aestivum, BBAADD). Ce blé allotétraploïde extrait est hybridé à son tour à l'espèce diploïde Ae. tauschii (DD) pour synthétiser un blé allohexaploïde.J'ai utilisé des méthodes d'analyse de l'expression des gènes basées sur les microarrays ainsi que le séquençage massif des ARN (RNA-Seq), basé sur les outils de nouvelles générations de séquençage (NGS) et rendu possible par la récente mise à disposition des séquences de trois copies homéologues (Ah, Bh, Dh) de 8605 gènes. Les méthodes bioinformatiques et statistiques appropriées ont été développées et/ou utilisées.Mes travaux révèlent un partitionnement de l'expression des gènes en celles des homéologues qui les composent dans les différents allopolyploïdes étudiés. La majorité des homéologues contribuent à l'expression globale des gènes de manière équivalente (1/3 chacun), d'autres présentent un biais d'expression spécifique vers un des homéologues, sans montrer de dominance d'un des sous-génomes. Une concertation dans le partitionnement et le niveau d'expression des homéologues est bien établie dans le blé: la majorité des homéologues augmentent leur expression lorsqu'ils sont séparés et la diminuent lorsqu'ils sont rassemblés dans un niveau de ploïdie supérieur. Ainsi, dans le blé allohexaploïde, pour la majorité des gènes, l'expression des homéologues Ah et Bh est égale au 2/3 de leur niveau d'expression dans le blé allotétraploïde extrait, et l'expression de l'homéoallèle Dh est égale au 1/3 du niveau d'expression dans le blé diploïde donneur du génome D. Cette concertation de l'expression des homéologues maintiendrait l'expression globale des gènes à des niveaux similaires dans les différentes espèces de blé de différents niveaux de ploïdie.Les résultats obtenus contribuent à la compréhension de la régulation de l'expression des gènes dans les polyploïdes du blé et la contribution des homéologues qui les composent. Les analyses futures des fonctions des différentes catégories d'expression des gènes permettraient d'identifier des fonctions particulières régulées en réponse à la polyploïdie

Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation

Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as Rag1, Mpeg1, and Dntt are expressed continuously from MPP2. Others, such as CD93, are CLP specific, suggesting their potential use as new markers to improve purification of lymphoid populations. Notably, a six-transcription factor network orchestrates the lymphoid differentiation program. Additionally, we pinpointed 24 long intergenic-non-coding RNA (lincRNA) differentially expressed through commitment and further identified seven novel forms. Collectively, our approach provides a comprehensive landscape of coding and non-coding transcriptomes expressed during lymphoid commitment

Characterization of genes expression reprogramming in allopolyploid wheats

La polyploïdie ou la duplication des génomes est une force majeure dans l'évolution et l'adaptation des espèces, notamment des angiospermes qui ont tous eu des évènements de polyploïdisation réccurrents au cours de leur évolution. Afin de comprendre la reprogrammation de l'expression des gènes en réponse à la polyploïdie chez les espèces économiquement importantes du blé (genres Triticum et Aegilops), j'ai utilisé un modèle original, qui consiste à caractériser les réponses à la diminution puis la ré-augmentation du niveau de ploïdie. Ainsi, le blé allotétraploïde (T. turgidum, BBAA) est extrait à partir du blé naturel allohexaploïde (T. aestivum, BBAADD). Ce blé allotétraploïde extrait est hybridé à son tour à l'espèce diploïde Ae. tauschii (DD) pour synthétiser un blé allohexaploïde.J'ai utilisé des méthodes d'analyse de l'expression des gènes basées sur les microarrays ainsi que le séquençage massif des ARN (RNA-Seq), basé sur les outils de nouvelles générations de séquençage (NGS) et rendu possible par la récente mise à disposition des séquences de trois copies homéologues (Ah, Bh, Dh) de 8605 gènes. Les méthodes bioinformatiques et statistiques appropriées ont été développées et/ou utilisées.Mes travaux révèlent un partitionnement de l'expression des gènes en celles des homéologues qui les composent dans les différents allopolyploïdes étudiés. La majorité des homéologues contribuent à l'expression globale des gènes de manière équivalente (1/3 chacun), d'autres présentent un biais d'expression spécifique vers un des homéologues, sans montrer de dominance d'un des sous-génomes. Une concertation dans le partitionnement et le niveau d'expression des homéologues est bien établie dans le blé: la majorité des homéologues augmentent leur expression lorsqu'ils sont séparés et la diminuent lorsqu'ils sont rassemblés dans un niveau de ploïdie supérieur. Ainsi, dans le blé allohexaploïde, pour la majorité des gènes, l'expression des homéologues Ah et Bh est égale au 2/3 de leur niveau d'expression dans le blé allotétraploïde extrait, et l'expression de l'homéoallèle Dh est égale au 1/3 du niveau d'expression dans le blé diploïde donneur du génome D. Cette concertation de l'expression des homéologues maintiendrait l'expression globale des gènes à des niveaux similaires dans les différentes espèces de blé de différents niveaux de ploïdie.Les résultats obtenus contribuent à la compréhension de la régulation de l'expression des gènes dans les polyploïdes du blé et la contribution des homéologues qui les composent. Les analyses futures des fonctions des différentes catégories d'expression des gènes permettraient d'identifier des fonctions particulières régulées en réponse à la polyploïdie.Polyploidy is a major evolutionary force, especially in angiosperms, all of which species have undergone recurrent polyploidization events during their evolution.In order to understand reprogramming of gene expression in response to polyploidy in the economically important wheat species (genera Triticum and Aegilops), I used an original model that consists in decreasing and reincreasing ploidy levels. Thus, the allotetraploid T. turgidum (BBAA) is extracted from the allohexaploid bread wheat T. aestivum (BBAADD), consisting in decreasing ploidy level. This extracted allotetraploid is crossed with the diploid species Ae. tauschii (DD) to synthesize an allohexaploid wheat, consisting in re-increasing ploidy level.The characterization of reprogramming of gene expression in response to decreasing and re-increasing ploidy levels was done here using first microarray technologies and then massive parallel mRNA sequencing (RNA-Seq), that has been rendered possible by the recent ‘draft' hexaploid wheat genome sequencing and subsequently the availability of the three homoeologs sequences (Ah, Bh, Dh) of 8605 genes. Adequate bioinformatics and statistics methods have been adopted and/or developed and used.My work reveals a partitioning of global expression of genes into that of their constituent homoeologs in different wheats allopolyploids. Most of homoeologs contribute equally to the overall gene expression and a low proportion reveals a bias towards one homoeolog, without showing a global dominance of a specific sub-genome. The partitioning and concerted expression of homoeologs is also established in wheat. Most homoeologs increase their expression when separated and reduce their expression levels when joined together in a higher ploidy level. For most genes, Ah and Bh homoeolog expression in allohexaploid wheat is equal to 2/3 of their expression level in the extracted allotetraploid wheat whereas the Dh homoeolog expression level is equal to 1/3 of that in the wheat diploid genome. This concerted change in homoeolog expression maintains the global gene expression at nearly similar levels in different ploidy levels.Results obtained in this work contribute to our understanding of global gene expression regulation and its partitioning between constituent homoeologs at different ploidy levels. Functional analysis of the different gene expression categories would reveal important gene functional categories that are regulated in response to polyploidy

