Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

Download Full-text

Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant conifer Pinus sylvestris

10.1101/2020.10.22.350058 ◽

2020 ◽

Author(s):

Sandra Cervantes ◽

Jaana Vuosku ◽

Dorota Paczesniak ◽

Tanja Pyhäjärvi

Keyword(s):

Gene Expression ◽

Pinus Sylvestris ◽

Tissue Specificity ◽

Expression Profiles ◽

Expression Patterns ◽

Biological Databases ◽

Ploidy Levels ◽

Tissue Specific ◽

Genomic Resources ◽

Wide Range

AbstractDespite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome.Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics, and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.

Download Full-text

Analyzing cancer gene expression data through the lens of normal tissue-specificity

10.1101/2021.01.25.428166 ◽

2021 ◽

Author(s):

H. Robert Frost

Keyword(s):

Gene Expression ◽

Normal Tissue ◽

Tissue Specificity ◽

Cancer Genomics ◽

Expression Profiles ◽

Genetic Alterations ◽

Cancer Type ◽

Tissue Specific ◽

Normal Tissues ◽

Cancer Types

AbstractThe genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that the biology of normal tissues carries important information regarding the pathophysiology of the associated cancers, information that can be leveraged to improve the power and accuracy of cancer genomic analyses. Research exploring the use of normal tissue data for the analysis of cancer genomics has primarily focused on the paired analysis of tumor and adjacent normal samples. Efforts to leverage the general characteristics of normal tissue for cancer analysis has received less attention with most investigations focusing on understanding the tissue-specific factors that lead to individual genomic alterations or dysregulated pathways within a single cancer type. To address this gap and support scenarios where adjacent normal tissue samples are not available, we explored the genome-wide association between the transcriptomes of 21 solid human cancers and their associated normal tissues as profiled in healthy individuals. While the average gene expression profiles of normal and cancerous tissue may appear distinct, with normal tissues more similar to other normal tissues than to the associated cancer types, when transformed into relative expression values, i.e., the ratio of expression in one tissue or cancer relative to the mean in other tissues or cancers, the close association between gene activity in normal tissues and related cancers is revealed. As we demonstrate through an analysis of tumor data from The Cancer Genome Atlas and normal tissue data from the Human Protein Atlas, this association between tissue-specific and cancer-specific expression values can be leveraged to improve the prognostic modeling of cancer, the comparative analysis of different cancer types, and the analysis of cancer and normal tissue pairs.

Download Full-text

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

10.1101/711127 ◽

2019 ◽

Cited By ~ 2

Author(s):

Charity Muriuki ◽

Stephen J. Bush ◽

Mazdak Salavati ◽

Mary E.B. McCulloch ◽

Zofia M. Lisowski ◽

...

Keyword(s):

Gene Expression ◽

Reference Genome ◽

Expression Profiles ◽

Expression Patterns ◽

Small Ruminants ◽

Capra Hircus ◽

Specific Cell ◽

Domestic Goat ◽

Protein Coding ◽

Genomic Resources

AbstractGoats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

Download Full-text

Tissue-specificity of gene expression diverges slowly between orthologs, and rapidly between paralogs

10.1101/065086 ◽

2016 ◽

Cited By ~ 1

Author(s):

Nadezda Kryuchkova-Mostacci ◽

Marc Robinson-Rechavi

Keyword(s):

