Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures

AbstractGenome-wide gene expression maps with a high spatial resolution have substantially accelerated molecular plant science. However, the number of characterized tissues and growth stages is still small because of the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterize transcriptomes of xylem vessels, fibers, the proximal and the distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classify more than 15,000 genes as being differentially expressed among different stem tissues and reveal known and novel tissue-specific cellular signatures. By determining transcription factor binding regions enriched in promoter regions of differentially expressed genes, we furthermore provide candidates for tissue-specific transcriptional regulators. Our datasets predict expression profiles of an exceptional amount of genes and allow generating hypotheses toward the spatial organization of physiological processes. Moreover, we demonstrate that information on gene expression in a broad range of mature plant tissues can be established with high spatial resolution by nuclear mRNA profiling.One sentence summaryA genome-wide high-resolution gene expression map of the Arabidopsis inflorescence stem is established.

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Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape

Translational Psychiatry ◽

10.1038/s41398-021-01270-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Divya Mehta ◽

Karen Grewen ◽

Brenda Pearson ◽

Shivangi Wani ◽

Leanne Wallace ◽

...

Keyword(s):

Gene Expression ◽

Depressive Symptoms ◽

Postpartum Depression ◽

Expression Profiles ◽

Depression Scale ◽

Well Being ◽

Health Concern ◽

Genome Wide ◽

A Genome ◽

Genome Wide Gene Expression

AbstractMaternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29–53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4–2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation

BMC Medical Genomics ◽

10.1186/s12920-020-0657-6 ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 2

Author(s):

Ieva Rauluseviciute ◽

Finn Drabløs ◽

Morten Beck Rye

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Dna Methylation ◽

Epigenetic Regulation ◽

Normal Tissue ◽

Expression Profiles ◽

Expression Data ◽

Dna Hypermethylation ◽

Genome Wide ◽

A Genome

Abstract Background Prostate cancer (PCa) has the highest incidence rates of cancers in men in western countries. Unlike several other types of cancer, PCa has few genetic drivers, which has led researchers to look for additional epigenetic and transcriptomic contributors to PCa development and progression. Especially datasets on DNA methylation, the most commonly studied epigenetic marker, have recently been measured and analysed in several PCa patient cohorts. DNA methylation is most commonly associated with downregulation of gene expression. However, positive associations of DNA methylation to gene expression have also been reported, suggesting a more diverse mechanism of epigenetic regulation. Such additional complexity could have important implications for understanding prostate cancer development but has not been studied at a genome-wide scale. Results In this study, we have compared three sets of genome-wide single-site DNA methylation data from 870 PCa and normal tissue samples with multi-cohort gene expression data from 1117 samples, including 532 samples where DNA methylation and gene expression have been measured on the exact same samples. Genes were classified according to their corresponding methylation and expression profiles. A large group of hypermethylated genes was robustly associated with increased gene expression (UPUP group) in all three methylation datasets. These genes demonstrated distinct patterns of correlation between DNA methylation and gene expression compared to the genes showing the canonical negative association between methylation and expression (UPDOWN group). This indicates a more diversified role of DNA methylation in regulating gene expression than previously appreciated. Moreover, UPUP and UPDOWN genes were associated with different compartments — UPUP genes were related to the structures in nucleus, while UPDOWN genes were linked to extracellular features. Conclusion We identified a robust association between hypermethylation and upregulation of gene expression when comparing samples from prostate cancer and normal tissue. These results challenge the classical view where DNA methylation is always associated with suppression of gene expression, which underlines the importance of considering corresponding expression data when assessing the downstream regulatory effect of DNA methylation.

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Gene expression profiles of oral leukoplakia and carcinoma: A genome-wide comparison analysis using an oligonucleotide microarray technology

International Journal of Oral and Maxillofacial Surgery ◽

10.1016/s0901-5027(05)81425-0 ◽

2005 ◽

Vol 34 ◽

pp. 137

Author(s):

T. Odani ◽

D. Ito ◽

M.-H. Li ◽

A. Kawamata ◽

T. Isobe ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Oligonucleotide Microarray ◽

Oral Leukoplakia ◽

Microarray Technology ◽

Comparison Analysis ◽

Genome Wide ◽

A Genome

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A genome-wide analysis of the gene expression profiles and alternative splicing events during the hypoxia-regulated osteogenic differentiation of human cartilage endplate-derived stem cells

Molecular Medicine Reports ◽

10.3892/mmr.2017.6846 ◽

2017 ◽

Vol 16 (2) ◽

pp. 1991-2001 ◽

Cited By ~ 2

Author(s):

Yuan Yao ◽

Qiyue Deng ◽

Chao Sun ◽

Weiling Song ◽

Huan Liu ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Alternative Splicing ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Human Cartilage ◽

Genome Wide Analysis ◽

Cartilage Endplate ◽

Genome Wide ◽

A Genome

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Early predictive biomarkers for postpartum depression point to a role for estrogen receptor signaling

Psychological Medicine ◽

10.1017/s0033291713003231 ◽

2014 ◽

Vol 44 (11) ◽

pp. 2309-2322 ◽

Cited By ~ 53

Author(s):

D. Mehta ◽

D. J. Newport ◽

G. Frishman ◽

L. Kraus ◽

M. Rex-Haffner ◽

...

