Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana

Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized protein sequence signatures for three family members in the HRGP superfamily: the hyperglycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). However, the mechanism of pollen-specific HRGP gene expression remains unexplored. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences to identify cis-regulatory motifs responsible for pollen-specific expression of HRGP genes in Arabidopsis thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery identified 15 conserved promoter elements between A.thaliana and A. lyrata. Motif scanning revealed two pollen related transcription factors: GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Finally, we performed a regression analysis and demonstrated that the 15 motifs provided a good model of HRGP gene expression in pollen (R = 0.61). In conclusion, we performed the first integrative analysis of cis-regulatory motifs in pollen-specific HRGP genes, revealing important insights into transcriptional regulation in pollen tissue.

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Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana

10.1101/2020.08.19.256693 ◽

2020 ◽

Author(s):

Yichao Li ◽

Maxwell Mullin ◽

Yingnan Zhang ◽

Frank Drews ◽

Lonnie Welch ◽

...

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Motif Discovery ◽

Plant Cell Wall ◽

Integrative Analysis ◽

Regulatory Sequences ◽

Rna Seq ◽

Motif Analysis ◽

Specific Expression ◽

Regulatory Motifs

ABSTRACTHydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall structural proteins that function in various aspects of plant growth and development, including pollen tube growth. We have previously characterized HRGP superfamily into three family members: the hyperglycosylated arabinogalactan-proteins, the moderately glycosylated extensins, and the lightly glycosylated proline-rich proteins. However, the mechanism of pollen-specific HRGP expression remains untouched. To this end, we developed an integrative analysis pipeline combining RNA-seq gene expression and promoter sequences that identified 15 transcriptional cis-regulatory motifs responsible for pollen-specific expression of HRGP in Arabidopsis Thaliana. Specifically, we mined the public RNA-seq datasets and identified 13 pollen-specific HRGP genes. Ensemble motif discovery with various filters identified 15 conserved promoter elements between Thaliana and Lyrata. Known motif analysis revealed pollen related transcription factors of GATA12 and brassinosteroid (BR) signaling pathway regulator BZR1. Lastly, we performed a machine learning regression analysis and demonstrated that the identified 15 motifs well captured the HRGP gene expression in pollen (R=0.61). In conclusion, we performed the integrative analysis as the first-of-its-kind study to identify cis-regulatory motifs in pollen-specific HRGP genes and shed light on its transcriptional regulation in pollen.

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Human globin gene promoter sequences are sufficient for specific expression of a hybrid gene transfected into tissue culture cells

Molecular and Cellular Biology ◽

10.1128/mcb.7.1.398-402.1987 ◽

1987 ◽

Vol 7 (1) ◽

pp. 398-402

Author(s):

T Rutherford ◽

A W Nienhuis

Keyword(s):

Gene Expression ◽

Globin Gene ◽

Gene Promoter ◽

Gene Promoters ◽

Globin Genes ◽

Specific Expression ◽

Tissue Specific ◽

Promoter Sequences ◽

Erythroleukemia Cells ◽

Murine Erythroleukemia

The contribution of the human globin gene promoters to tissue-specific transcription was studied by using globin promoters to transcribe the neo (G418 resistance) gene. After transfection into different cell types, neo gene expression was assayed by scoring colony formation in the presence of G418. In K562 human erythroleukemia cells, which express fetal and embryonic globin genes but not the adult beta-globin gene, the neo gene was expressed strongly from a fetal gamma- or embryonic zeta-globin gene promoter but only weakly from the beta promoter. In murine erythroleukemia cells which express the endogenous mouse beta genes, the neo gene was strongly expressed from both beta and gamma promoters. In two nonerythroid cell lines, human HeLa cells and mouse 3T3 fibroblasts, the globin gene promoters did not allow neo gene expression. Globin-neo genes were integrated in the erythroleukemia cell genomes mostly as a single copy per cell and were transcribed from the appropriate globin gene cap site. We conclude that globin gene promoter sequences extending from -373 to +48 base pairs (bp) (relative to the cap site) for the beta gene, -385 to +34 bp for the gamma gene, and -555 to +38 bp for the zeta gene are sufficient for tissue-specific and perhaps developmentally specific transcription.