Gene Expression ◽

Tissue Specificity ◽

Pearson Correlation ◽

Expression Patterns ◽

Divergence Time ◽

Gene Copy ◽

Strong Increase ◽

Small Scale ◽

Ontology Term ◽

Tissue Specific

AbstractThe ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs. It has been supported using levels of expression and Gene Ontology term analysis, although the evidence was rather weak and there were also conflicting reports. In this study on 12 species we provide strong evidence of high conservation in tissue-specificity between orthologs, in contrast to low conservation between within-species paralogs. This allows us to shed a new light on the evolution of gene expression patterns. While there have been several studies of the correlation of expression between species, little is known about the evolution of tissue-specificity itself. Ortholog tissue-specificity is strongly conserved between all tetrapod species, with the lowest Pearson correlation between mouse and frog at r = 0.66. Tissue-specificity correlation decreases strongly with divergence time. Paralogs in human show much lower conservation, even for recent Primate-specific paralogs. When both paralogs from ancient whole genome duplication tissue-specific paralogs are tissue-specific, it is often to different tissues, while other tissue-specific paralogs are mostly specific to the same tissue. The same patterns are observed using human or mouse as focal species, and are robust to choices of datasets and of thresholds. Our results support the following model of evolution: in the absence of duplication, tissue-specificity evolves slowly, and tissue-specific genes do not change their main tissue of expression; after small-scale duplication the less expressed paralog loses the ancestral specificity, leading to an immediate difference between paralogs; over time, both paralogs become more broadly expressed, but remain poorly correlated. Finally, there is a small number of paralog pairs which stay tissue-specific with the same main tissue of expression, for at least 300 million years.Author summaryFrom specific examples, it has been assumed by comparative biologists that the same gene in different species has the same function, whereas duplication of a gene inside one species to create several copies allows them to acquire different functions. Yet this model was little tested until recently, and then has proven harder than expected to confirm. One of the problems is defining “function” in a way which can be easily studied. We introduce a new way of considering function: how specific is the activity (“expression”) of a gene? Genes which are specific to certain tissues have functions related to these tissues, whereas genes which are broadly active over many or all tissues have more general functions for the organism. We find that this “tissue-specificity” evolves very slowly in the absence of duplication, while immediately after duplication the new gene copy differs. This shows that indeed duplication leads to a strong increase in the evolution of new functions.

Download Full-text

Conservation of expression regulation throughout the animal kingdom

10.1101/007252 ◽

2014 ◽

Cited By ~ 1

Author(s):

Michael Kuhn ◽

Andreas Beyer

Keyword(s):

Gene Expression ◽

Related Species ◽

Expression Patterns ◽

Gene Families ◽

Tissue Expression ◽

Rate Of Change ◽

Gene Expression Patterns ◽

Transfer Of Knowledge ◽

Tissue Specific ◽

Wide Range

Following the increase in available sequenced genomes, tissue-specific transcriptomes are being determined for a rapidly growing number of highly diverse species. Traditionally, only the transcriptomes of related species with equivalent tissues have been compared. Such an analysis is much more challenging over larger evolutionary distances when complementary tissues cannot readily be defined. Here, we present a method for the cross-species mapping of tissue-specific and developmental gene expression patterns across a wide range of animals, including many non-model species. Our approach maps gene expression patterns between species without requiring the definition of homologous tissues. With the help of this mapping, gene expression patterns can be compared even across distantly related species. In our survey of 36 datasets across 27 species, we detected conserved expression programs on all taxonomic levels, both within animals and between the animals and their closest unicellular relatives, the choanoflagellates. We found that the rate of change in tissue expression patterns is a property of gene families. Our findings open new avenues of study for the comparison and transfer of knowledge between different species.

Download Full-text

Analyzing cancer gene expression data through the lens of normal tissue-specificity

PLoS Computational Biology ◽

10.1371/journal.pcbi.1009085 ◽

2021 ◽

Vol 17 (6) ◽

pp. e1009085

Author(s):

H. Robert Frost

Keyword(s):

