Rapid muscle-specific gene expression changes after a single bout of eccentric contractions in the mouse

2004 ◽  
Vol 286 (2) ◽  
pp. C355-C364 ◽  
Author(s):  
Ilona A. Barash ◽  
Liby Mathew ◽  
Allen F. Ryan ◽  
Ju Chen ◽  
Richard L. Lieber
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Biological Response ◽  
Exercise Bout ◽  
Ankyrin Repeat ◽  
Eccentric Contractions ◽  
Specific Gene ◽  
Muscle Strengthening ◽  
Time Courses ◽  
Ankyrin Repeat Proteins

Eccentric contractions (ECs), in which a muscle is forced to lengthen while activated, result in muscle injury and, eventually, muscle strengthening and prevention of further injury. Although the mechanical basis of EC-induced injury has been studied in detail, the biological response of muscle is less well characterized. This study presents the development of a minimally invasive model of EC injury in the mouse, follows the time course of torque recovery after an injurious bout of ECs, and uses Affymetrix microarrays to compare the gene expression profile 48 h after ECs to both isometrically stimulated muscles and contralateral muscles. Torque dropped by ∼55% immediately after the exercise bout and recovered to initial levels 7 days later. Thirty-six known genes were upregulated after ECs compared with contralateral and isometrically stimulated muscles, including five muscle-specific genes: muscle LIM protein (MLP), muscle ankyrin repeat proteins (MARP1 and -2; also known as cardiac ankyrin repeat protein and Arpp/Ankrd2, respectively), Xin, and myosin binding protein H. The time courses of MLP and MARP expression after the injury bout (determined by quantitative real-time polymerase chain reaction) indicate that these genes are rapidly induced, reaching a peak expression level of 6–11 times contralateral values 12–24 h after the EC bout and returning to baseline within 72 h. Very little gene induction was seen after either isometric activation or passive stretch, indicating that the MLP and MARP genes may play an important and specific role in the biological response of muscle to EC-induced injury.

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.

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 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.

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 Ankyrin Repeat Proteins of Orf Virus Influence the Cellular Hypoxia Response Pathway

2016 ◽  
Vol 91 (1) ◽  
Author(s):  
Da-Yuan Chen ◽  
Jacqueline-Alba Fabrizio ◽  
Sarah E. Wilkins ◽  
Keyur A. Dave ◽  
Jeffrey J. Gorman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Hypoxia Inducible Factor ◽  
Ankyrin Repeat ◽  
Orf Virus ◽  
Binding Motif ◽  
Target Gene Expression ◽  
Cellular Environment ◽  
Ankyrin Repeat Proteins

ABSTRACT Hypoxia-inducible factor (HIF) is a transcriptional activator with a central role in regulating cellular responses to hypoxia. It is also emerging as a major target for viral manipulation of the cellular environment. Under normoxic conditions, HIF is tightly suppressed by the activity of oxygen-dependent prolyl and asparaginyl hydroxylases. The asparaginyl hydroxylase active against HIF, factor inhibiting HIF (FIH), has also been shown to hydroxylate some ankyrin repeat (ANK) proteins. Using bioinformatic analysis, we identified the five ANK proteins of the parapoxvirus orf virus (ORFV) as potential substrates of FIH. Consistent with this prediction, coimmunoprecipitation of FIH was detected with each of the ORFV ANK proteins, and for one representative ORFV ANK protein, the interaction was shown to be dependent on the ANK domain. Immunofluorescence studies revealed colocalization of FIH and the viral ANK proteins. In addition, mass spectrometry confirmed that three of the five ORFV ANK proteins are efficiently hydroxylated by FIH in vitro. While FIH levels were unaffected by ORFV infection, transient expression of each of the ORFV ANK proteins resulted in derepression of HIF-1α activity in reporter gene assays. Furthermore, ORFV-infected cells showed upregulated HIF target gene expression. Our data suggest that sequestration of FIH by ORFV ANK proteins leads to derepression of HIF activity. These findings reveal a previously unknown mechanism of viral activation of HIF that may extend to other members of the poxvirus family. IMPORTANCE The protein-protein binding motif formed from multiple repeats of the ankyrin motif is common among chordopoxviruses. However, information on the roles of these poxviral ankyrin repeat (ANK) proteins remains limited. Our data indicate that the parapoxvirus orf virus (ORFV) is able to upregulate hypoxia-inducible factor (HIF) target gene expression. This response is mediated by the viral ANK proteins, which sequester the HIF regulator FIH (factor inhibiting HIF). This is the first demonstration of any viral protein interacting directly with FIH. Our data reveal a new mechanism by which viruses reprogram HIF, a master regulator of cellular metabolism, and also show a new role for the ANK family of poxvirus proteins.

scholarly journals Multiple synapsin I messenger RNAs are differentially regulated during neuronal development.