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Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Plants ◽

10.3390/plants9091176 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1176

Author(s):

Ivan Tsers ◽

Vladimir Gorshkov ◽

Natalia Gogoleva ◽

Olga Parfirova ◽

Olga Petrova ◽

...

Keyword(s):

Gene Expression ◽

Plant Cell Wall ◽

Soft Rot ◽

Regulatory Elements ◽

Plant Responses ◽

Gene Promoters ◽

Rna Seq ◽

Induced Plant Responses ◽

Regulatory Systems ◽

Genome Level

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

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Human glucagon gene promoter sequences regulating tissue-specific versus nutrient-regulated gene expression

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00215.2001 ◽

2002 ◽

Vol 282 (1) ◽

pp. R173-R183 ◽

Cited By ~ 23

Author(s):

Min Nian ◽

Jun Gu ◽

David M. Irwin ◽

Daniel J. Drucker

Keyword(s):

Gene Expression ◽

Gene Promoter ◽

Regulatory Sequences ◽

Dependent Manner ◽

Specific Expression ◽

Tissue Specific ◽

High Fiber ◽

Fiber Diet ◽

Regulated Gene Expression

The glucagon-like peptides (GLPs) are synthesized and secreted in a nutrient-dependent manner in rodents; however, the factors regulating human GLP-1 and GLP-2 biosynthesis remain unclear. To understand how nutrients regulate human proglucagon gene expression, we studied the expression of a human proglucagon promoter-growth hormone (GH) transgene in 1.6 human glucagon-GH transgenic mice. Fasting-refeeding significantly decreased and increased the levels of circulating mouse insulin and transgene-derived hGH ( P < 0.05 fasting vs. refeeding) and decreased and upregulated, respectively, the levels of endogenous mouse proglucagon RNA in the ileum but not in the jejunum or colon. High-fiber feeding significantly increased the levels of glucose-stimulated circulating hGH and upregulated levels of mouse intestinal proglucagon gene expression in the jejunum, ileum, and colon ( P < 0.05, 0 vs. 30% fiber diet). In contrast, neither fasting-refeeding nor a high-fiber diet upregulated the expression of the human proglucagon promoter-hGH transgene. These findings demonstrate that human proglucagon gene regulatory sequences specifying tissue-specific expression in gut endocrine cells are not sufficient for recognition of energy-derived signals regulating murine glucagon gene expression in enteroendocrine cells in vivo.

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Different regulatory sequences control creatine kinase-M gene expression in directly injected skeletal and cardiac muscle.

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.1264 ◽

1993 ◽

Vol 13 (2) ◽

pp. 1264-1272 ◽

Cited By ~ 61

Author(s):

C K Vincent ◽

A Gualberto ◽

C V Patel ◽

K Walsh

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Creatine Kinase ◽

Cardiac Muscle ◽

Serum Response Factor ◽

Sequence Motif ◽

Regulatory Sequences ◽

Response Factor ◽

Specific Expression ◽

Serum Response

Regulatory sequences of the M isozyme of the creatine kinase (MCK) gene have been extensively mapped in skeletal muscle, but little is known about the sequences that control cardiac-specific expression. The promoter and enhancer sequences required for MCK gene expression were assayed by the direct injection of plasmid DNA constructs into adult rat cardiac and skeletal muscle. A 700-nucleotide fragment containing the enhancer and promoter of the rabbit MCK gene activated the expression of a downstream reporter gene in both muscle tissues. Deletion of the enhancer significantly decreased expression in skeletal muscle but had no detectable effect on expression in cardiac muscle. Further deletions revealed a CArG sequence motif at position -179 within the promoter that was essential for cardiac-specific expression. The CArG element of the MCK promoter bound to the recombinant serum response factor and YY1, transcription factors which control expression from structurally similar elements in the skeletal actin and c-fos promoters. MCK-CArG-binding activities that were similar or identical to serum response factor and YY1 were also detected in extracts from adult cardiac muscle. These data suggest that the MCK gene is controlled by different regulatory programs in adult cardiac and skeletal muscle.

