scholarly journals Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius–Pinus Symbioses

2021 ◽  
Vol 12 ◽  
Author(s):  
Nianwu Tang ◽  
Annie Lebreton ◽  
Wenjun Xu ◽  
Yucheng Dai ◽  
Fuqiang Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Symbiotic Gene ◽  
Mutualistic Symbiosis ◽  
Secreted Proteases ◽  
Fungal Genes

Ectomycorrhizal fungi establish a mutualistic symbiosis in roots of most woody plants. The molecular underpinning of ectomycorrhizal development was only explored in a few lineages. Here, we characterized the symbiotic transcriptomes of several milkcap species (Lactarius, Russulales) in association with different pine hosts. A time-course study of changes in gene expression during the development of L. deliciosus–Pinus taeda symbiosis identified 6 to 594 differentially expressed fungal genes at various developmental stages. Up- or down-regulated genes are involved in signaling pathways, nutrient transport, cell wall modifications, and plant defenses. A high number of genes coding for secreted proteases, especially sedolisins, were induced during root colonization. In contrast, only a few genes encoding mycorrhiza-induced small secreted proteins were identified. This feature was confirmed in several other Lactarius species in association with various pines. Further comparison among all these species revealed that each Lactarius species encodes a highly specific symbiotic gene repertoire, a feature possibly related to their host-specificity. This study provides insights on the genetic basis of symbiosis in an ectomycorrhizal order, the Russulales, which was not investigated so far.

scholarly journals Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks

2016 ◽  
Vol 25 (4) ◽  
pp. 943-958 ◽  
Author(s):  
Yun Huang ◽  
Frédéric J. J. Chain ◽  
Mahesh Panchal ◽  
Christophe Eizaguirre ◽  
Martin Kalbe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Immune Tissues

scholarly journals Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11875
Author(s):  
Tomoko Matsuda
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Time Course ◽  
Sequence Data ◽  
Specific Gene ◽  
Time Interval ◽  
Short Time Interval ◽  
Rna Seq ◽  
Lysis Buffer ◽  
Rna Protection

Large volumes of high-throughput sequencing data have been submitted to the Sequencing Read Archive (SRA). The lack of experimental metadata associated with the data makes reuse and understanding data quality very difficult. In the case of RNA sequencing (RNA-Seq), which reveals the presence and quantity of RNA in a biological sample at any moment, it is necessary to consider that gene expression responds over a short time interval (several seconds to a few minutes) in many organisms. Therefore, to isolate RNA that accurately reflects the transcriptome at the point of harvest, raw biological samples should be processed by freezing in liquid nitrogen, immersing in RNA stabilization reagent or lysing and homogenizing in RNA lysis buffer containing guanidine thiocyanate as soon as possible. As the number of samples handled simultaneously increases, the time until the RNA is protected can increase. Here, to evaluate the effect of different lag times in RNA protection on RNA-Seq data, we harvested CHO-S cells after 3, 5, 6, and 7 days of cultivation, added RNA lysis buffer in a time course of 15, 30, 45, and 60 min after harvest, and conducted RNA-Seq. These RNA samples showed high RNA integrity number (RIN) values indicating non-degraded RNA, and sequence data from libraries prepared with these RNA samples was of high quality according to FastQC. We observed that, at the same cultivation day, global trends of gene expression were similar across the time course of addition of RNA lysis buffer; however, the expression of some genes was significantly different between the time-course samples of the same cultivation day; most of these differentially expressed genes were related to apoptosis. We conclude that the time lag between sample harvest and RNA protection influences gene expression of specific genes. It is, therefore, necessary to know not only RIN values of RNA and the quality of the sequence data but also how the experiment was performed when acquiring RNA-Seq data from the database.

scholarly journals Transcriptome profiling reveals phase-specific gene expression in the developing barley inflorescence

2020 ◽  
Vol 8 (1) ◽  
pp. 71-86 ◽  
Author(s):  
Huiran Liu ◽  
Gang Li ◽  
Xiujuan Yang ◽  
Hendrik N.J. Kuijer ◽  
Wanqi Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Profiling ◽  
Specific Gene ◽  
Specific Gene Expression

Gene expression after resumption of development of Artemia franciscana cryptobiotic embryos

1994 ◽  
Vol 72 (3-4) ◽  
pp. 78-83 ◽  
Author(s):  
Ricardo Escalante ◽  
Alberto García-Sáez ◽  
Maria-Asunción Ortega ◽  
Leandro Sastre
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Developmental Stages ◽  
Artemia Franciscana ◽  
Mrna Levels ◽  
Muscle Actin ◽  
Mrna Accumulation ◽  
Α Subunit ◽  
Steady State Levels ◽  
Cyst Development

The steady-state levels of six different mRNAs have been studied during Artemia franciscana development. Some of these mRNAs are present in the cryptobiotic cyst, like those coding for cytoplasmic actins, sarcoplasmic/endoplasmic reticulum Ca2+-ATPase, and the Na+,K+-ATPase α-subunit isoform coded by the clone pArATNa136. The expression of these mRNAs is markedly induced during cyst development. A small increase in mRNA levels can be observed for some genes at very early stages of development (2 h). The main increase is observed between 4 and 16 h of development for all these genes, although the time course of mRNA accumulation is different for each one of the genes studied. Some other genes, like those coding for muscle actin (actin 3) or the Na+,K+-ATPase α-subunit isoform coded by the cDNA clone α2850, are not expressed in the cyst before resumption of development and their expression is induced after 10 or 6 h of development, respectively. These data on the kinetic of mRNA accumulation provide the information required to determine transcriptionally active developmental stages, necessary to study in more detail the mechanisms of transcriptional regulation during activation of cryptobiotic cysts and resumption of embryonic development.Key words: Artemia, gene expression, actin, Na,K-ATPase, Ca2+-ATPase.

