A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

AbstractRNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.

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An R Package for Data Mining Chili Pepper Fruit Transcriptomes

10.21203/rs.3.rs-130806/v1 ◽

2020 ◽

Author(s):

Christian Escoto-Sandoval ◽

Alan Flores-Díaz ◽

M. Humberto Reyes-Valdés ◽

Neftalí Ochoa-Alejo ◽

Octavio Martinez

Keyword(s):

Gene Expression ◽

Data Mining ◽

Fruit Development ◽

Expression Profiles ◽

Open Data ◽

Enrichment Analysis ◽

R Package ◽

Chili Pepper ◽

Rna Seq ◽

Pepper Fruit

Abstract Background: Open data sharing is instrumental for the advance of biological sciences. Gene expression is the primary molecular phenotype, usually estimated through RNA-Seq experiments. Large scope interpretation of RNA-Seq results is complicated by the extensive gene expression range, as well as by the diversity of biological sources and experimental treatments. Here we present “Salsa”, an auto-contained R package for extracting useful knowledge about gene expression during the development of chili pepper fruit. Methods and Results: Data from 168 RNA-Seq libraries, comprising more than 3.4 billion reads, were analyzed and curated to represent standardized expression profiles (SEPs) for all genes expressed during fruit development in 12 chili pepper accessions. Accessions have representatives of domesticated varieties, wild ancestors and crosses, covering a broad spectrum of genotypes. Data are organized in a relational way, and functions allow data mining from the level of single genes up to whole genomes, grouping profiles by different criteria. Those include any combination of expression model, accession, protein description and gene ontology (GO) term, among others. Also, GO enrichment analysis can be performed over any set of genes. Conclusions: “Salsa” opens endless possibilities for mining the transcriptome of chili pepper during fruit development.

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Transcriptome Analyses throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process

Plants ◽

10.3390/plants10030585 ◽

2021 ◽

Vol 10 (3) ◽

pp. 585

Author(s):

Octavio Martínez ◽

Magda L. Arce-Rodríguez ◽

Fernando Hernández-Godínez ◽

Christian Escoto-Sandoval ◽

Felipe Cervantes-Hernández ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Fruit Development ◽

Time Course ◽

Expression Profiles ◽

Fruit Size ◽

Gene Expression Profiles ◽

Chili Pepper ◽

Time Shift ◽

The Mean

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

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Inheritance of gene expression throughout fruit development in chili pepper

Scientific Reports ◽

10.1038/s41598-021-02151-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Christian Escoto-Sandoval ◽

Neftalí Ochoa-Alejo ◽

Octavio Martínez

Keyword(s):

Gene Expression ◽

Fruit Development ◽

Gene Expression Regulation ◽

R Package ◽

Chili Pepper ◽

Wild Accession ◽

Biological Processes ◽

Genome Wide ◽

Cell Components

AbstractGene expression is the primary molecular phenotype and can be estimated in specific organs or tissues at particular times. Here we analyzed genome-wide inheritance of gene expression in fruits of chili pepper (Capsicum annuum L.) in reciprocal crosses between a domesticated and a wild accession, estimating this parameter during fruit development. We defined a general hierarchical schema to classify gene expression inheritance which can be employed for any quantitative trait. We found that inheritance of gene expression is affected by both, the time of fruit development as well as the direction of the cross, and propose that such variations could be common in many developmental processes. We conclude that classification of inheritance patterns is important to have a better understanding of the mechanisms underlying gene expression regulation, and demonstrate that sets of genes with specific inheritance pattern at particular times of fruit development are enriched in different biological processes, molecular functions and cell components. All curated data and functions for analysis and visualization are publicly available as an R package.

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Transcriptomic Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into Domestication Process

10.1101/2020.10.05.326470 ◽

2020 ◽

Author(s):

Octavio Martínez ◽

Magda L. Arce-Rodríguez ◽

Fernando Hernández-Godínez ◽

Christian Escoto-Sandoval ◽

Felipe Cervantes-Hernández ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Fruit Development ◽

Time Course ◽

Expression Profiles ◽

Fruit Size ◽

Gene Expression Profiles ◽

Chili Pepper ◽

Time Shift ◽

The Mean

ABSTRACTChili pepper (Capsicum spp.) is both an important crop and a model for domestication studies. Here we performed a time course experiment to estimate standardized gene expression profiles across fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptome every 10 days, from flower to fruit at 60 Days After Anthesis (DAA), and found that the mean standardized expression profile for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time-shift in expression which explains some of the differences between domesticated and wild phenotypes.