Region-specific expression of young small-scale duplications in the human central nervous system

International audienceBackground. The duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the implication of duplicated gene expression in brain evolution was extensively studied through comparisons between organs, their role in the regional specialization of the adult human central nervous system has not yet been well described. Results. Our work explored intra-organ expression properties of paralogs through multiple territories of the human central nervous system (CNS) using transcriptome data generated by the Genotype-Tissue Expression (GTEx) consortium. Interestingly, we found that paralogs were associated with region-specific expression in CNS, suggesting their involvement in the differentiation of these territories. Beside the influence of gene expression level on region-specificity, we observed the contribution of both duplication age and duplication type to the CNS region-specificity of paralogs. Indeed, we found that small scale duplicated genes (SSDs) and in particular ySSDs (SSDs younger than the 2 rounds of whole genome duplications) were more CNS region-specific than other paralogs. Next, by studying the two paralogs of ySSD pairs, we observed that when they were region-specific, they tend to be specific to the same region more often than for other paralogs, showing the high co-expression of ySSD pairs. The extension of this analysis to families of paralogs showed that the families with co-expressed gene members (i.e. homogeneous families) were enriched in ySSDs. Furthermore, these homogeneous families tended to be region-specific families, where the majority of their gene members were specifically expressed in the same region. Conclusions Overall, our study suggests the involvement of ySSDs in the differentiation of human central nervous system territories. Therefore, we show the relevance of exploring region-specific expression of paralogs at the intra-organ level

Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation

Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as Rag1, Mpeg1, and Dntt are expressed continuously from MPP2. Others, such as CD93, are CLP specific, suggesting their potential use as new markers to improve purification of lymphoid populations. Notably, a six-transcription factor network orchestrates the lymphoid differentiation program. Additionally, we pinpointed 24 long intergenic-non-coding RNA (lincRNA) differentially expressed through commitment and further identified seven novel forms. Collectively, our approach provides a comprehensive landscape of coding and non-coding transcriptomes expressed during lymphoid commitment

Co-Transplantation of Barcoded Lymphoid-Primed Multipotent (LMPP) and Common Lymphocyte (CLP) Progenitors Reveals a Major Contribution of LMPP to the Lymphoid Lineage

International audienceT cells have the potential to maintain immunological memory and self-tolerance by recognizing antigens from pathogens or tumors. In pathological situations, failure to generate de novo T cells causes immunodeficiency resulting in acute infections and complications. Hematopoietic stem cells (HSC) transplantation constitutes a valuable option to restore proper immune function. However, delayed T cell reconstitution is observed compared to other lineages. To overcome this difficulty, we developed a new approach to identify populations with efficient lymphoid reconstitution properties. To this end, we use a DNA barcoding strategy based on the insertion into a cell chromosome of a lentivirus (LV) carrying a non-coding DNA fragment named barcode (BC). These will segregate through cell divisions and be present in cells' progeny. The remarkable characteristic of the method is that different cell types can be tracked simultaneously in the same mouse. Thus, we in vivo barcoded LMPP and CLP progenitors to test their ability to reconstitute the lymphoid lineage. Barcoded progenitors were co-grafted in immuno-compromised mice and their fate analyzed by evaluating the BC composition in transplanted mice. The results highlight the predominant role of LMPP progenitors for lymphoid generation and reveal valuable novel insights to be reconsidered in clinical transplantation assays

Prevalence of gene expression additivity in genetically stable wheat allohexaploids

International audienceThe reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids