Identification of DNA Regulatory Motifs and Regulators by Integrating Gene Expression and Sequence Data

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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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 ◽

10.7717/peerj.11875 ◽

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.

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Single pass cDNA sequencing - a powerful tool to analyse gene expression in preparasitic juveniles of the southern root-knot nematode Meloidogyne incognita

Nematology ◽

10.1163/156854101750236259 ◽

2001 ◽

Vol 3 (2) ◽

pp. 129-139 ◽

Cited By ~ 38

Author(s):

Jaap Bakker ◽

Fred Gommers ◽

Geert Smant ◽

Pierre Abad ◽

Marie-Noëlle Rosso ◽

...

Keyword(s):

Gene Expression ◽

Cdna Library ◽

Meloidogyne Incognita ◽

Sequence Data ◽

Homo Sapiens ◽

Large Fraction ◽

Nematode Species ◽

Cdna Libraries ◽

Parasitic Nematodes ◽

Root Knot Nematode

AbstractExpressed sequence tags (EST) have been widely used to assist in gene discovery in various organisms (e.g., Arabidopsis thaliana, Caenorhabditis elegans, Mus musculus, and Homo sapiens). In this paper we describe an EST project, which aims to investigate gene expression in Meloidogyne incognita at the onset of parasitism. Approximately 1000 5′-end sequence tags were produced from a cDNA library made of freshly hatched preparasitic second stage juveniles (J2). The EST were identified in the primary transformants of the cDNA library, and assigned to nine different functional groups, including (candidate) parasitism genes. A large fraction of the EST (45%) did not have a putative homologue in public databases. Sixty five percent of the EST that could be clustered into a functional group had putative homologues in other nematode species. EST were found for virtually all parasitism related genes that have been cloned from M. incognita to date. In addition, several novel genes were tagged, including a xylanase and a chitinase gene. The efficiency of EST projects, which produce sequence data for thousands of genes in months time without any difficult pre-selections of mRNA pools, makes random sequencing cDNA libraries a superior method to identify candidates for parasitism related genes in plant-parasitic nematodes. The sequences in this paper are retrievable from Genbank with the accession numbers BE191640 to BE191741, BE217592 to BE217720, BE225324 to BE225598, BE238852 to BE239221, and BE240829 to BE240865.

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Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

PLoS Genetics ◽

10.1371/journal.pgen.1006278 ◽

2016 ◽

Vol 12 (9) ◽

pp. e1006278 ◽

Cited By ~ 12

Author(s):

Michalis Barkoulas ◽

Amhed M. Vargas Velazquez ◽

Alexandre E. Peluffo ◽

Marie-Anne Félix

Keyword(s):

Gene Expression ◽

Specific Gene ◽

Regulatory Motifs ◽

Specific Gene Expression

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DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola

Genes ◽

10.3390/genes10020137 ◽

2019 ◽

Vol 10 (2) ◽

pp. 137 ◽

Cited By ~ 16

Author(s):

Shenglin Liu ◽

Anne Aagaard ◽

Jesper Bechsgaard ◽

Trine Bilde

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Sequence Data ◽

Social Spider ◽

The Social ◽

Genome Bisulfite Sequencing ◽

Differential Gene ◽

Methylation Patterns ◽

Comparative Phylogenetic Analysis

Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.

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GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

Nucleic Acids Research ◽

10.1093/nar/29.7.1616 ◽

2001 ◽

Vol 29 (7) ◽

pp. 1616-1622 ◽

Cited By ~ 28

Author(s):

L. Qin

Keyword(s):

Gene Expression ◽

Cdna Sequence ◽

Sequence Data ◽

Expression Profiles ◽

Gene Expression Profiles

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Distinct Patterns of Gene Expression Associated with Development of Fluconazole Resistance in Serial Candida albicansIsolates from Human Immunodeficiency Virus-Infected Patients with Oropharyngeal Candidiasis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.11.2932 ◽

1998 ◽

Vol 42 (11) ◽

pp. 2932-2937 ◽

Cited By ~ 147

Author(s):

Jose L. Lopez-Ribot ◽

Robert K. McAtee ◽

Linda N. Lee ◽

William R. Kirkpatrick ◽

Theodore C. White ◽

...

Keyword(s):

Gene Expression ◽

Human Immunodeficiency Virus ◽

Sequence Data ◽

Point Mutations ◽

Oropharyngeal Candidiasis ◽

Fluconazole Resistance ◽

Expression Of Genes ◽

Immunodeficiency Virus ◽

Major Facilitator ◽

Abc Transporter Genes

ABSTRACT Resistance to fluconazole is becoming an increasing problem in the management of oropharyngeal candidiasis in human immunodeficiency virus-infected patients. Strains obtained from five patients developed decreased fluconazole susceptibility over time. DNA strain typing confirmed the high degree of relatedness among isolates from one patient and the variability among isolates from different patients. Expression of genes involved in development of fluconazole resistance was monitored in each isolate using probes specific for ERG11 (lanosterol 14α-demethylase), MDR1 (a major facilitator), andCDR (ATP-binding cassette or ABC transporter) genes. Increased expression of CDR genes was detected in the series of isolates from two patients. Isolates from one of the two patients also demonstrated increased ERG11 expression, whereas isolates from the other patient did not. Increased levels ofMDR1 mRNA correlated with increased resistance in sequential isolates from another patient. Initial overexpression ofMDR1 with subsequent overexpression of CDRgenes and a final isolate again overexpressing MDR1 were detected in serial isolates from another patient. In another patient, overexpression of these genes was not detected despite an eightfold increase in fluconazole MIC. In this patient, sequence data of theERG11 gene revealed no point mutations associated with decreased susceptibility. Five different patterns of gene expression were observed in isolates recovered from five patients who developed resistance. Therefore, these experiments demonstrate that a variety of mechanisms or combinations of mechanisms are associated with the development of fluconazole drug resistance. Additional studies are needed to estimate the frequency and clinical impact of these mechanisms of resistance.

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The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli

PLoS ONE ◽

10.1371/journal.pone.0114347 ◽

2014 ◽

Vol 9 (12) ◽

pp. e114347 ◽

Cited By ~ 19

Author(s):

Mattias Rydenfelt ◽

Hernan G. Garcia ◽

Robert Sidney Cox ◽

Rob Phillips

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Regulatory Motifs ◽

Expression In Escherichia Coli

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Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Nature Biotechnology ◽

10.1038/nbt1098-939 ◽

1998 ◽

Vol 16 (10) ◽

pp. 939-945 ◽

Cited By ~ 559

Author(s):

Frederick P. Roth ◽

Jason D. Hughes ◽

Preston W. Estep ◽

George M. Church

Keyword(s):

Whole Genome ◽

Noncoding Sequences ◽

Regulatory Motifs ◽

Mrna Quantitation ◽

Dna Regulatory Motifs

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Regulatory motifs identified from a maize developmental coexpression network

Genome ◽

10.1139/gen-2013-0177 ◽

2014 ◽

Vol 57 (3) ◽

pp. 181-184 ◽

Cited By ~ 3

Author(s):

Gregory S. Downs ◽

Christophe Liseron-Monfils ◽

Lewis N. Lukens

Keyword(s):

Gene Expression ◽

Transcriptional Control ◽

Important Determinant ◽

Gene Expression Pattern ◽

Transcript Level ◽

Regulatory Sequences ◽

Regulatory Motifs ◽

Control Gene Expression ◽

Maize Gene ◽

Upstream Regulatory Sequences

Transcriptional control is an important determinant of plant development, and distinct modules of coordinated genes characterize the maize developmental transcriptome. Upstream regulatory sequences are often the primary factors that control gene expression pattern and abundance. Here, we identify 244 regulatory motifs that are significantly enriched within 24 gene expression modules previously constructed from transcript abundances of 34 876 Zea mays (maize) gene models from embryogenesis to senescence. Within modules, we identify motifs that have not been characterized. In addition, we identify motifs similar to experimentally verified motifs, and the functions of these motifs overlap with predicted module functions. This work demonstrates the power of transcript-level coexpression modules to identify both variants of known regulatory motifs and novel motifs that control a species’ developmental transcriptome.

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