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SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency

BMC Bioinformatics ◽

10.1186/s12859-021-04282-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Verônica R. de Melo Costa ◽

Julianus Pfeuffer ◽

Annita Louloupi ◽

Ulf A. V. Ørom ◽

Rosario M. Piro

Keyword(s):

Gene Expression ◽

Cancer Progression ◽

Time Course ◽

Progressive Increase ◽

Rna Seq ◽

Transcript Processing ◽

Aberrant Transcript ◽

Genome Wide ◽

Splicing Efficiency ◽

Nascent Rna

Abstract Background Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene expression and its misregulation is related to numerous human diseases. Thus, to better understand the dynamics of this process and the perturbations that might be caused by aberrant transcript processing it is important to quantify splicing efficiency. Results Here, we introduce SPLICE-q, a fast and user-friendly Python tool for genome-wide SPLICing Efficiency quantification. It supports studies focusing on the implications of splicing efficiency in transcript processing dynamics. SPLICE-q uses aligned reads from strand-specific RNA-seq to quantify splicing efficiency for each intron individually and allows the user to select different levels of restrictiveness concerning the introns’ overlap with other genomic elements such as exons of other genes. We applied SPLICE-q to globally assess the dynamics of intron excision in yeast and human nascent RNA-seq. We also show its application using total RNA-seq from a patient-matched prostate cancer sample. Conclusions Our analyses illustrate that SPLICE-q is suitable to detect a progressive increase of splicing efficiency throughout a time course of nascent RNA-seq and it might be useful when it comes to understanding cancer progression beyond mere gene expression levels. SPLICE-q is available at: https://github.com/vrmelo/SPLICE-q

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Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

10.1101/2021.09.16.460328 ◽

2021 ◽

Author(s):

Dennis A Sun ◽

Nipam H Patel

Keyword(s):

Gene Expression ◽

Genome Annotation ◽

Time Course ◽

Regulatory Elements ◽

Rna Seq ◽

Genome Wide ◽

Long Read ◽

Amphipod Crustacean ◽

Accessible Chromatin

AbstractEmerging research organisms enable the study of biology that cannot be addressed using classical “model” organisms. The development of novel data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.Primary Findings-Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis-Combined short- and long-read RNA-Seq improves the Parhyale genome annotation-ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements-NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding-Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics-Integration of accessibility and gene expression reveals possible enhancers and repressors-Omni-ATAC can identify known and novel regulatory elements

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Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

10.1101/2021.01.15.426908 ◽

2021 ◽

Author(s):

Jakub Jankowski ◽

Hye Kyung Lee ◽

Julia Wilflingseder ◽

Lothar Hennighausen

Keyword(s):

Gene Expression ◽

Proximal Tubule ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Regulatory Elements ◽

Rna Seq ◽

Angiotensin Converting Enzyme 2 ◽

Genome Wide ◽

Cytokine Stimulation

SummaryRecently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFNα and IFNβ, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.

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The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

10.1101/2021.03.03.433814 ◽

2021 ◽

Author(s):

Chaoyang Li ◽

Jiangwen Sun ◽

Qianglin Liu ◽

Sanjeeva Dodlapati ◽

Hao Ming ◽

...

Keyword(s):

Gene Expression ◽

Myocardial Infarction ◽

High Throughput Sequencing ◽

Cardiac Fibroblasts ◽

Expression Profiles ◽

Integrated Analysis ◽

Matrix Remodeling ◽

Rna Seq ◽

Genome Wide ◽

Accessible Chromatin

AbstractAfter myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

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Transcriptome analysis of Plasmodium berghei during exo-erythrocytic development

10.1101/543207 ◽

2019 ◽

Author(s):

Reto Caldelari ◽

Sunil Dogga ◽

Marc W. Schmid ◽

Blandine Franke-Fayard ◽

Chris J Janse ◽

...