Keyword(s):

Gene Expression ◽

High Risk ◽

Postpartum Depression ◽

Expression Profiles ◽

Predictive Biomarkers ◽

Estrogen Signaling ◽

Third Trimester ◽

The Third ◽

Genome Wide ◽

A Genome

BackgroundPostpartum depression (PPD) affects approximately 13% of women and has a negative impact on mother and infant, hence reliable biological tests for early detection of PPD are essential. We aimed to identify robust predictive biomarkers for PPD using peripheral blood gene expression profiles in a hypothesis-free genome-wide study in a high-risk, longitudinal cohort.MethodWe performed a genome-wide association study in a longitudinal discovery cohort comprising 62 women with psychopathology. Gene expression and hormones were measured in the first and third pregnancy trimesters and early postpartum (201 samples). The replication cohort comprised 24 women with third pregnancy trimester gene expression measures. Gene expression was measured on Illumina-Human HT12 v4 microarrays. Plasma estradiol and estriol were measured. Statistical analysis was performed in R.ResultsWe identified 116 transcripts differentially expressed between the PPD and euthymic women during the third trimester that allowed prediction of PPD with an accuracy of 88% in both discovery and replication cohorts. Within these transcripts, significant enrichment of transcripts implicated that estrogen signaling was observed and such enrichment was also evident when analysing published gene expression data predicting PPD from a non-risk cohort. While plasma estrogen levels were not different across groups, women with PPD displayed an increased sensitivity to estrogen signaling, confirming the previously proposed hypothesis of increased sex-steroid sensitivity as a susceptibility factor for PPD.ConclusionsThese results suggest that PPD can be robustly predicted in currently euthymic women as early as the third trimester and these findings have implications for predictive testing of high-risk women and prevention and treatment for PPD.

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Comparison of gene-expression profiles between diffuse- and intestinal-type gastric cancers using a genome-wide cDNA microarray

Oncogene ◽

10.1038/sj.onc.1207886 ◽

2004 ◽

Vol 23 (40) ◽

pp. 6830-6844 ◽

Cited By ~ 77

Author(s):

Natini Jinawath ◽

Yoichi Furukawa ◽

Suguru Hasegawa ◽

Meihua Li ◽

Tatsuhiko Tsunoda ◽

...

Keyword(s):

Gene Expression ◽

Cdna Microarray ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Intestinal Type ◽

Gastric Cancers ◽

Genome Wide ◽

A Genome

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Genome-Wide Expression Profiling in Malaria Infection Reveals Transcriptional Changes Associated with Lethal and Nonlethal Outcomes

Infection and Immunity ◽

10.1128/iai.73.9.6091-6100.2005 ◽

2005 ◽

Vol 73 (9) ◽

pp. 6091-6100 ◽

Cited By ~ 24

Author(s):

Kurt Schaecher ◽

Sanjai Kumar ◽

Anjali Yadava ◽

Maryanne Vahey ◽

Christian F. Ockenhouse

Keyword(s):

Gene Expression ◽

Immune Responses ◽

Transcriptional Activation ◽

Malaria Infection ◽

Target Genes ◽

Expression Profiles ◽

Plasmodium Yoelii ◽

Differentially Expressed ◽

Genome Wide ◽

Study Gene Expression

ABSTRACT High-density oligonucleotide microarrays are widely used to study gene expression in cells exposed to a variety of pathogens. This study addressed the global genome-wide transcriptional activation of genes in hosts infected in vivo, which result in radically different clinical outcomes. We present an analysis of the gene expression profiles that identified a set of host biomarkers which distinguish between lethal and nonlethal blood stage Plasmodium yoelii malaria infections. Multiple biological replicates sampled during the course of infection were used to establish statistically valid sets of differentially expressed genes. These genes that correlated with the intensity of infection were used to identify pathways of cellular processes related to metabolic perturbations, erythropoiesis, and B-cell immune responses and other innate and cellular immune responses. The transcriptional apparatus that controls gene expression in erythropoiesis was also differentially expressed and regulated the expression of target genes involved in the host's response to malaria anemia. The biological systems approach provides unprecedented opportunities to explore the pathophysiology of host-pathogen interactions in experimental malaria infection and to decipher functionally complex networks of gene and protein interactions.

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