1988 ◽  
Vol 106 (1) ◽  
pp. 195-203 ◽  
Author(s):  
C A Haas ◽  
L J DeGennaro
Keyword(s):  
Gene Expression ◽  
Rna Splicing ◽  
Time Course ◽  
Granule Cells ◽  
Developmental Time ◽  
Rnase H ◽  
Granule Cell Layer ◽  
Specific Gene ◽  
Synapsin I ◽  
Messenger Rnas

Synapsin I is a neuron-specific protein consisting of two isoforms Ia and Ib. It is thought to play a role in the regulation of neurotransmitter release. In this study the structure and expression of two classes of synapsin I mRNA have been examined. The two mRNA classes have molecular sizes of 3.4 and 4.5 kb, respectively. Both classes translate into synapsin I polypeptides and display a high degree of base sequence homology. Utilizing an oligonucleotide-directed RNase H assay we have shown that both mRNA classes have a common start site of transcription and differ from one another toward their 3' ends. The expression of the two synapsin I mRNA classes is differentially regulated during the development of the rat brain and cerebellum. In the cerebellum the 4.5-kb transcript is expressed until postnatal day 7, after which it decreases to an undetectable level. The 3.4-kb mRNA is found throughout cerebellar development and in the adult. This suggests that the 3.4-kb mRNA class consists of messages which can encode both synapsin I polypeptides. Using quantitative Northern blot analysis a peak in the expression of this mRNA was observed at postnatal day 20. The maximum expression of the 3.4-kb class coincides with the period of synaptogenesis in the cerebellum. In addition to the developmental time course of synapsin mRNA expression a description of its spatial distribution throughout the cerebellum was performed using in situ hybridization histochemistry. From postnatal day 15 onwards, with a maximum at postnatal day 20, synapsin mRNA was localized in the internal granule cell layer of the cerebellum. On a cellular level, the granule cells, but not the neighboring Purkinje cells, express high levels of synapsin mRNA. These observations implicate developmentally coordinated differential RNA splicing in the regulation of neuron-specific gene expression and substantiate the correlation of synapsin gene expression with the period of synaptogenic differentiation of neurons.

Structural and regulatory roles of muscle ankyrin repeat protein family in skeletal muscle

2007 ◽  
Vol 293 (1) ◽  
pp. C218-C227 ◽  
Author(s):  
Ilona A. Barash ◽  
Marie-Louise Bang ◽  
Liby Mathew ◽  
Marion L. Greaser ◽  
Ju Chen ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Time Course ◽  
Fiber Type ◽  
Biological Response ◽  
Ankyrin Repeat ◽  
Wild Type ◽  
Repeat Protein ◽  
Ankyrin Repeat Protein ◽  
Enhanced Expression ◽  
Torque Loss

The biological response of muscle to eccentric contractions (ECs) results in strengthening and protection from further injury. However, the cellular basis for this response remains unclear. Previous studies identified the muscle ankyrin repeat protein ( MARP) family, consisting of cardiac ankyrin repeat protein ( CARP), ankyrin repeat domain 2/ankyrin repeat protein with PEST and proline-rich region ( Ankrd2/Arpp), and diabetes-associated ankyrin repeat protein ( DARP), as rapidly and specifically upregulated in mice after a single bout of EC. To determine the role of these genes in skeletal muscle, a survey of skeletal muscle structural and functional characteristics was performed on mice lacking all three MARP family members (MKO). There was a slight trend toward MKO muscles having a slower fiber type distribution but no differences in muscle fiber size. Single MKO fibers were less stiff, tended to have longer resting sarcomere lengths, and expressed a longer isoform of titin than their wild-type counterparts, indicating that these proteins may play a role in the passive mechanical behavior of muscle. Finally, MKO mice showed a greater degree of torque loss after a bout of ECs compared with wild-type mice, although they recovered from the injury with the same or even improved time course. This recovery was associated with enhanced expression of the muscle regulatory genes MyoD and muscle LIM protein ( MLP), suggesting that the MARP family may play both important structural and gene regulatory roles in skeletal muscle.

scholarly journals Class II Histone Deacetylases Confer Signal Responsiveness to the Ankyrin-Repeat Proteins ANKRA2 and RFXANK

2006 ◽  
Vol 17 (1) ◽  
pp. 438-447 ◽  
Author(s):  
Timothy A. McKinsey ◽  
Koichiro Kuwahara ◽  
Svetlana Bezprozvannaya ◽  
Eric N. Olson
Keyword(s):  
Gene Expression ◽  
Transcriptional Repression ◽  
Nuclear Export ◽  
Histone Deacetylases ◽  
Class Ii ◽  
Ankyrin Repeat ◽  
Amino Terminal ◽  
Mhc Ii ◽  
Repeat Proteins ◽  
Ankyrin Repeat Proteins