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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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Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

10.1101/238691 ◽

2017 ◽

Cited By ~ 1

Author(s):

Seth Polydore ◽

Michael J. Axtell

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Small Rna ◽

Small Rnas ◽

Rna Seq ◽

Triple Mutant ◽

Physiological Mechanisms ◽

Protein Coding ◽

Regulate Gene Expression ◽

Rna Biogenesis

SummaryPlant small RNAs regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs and other hairpin-derived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, −2, or −6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.Significance StatementSmall RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

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Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

10.1101/136614 ◽

2017 ◽

Cited By ~ 3

Author(s):

Douglas R. Wilson ◽

Wei Sun ◽

Joseph G. Ibrahim

Keyword(s):

Gene Expression ◽

Type I Error ◽

The Cancer Genome Atlas ◽

Type I ◽

Eqtl Mapping ◽

Rna Seq ◽

Specific Expression ◽

Normal Cells ◽

Technology Application ◽

Tumor Tissues

AbstractThe study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g. immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells.

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Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species

10.1101/2020.07.29.227397 ◽

2020 ◽

Author(s):

Thomas M. Winkelmüller ◽

Frederickson Entila ◽

Shajahan Anver ◽

Anna Piasecka ◽

Baoxing Song ◽

...

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Binding Sites ◽

Microbial Control ◽

Purifying Selection ◽

Wrky Transcription Factor ◽

Specific Gene ◽

Specific Expression ◽

Brassicaceae Species ◽

Species Specific

AbstractPlants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Employing comparative transcriptomics of six Arabidopsis thaliana accessions and three additional Brassicaceae species for PTI responses to the MAMP flg22, we identified a set of genes with expression changes under purifying selection in the Brassicaceae species and genes exhibiting species-specific expression signatures. Variation in flg22-triggered transcriptome and metabolome responses across Brassicaceae species was incongruent with their phylogeny while expression changes were strongly conserved within A. thaliana, suggesting directional selection for some species-specific gene expression. We found the enrichment of WRKY transcription factor binding sites in 5’-regulatory regions in conserved and species-specific responsive genes, linking the emergence of WRKY-binding sites with the evolution of gene responses in PTI. Our findings advance our understanding of transcriptome evolution during biotic stress.

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Integrative Analysis of Axolotl Gene Expression Data From Regenerative and Wound Healing Limb Tissues

10.1101/693523 ◽

2019 ◽

Author(s):

Mustafa Sibai ◽

Cüneyd Parlayan ◽

Pelin Tuğlu ◽

Gürkan Öztürk ◽

Turan Demircan

Keyword(s):

Gene Expression ◽

Wound Healing ◽

Differential Expression Analysis ◽

Limb Regeneration ◽

Ambystoma Mexicanum ◽

Integrative Analysis ◽

Control Group ◽

Rna Seq ◽

Amputation Injury ◽

Study Designs

ABSTRACTAxolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and full restoration of amputated limbs. Several regenerative cues of the axolotl limb were successfully unraveled due to the advent of high-throughput technologies and their employment in tackling research questions on several OMICS levels. The field of regenerative biology and medicine has therefore utilized the axolotl as a major and powerful experimental model. Studies which have previously unraveled differentially expressed (DE) genes en masse in different phases of the axolotl limb regeneration have primarily used microarrays and RNA-Seq technologies. However, as different labs are conducting such experiments, sufficient consistency may be lacking due to statistical limitations arising from limited number of sample replicates as well as possible differences in study designs. This study, therefore, aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs. Three biological groups were conceived for the analysis; homeostatic tissues (control group), from amputation/injury timepoint up to around 50 hours post amputation (wound healing group), and from 50 hours to 28 days post amputation/injury (regenerative group). Integrative analysis was separately carried out on the selected microarray and RNA-Seq data from axolotl limb samples using the “merging” method. Differential expression analysis was separately implemented on the processed data from both technologies using the R/Bioconductor “limma” package. A total of 1254 genes (adjusted P < 0.01) were found DE in regenerative samples compared to the control, out of which 351 showed magnitudes of Log Fold Changes (LogFC) > 1 and were identified as the top DE genes from data of both technologies. Downstream analyses illustrated consistent correlations of the logFCs of DE genes distributed among the biological comparisons, within and between both technologies. Gene ontology annotations demonstrated concordance with the literature on the biological process involved in the axolotl limb regeneration. qPCR analysis validated the observed gene expression level differences between regenerative and control samples for a set of five genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.

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