Gene Expression ◽

Normal Tissue ◽

Tissue Specificity ◽

Cancer Genomics ◽

Expression Profiles ◽

Genetic Alterations ◽

Cancer Type ◽

Tissue Specific ◽

Normal Tissues ◽

Cancer Types

The genetic alterations that underlie cancer development are highly tissue-specific with the majority of driving alterations occurring in only a few cancer types and with alterations common to multiple cancer types often showing a tissue-specific functional impact. This tissue-specificity means that the biology of normal tissues carries important information regarding the pathophysiology of the associated cancers, information that can be leveraged to improve the power and accuracy of cancer genomic analyses. Research exploring the use of normal tissue data for the analysis of cancer genomics has primarily focused on the paired analysis of tumor and adjacent normal samples. Efforts to leverage the general characteristics of normal tissue for cancer analysis has received less attention with most investigations focusing on understanding the tissue-specific factors that lead to individual genomic alterations or dysregulated pathways within a single cancer type. To address this gap and support scenarios where adjacent normal tissue samples are not available, we explored the genome-wide association between the transcriptomes of 21 solid human cancers and their associated normal tissues as profiled in healthy individuals. While the average gene expression profiles of normal and cancerous tissue may appear distinct, with normal tissues more similar to other normal tissues than to the associated cancer types, when transformed into relative expression values, i.e., the ratio of expression in one tissue or cancer relative to the mean in other tissues or cancers, the close association between gene activity in normal tissues and related cancers is revealed. As we demonstrate through an analysis of tumor data from The Cancer Genome Atlas and normal tissue data from the Human Protein Atlas, this association between tissue-specific and cancer-specific expression values can be leveraged to improve the prognostic modeling of cancer, the comparative analysis of different cancer types, and the analysis of cancer and normal tissue pairs.

Download Full-text

Tissue-Wide Gene Expression Analysis of Sodium/Phosphate Co-Transporters in Pigs

International Journal of Molecular Sciences ◽

10.3390/ijms20225576 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5576 ◽

Cited By ~ 4

Author(s):

Aisanjiang Wubuli ◽

Henry Reyer ◽

Eduard Muráni ◽

Siriluck Ponsuksili ◽

Petra Wolf ◽

...

Keyword(s):

Gene Expression ◽

Sodium Phosphate ◽

Expression Patterns ◽

Distal Colon ◽

Kidney Cortex ◽

Specific Expression ◽

Tissue Specific ◽

Commercial Diet ◽

Wide Range ◽

P Supply

Sodium/phosphate co-transporters are considered to be important mediators of phosphorus (P) homeostasis. The expression of specific sodium/phosphate co-transporters is routinely used as an immediate response to dietary interventions in different species. However, a general understanding of their tissue-specificity is required to elucidate their particular contribution to P homeostasis. In this study, the tissue-wide gene expression status of all currently annotated sodium/phosphate co-transporters were investigated in two pig trials focusing on a standard commercial diet (trial 1) or divergent P-containing diets (trial 2). A wide range of tissues including the gastrointestinal tract (stomach, duodenum, jejunum, ileum, caecum, and colon), kidney, liver, bone, muscle, lung, and aorta were analyzed. Both trials showed consistent patterns in the overall tissue-specific expression of P transporters. While SLC34A2 was considered as the most important intestinal P transporter in other species including humans, SLC34A3 appeared to be the most prominent intestinal P transporter in pigs. In addition, the P transporters of the SLC17 family showed basal expression in the pig intestine and might have a contribution to P homeostasis. The expression patterns observed in the distal colon provide evidence that the large intestine may also be relevant for intestinal P absorption. A low dietary P supply induced higher expressions of SLC20A1, SLC20A2, SLC34A1, and SLC34A3 in the kidney cortex. The results suggest that the expression of genes encoding transcellular P transporters is tissue-specific and responsive to dietary P supply, while underlying regulatory mechanisms require further analyses.

Download Full-text

SELECTION DRIVES THE EVOLUTION OF CONVERGENT GENE EXPRESSION CHANGES DURING TRANSITIONS TO CO-SEXUALITY IN HAPLOID SEXUAL SYSTEMS

10.1101/2021.07.05.451104 ◽

2021 ◽

Author(s):