Class II histone deacetylases (HDACs) contain unique amino-terminal extensions that mediate interactions with members of the myocyte enhancer factor-2 (MEF2) family of transcription factors and responsiveness to kinases, including Ca2+/calmodulin-dependent kinase (CaMK). Despite intense investigation of class II HDACs, little is known of MEF2-independent mechanisms for transcriptional repression by these chromatin-modifying enzymes. Here, we demonstrate that class II HDACs 4 and 5 physically associate with ankyrin-repeat proteins ANKRA2 and RFXANK (RFX-B/Tvl-1/ANKRA1). ANKRA2 is a megalin- and BKCa potassium channel-interacting factor, whereas RFXANK is a positive regulator of major histocompatibility complex II (MHC II) gene expression. HDAC4 and HDAC5 interact with the ankyrin repeats of ANKRA2 and RFXANK and, through association with RFXANK, repress MHC II promoter activation. HDACs 4 and 5 also repress endogenous HLA-DRA gene expression induced by CIITA. Phosphorylation of class II HDACs by CaMK results in CRM1-dependent nuclear export of HDAC/RFXANK complexes. These results define a novel transcriptional pathway under the control of class II HDACs and suggest a role for these transcriptional repressors as signal-responsive regulators of antigen presentation.

scholarly journals A recently formed triploid Cardamine insueta inherits leaf vivipary and submergence tolerance traits of parents

2020 ◽  
Author(s):  
Jianqiang Sun ◽  
Rie Shimizu-Inatsugi ◽  
Hugo Hofhuis ◽  
Kentaro Shimizu ◽  
Angela Hay ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Field Studies ◽  
Specific Gene ◽  
Niche Separation ◽  
Expression Ratio ◽  
Specific Gene Expression ◽  
Meristem Development ◽  
Environmental Robustness ◽  
Trans Regulation

AbstractContemporary speciation provides a unique opportunity to directly observe the traits and environmental responses of a new species. Cardamine insueta is an allotriploid species that appeared within the past 150 years in a Swiss village, Urnerboden. In contrast to its two progenitor species, C. amara and C. rivularis that live in wet and open habitats, respectively, C. insueta is found in-between their habitats with temporal water level fluctuation. This triploid species propagates clonally and serves as a triploid bridge to form higher ploidy species. Although niche separation is observed in field studies, the mechanisms underlying the environmental robustness of C. insueta are not clear. To characterize responses to a fluctuating environment, we performed a time-course analysis of homeolog gene expression in C. insueta in response to submergence treatment. For this purpose, the two parental (C. amara and C. rivularis) genome sequences were assembled with a reference-guided approach, and homeolog-specific gene expression was quantified by using HomeoRoq software. We found that C. insueta and C. rivularis initiated vegetative propagation by forming ectopic meristems on leaves, while C. amara did not. We examined homeolog-specific gene expression of three species at nine time points during the treatment. The genome-wide expression ratio of homeolog pairs was 2:1 over the time-course, consistent with the ploidy number. By searching the genes with high coefficient of variation of expression over time-course transcriptome data, we found many known key transcriptional factors related to meristem development and formation upregulated in both C. rivularis and rivularis-homeolog of C. insueta, but not in C. amara. Moreover, some amara-homeologs of these genes were also upregulated in the triploid, suggesting trans-regulation. In turn, Gene Ontology analysis suggested that the expression pattern of submergence tolerant genes in the triploid was inherited from C. amara. These results suggest that the triploid C. insueta combined advantageous patterns of parental transcriptomes to contribute to its establishment in a new niche along a water-usage gradient.

scholarly journals Expression of muscle genes in heterokaryons depends on gene dosage.

1986 ◽  
Vol 102 (1) ◽  
pp. 124-130 ◽  
Author(s):  
G K Pavlath ◽  
H M Blau
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Gene Dosage ◽  
Cell Types ◽  
Threshold Concentration ◽  
Specific Gene ◽  
Mouse Muscle ◽  
Muscle Gene Expression ◽  
Muscle Genes ◽  
Muscle Gene

We report that gene dosage, or the ratio of nuclei from two cell types fused to form a heterokaryon, affects the time course of differentiation-specific gene expression. The rate of appearance of the human muscle antigen, 5.1H11, is significantly faster in heterokaryons with equal or near-equal numbers of mouse muscle and human fibroblast nuclei than in heterokaryons with increased numbers of nuclei from either cell type. By 4 d after fusion, a high frequency of gene expression is evident at all ratios and greater than 75% of heterokaryons express the antigen even when the nonmuscle nuclei greatly outnumber the muscle nuclei. The kinetic differences observed with different nuclear ratios suggest that the concentration of putative trans-acting factors significantly influences the rate of muscle gene expression: a threshold concentration is necessary, but an excess may be inhibitory.

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