Dynamics of Genomic Organization.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. SCI-17-SCI-17
Author(s):  
Mark T. Groudine ◽  
Indika Rajapakse ◽  
David Scalzo ◽  
Michael Perlman ◽  
Charles L. Kooperberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Genomic Organization ◽  
Conflicts Of Interest ◽  
Cell Types ◽  
Specific Gene ◽  
Chromosomal Association ◽  
Regulated Gene Expression ◽  
Lineage Specific Gene ◽  
Ordered State

Abstract Abstract SCI-17 We have investigated the relationships between lineage-specific gene expression, and total genomic organization during hematopoiesis. First, we determined the linear chromosomal distribution of genes that are co-regulated (identified via microarray analysis) when murine hematopoietic progenitor cells (FDCP-mixA) are differentiated to the erythroid and neutrophil lineages, as well as the organization of all chromosomes (in the form of rosettes) in the three cell types. Our analysis revealed a significant tendency for co-regulated genes to be proximal, which is related to the association of homologous chromosomes and the spatial juxtaposition of lineage-specific gene domains. This led us to hypothesize that the genome—at the level of chromosomes—may self-organize to facilitate coordinate gene regulation during cellular differentiation. We tested this hypothesis by applying the approaches of distance matrices and coupled oscillators to our datasets of gene expression and chromosomal associations from the differentiation of the progenitor to the erythroid and neutrophil lineages. Our analysis revealed that coordinate gene expression undergoes a phase transition—characterized by an increase in entropy—upon commitment of the progenitor. As differentiation continues, there is a gradual loss of entropy, culminating in a highly ordered state in the differentiated cell types. The coregulated gene sets of the semi-ordered progenitor and ordered erythroid and neutrophil lineages are significantly correlated with lineage-specific chromosomal association patterns. Furthermore, by transforming the gene expression networks along the time course to corresponding chromosomal association matrices, we found that chromosomal topologies change dynamically during differentiation but, as with gene expression, result in a more highly ordered state in the differentiated cell types. Our analysis demonstrates that the networks of co-regulated gene expression and chromosomal association are mutually related during differentiation, resulting in the self-organization of lineage-specific chromosomal topologies. Disclosures No relevant conflicts of interest to declare.

scholarly journals Transcriptome profiling of the ventral pallidum reveals a role for pallido-thalamic neurons in cocaine reward

2021 ◽  
Author(s):  
Michel Engeln ◽  
Megan E Fox ◽  
Ramesh Chandra ◽  
Eric Y Choi ◽  
Hyungwoo Nam ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Drug Use ◽  
Dendritic Spine ◽  
Transcriptome Profiling ◽  
Ventral Pallidum ◽  
Projection Neurons ◽  
Specific Gene ◽  
Thalamic Neurons ◽  
Spine Dynamics

Psychostimulant exposure alters the activity of ventral pallidum (VP) projection-neurons. However, the molecular underpinnings of these circuit dysfunctions are unclear. Using RNA-sequencing followed by circuit-specific gene expression assays, we revealed a key role for the VP to mediodorsal thalamus (VP-MDT) projection neurons in cocaine-related behaviors in mice. Our analyses demonstrated that the transcription factor Nr4a1 bidirectionally modulated dendritic spine dynamics in VP-MDT neurons and positively regulated pathological drug use.

scholarly journals dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using single cell time-course gene expression data

2021 ◽  
Author(s):  
Yu Xu ◽  
Jiaxing Chen ◽  
Aiping Lyu ◽  
William K Cheung ◽  
Lu Zhang
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Gene Expression Data ◽  
Time Course ◽  
Target Genes ◽  
Neighborhood Context ◽  
Specific Gene ◽  
Expression Data ◽  
Regulatory Interactions ◽  
Gene Functions

Time-course single-cell RNA sequencing (scRNA-seq) data have been widely applied to reconstruct the cell-type-specific gene regulatory networks by exploring the dynamic changes of gene expression between transcription factors (TFs) and their target genes. The existing algorithms were commonly designed to analyze bulk gene expression data and could not deal with the dropouts and cell heterogeneity in scRNA-seq data. In this paper, we developed dynDeepDRIM that represents gene pair joint expression as images and considers the neighborhood context to eliminate the transitive interactions. dynDeepDRIM integrated the primary image, neighbor images with time-course into a four-dimensional tensor and trained a convolutional neural network to predict the direct regulatory interactions between TFs and genes. We evaluated the performance of dynDeepDRIM on five time-course gene expression datasets. dynDeepDRIM outperformed the state-of-the-art methods for predicting TF-gene direct interactions and gene functions. We also observed gene functions could be better performed if more neighbor images were involved.

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