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Plasmodium Berghei ◽

Expression Profiles ◽

Specific Gene ◽

Rna Seq ◽

Erythrocytic Stage ◽

Liver Stage ◽

Specific Gene Expression ◽

Genome Wide

SummaryThe complex life cycle of malaria parasites requires well-orchestrated stage specific gene expression. In the vertebrate host the parasites grow and multiply by schizogony in two different environments: within erythrocytes and within hepatocytes. Whereas erythrocytic parasites are rather well-studied in this respect, relatively little is known about the exo-erythrocytic stages. In an attempt to fill this gap, we performed genome wide RNA-seq analyses of various exo-erythrocytic stages of Plasmodium berghei including sporozoites, samples from a time-course of liver stage development and detached cells, which contain infectious merozoites and represent the final step in exo-erythrocytic development. The analysis represents the completion of the transcriptome of the entire life cycle of P. berghei parasites with temporal detailed analysis of the liver stage allowing segmentation of the transcriptome across the progression of the life cycle. We have used these RNA-seq data from different developmental stages to cluster genes with similar expression profiles, in order to infer their functions. A comparison with published data of other parasite stages confirmed stage-specific gene expression and revealed numerous genes that are expressed differentially in blood and exo-erythrocytic stages. One of the most exo-erythrocytic stage-specific genes was PBANKA_1003900, which has previously been annotated as a “gametocyte specific protein”. The promoter of this gene drove high GFP expression in exo-erythrocytic stages, confirming its expression profile seen by RNA-seq. The comparative analysis of the genome wide mRNA expression profiles of erythrocytic and different exo-erythrocytic stages improves our understanding of gene regulation of Plasmodium parasites and can be used to model exo-erythrocytic stage metabolic networks and identify differences in metabolic processes during schizogony in erythrocytes and hepatocytes.

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Genome-wide alterations in gene expression of prostate cancer (PC) cells surviving neoadjuvant androgen deprivation therapy (ADT).

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.6_suppl.88 ◽

2017 ◽

Vol 35 (6_suppl) ◽

pp. 88-88

Author(s):

Anna C. Ferrari ◽

Ying Chen ◽

Hatem E. Sabaawy ◽

Mark N. Stein ◽

David Foran ◽

...

Keyword(s):

Gene Expression ◽

Androgen Deprivation Therapy ◽

Unsaturated Fatty Acids ◽

R Package ◽

Tumor Burden ◽

Androgen Deprivation ◽

Rna Seq ◽

Genome Wide ◽

Wide Range ◽

Castrate Resistant

88 Background: Although androgen deprivation therapy initially decreases PC tumor burden, resistance to further androgen receptor (AR)-directed treatments or chemotherapy is inevitable once CRPC is established. We postulated that the stress of ADT triggers widespread alterations in expression that renders a metastable physiologic state conditioned by epigenetic changes that might be initially reversible by targeting non-androgen pathways. We conducted a pilot study to explore genome-wide expression alterations in PC foci surviving 3 months ADT (eADT). Methods: mRNA from 7 frozen microdissected PC foci and normal counterparts (NC) were processed for RNA-seq. RNA-seq changes in eADT specimens were compared first with NC and the untreated PC in the TCGA PRAD (TCGA) database to castrate resistant (mCRPC) specimens in the dbGAP study phs000915.v1.p1database. The raw data (fastq files) was quantified using kallisto, normalized by TMM using R package edgeR, batch effects corrected using R package SVA. Analysis of differential gene expression by R package sleuth. Pathway and gene set by GSEA, GAGE/pathview packages for Gene Ontology (GO) and KEGG. Results: TMPRSS2-ERG+, 5/7. Highest DEG in eADT vs. TCGA vs mCRPC were non-coding RNA’s. Among 17431 differentially regulated paths; GSEA of eADT vs TCGA or mCRPC: 341 (1.95%) and 1366 (7.84%) up- vs 46 (0.26%) and 59 (0.34%) down-regulated. KEGG paths, eADT vs. TCGA or mCRPC, 11 and 53 up vs. 2 and 3 down- respectively. Highly down- path in eADT vs TCGA (log q < 10-17) was ribosomal vs. cell cycle and DNA replication in mCRPC. Six paths significantly up- in eADT vs TCGA or mCRPC: Wnt, adherence junction, steroid biosynthesis, unsaturated fatty acids, citrate cycle, ErbB. Calcium, MAPK, insulin, GnRH and Hedgehog were also up- in eADT vs mCRPC. AR full-length was marginally higher in eADT than TCGA and lower than mCRPC, no differences in gene targets. Conclusions: This pilot data shows that ADT triggers a wide range of gene expression alterations that support PC cell survival and may be vulnerable to therapeutic targeting in addition to the androgen pathway. Validation of these findings is planned in a larger set of samples from the same bank.

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