Guillaume Cossard ◽

Olivier Godfroy ◽

Zofia Nehr ◽

Corinne Crouaud ◽

J. Mark Cock ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Sequence Evolution ◽

High Turnover ◽

Sexual Systems ◽

Independent Events ◽

Wide Range ◽

Degree Of Convergence

Co-sexuality has evolved repeatedly from ancestors with separate sexes across a wide range of taxa. The switch to co-sexuality is expected to involve major molecular readjustments at the level of gene expression patterns, as modified males or females will express the opposite sexual function for which their phenotypes have been optimized. However, the molecular changes underpinning this important transition remain unknown, particularly in organisms with haploid sexual systems such as bryophytes, red and brown algae. Here, we explore four independent events of emergence of co-sexuality from uni-sexual (dioicous) ancestors in brown algal clades in order to examine the nature, evolution and degree of convergence of gene expression changes that accompany the breakdown of dioicy. The amount of male versus female phenotypic differences in dioicous species were not correlated with the extent of sex-biased gene expression, in strike contrast to what is observed in animals. Although sex-biased genes exhibited a high turnover rate during brown alga diversification, their predicted functions were remarkably conserved. Transition to co-sexuality consistently involved adaptive gene expression shifts and rapid sequence evolution, particularly of male-biased genes. The gene expression profiles of co-sexual species were more similar to those of females than to males of related dioicous species, suggesting that the former may have arisen from ancestral females. Finally, we identified extensive convergent gene expression changes associated with the transition to co-sexuality, and these changes appear to be driven by selection. Together, our observations provide novel insights on how co-sexual systems arise from ancestral, haploid UV sexual systems.

Download Full-text

Comprehensive Comparison of Amnion Stromal Cells and Chorion Stromal Cells by RNA-Seq

International Journal of Molecular Sciences ◽

10.3390/ijms22041901 ◽

2021 ◽

Vol 22 (4) ◽

pp. 1901

Author(s):

Brielle Jones ◽

Chaoyang Li ◽

Min Sung Park ◽

Anne Lerch ◽

Vimal Jacob ◽

...

Keyword(s):

Gene Expression ◽

Stromal Cells ◽

Expression Profiles ◽

Expression Patterns ◽

Principal Component ◽

Differentially Expressed ◽

Inflammatory Factor ◽

Next Generation Sequencing Technology ◽

Angiogenic Potential ◽

Anti Inflammatory

Mesenchymal stromal cells derived from the fetal placenta, composed of an amnion membrane, chorion membrane, and umbilical cord, have emerged as promising sources for regenerative medicine. Here, we used next-generation sequencing technology to comprehensively compare amniotic stromal cells (ASCs) with chorionic stromal cells (CSCs) at the molecular and signaling levels. Principal component analysis showed a clear dichotomy of gene expression profiles between ASCs and CSCs. Unsupervised hierarchical clustering confirmed that the biological repeats of ASCs and CSCs were able to respectively group together. Supervised analysis identified differentially expressed genes, such as LMO3, HOXA11, and HOXA13, and differentially expressed isoforms, such as CXCL6 and HGF. Gene Ontology (GO) analysis showed that the GO terms of the extracellular matrix, angiogenesis, and cell adhesion were significantly enriched in CSCs. We further explored the factors associated with inflammation and angiogenesis using a multiplex assay. In comparison with ASCs, CSCs secreted higher levels of angiogenic factors, including angiogenin, VEGFA, HGF, and bFGF. The results of a tube formation assay proved that CSCs exhibited a strong angiogenic function. However, ASCs secreted two-fold more of an anti-inflammatory factor, TSG-6, than CSCs. In conclusion, our study demonstrated the differential gene expression patterns between ASCs and CSCs. CSCs have superior angiogenic potential, whereas ASCs exhibit increased anti-inflammatory properties.

Download Full-text

Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽

10.1186/s12864-021-07545-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Jorge A. Ramírez-Tejero ◽

Jaime Jiménez-Ruiz ◽

Alicia Serrano ◽

Angjelina Belaj ◽

Lorenzo León ◽

...

Keyword(s):

Gene Expression ◽

Expression Pattern ◽

Growth And Development ◽

Expression Patterns ◽

Gene Expression Pattern ◽

Expression Level ◽

Resistant Cultivars ◽

Pathogen Invasion ◽

Wide Range ◽

Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

Download Full-text