scholarly journals Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis

2019 ◽  
Vol 116 (7) ◽  
pp. 2761-2766 ◽  
Author(s):  
Ryan C. Kirkbride ◽  
Jie Lu ◽  
Changqing Zhang ◽  
Rebecca A. Mosher ◽  
David C. Baulcombe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Seed Development ◽  
Seed Coat ◽  
Target Genes ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Small Interfering Rnas ◽  
Altered Expression ◽  
Temporal Regulation ◽  
Laser Capture

Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatial-temporal activity of the NRPD1-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternal NRPD1 allele in the endosperm or seed coat. A group of maternally expressed NRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by the NRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

microRNAs in seeds: modified detection techniques and potential applications

2006 ◽  
Vol 84 (2) ◽  
pp. 189-198 ◽  
Author(s):  
Ruth C. Martin ◽  
Po-Pu Liu ◽  
Hiroyuki Nonogaki
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Environmental Signals ◽  
Detection Techniques ◽  
Potential Applications ◽  
Technical Advances ◽  
Spatio Temporal ◽  
Germinating Seeds

microRNAs (miRNAs) are small (21–24 nucleotides), single-stranded RNAs that regulate target gene expression at transcriptional and posttranscriptional levels. miRNAs play crucial roles in plant development, maintenance of homeostasis, and responses to environmental signals. miRNAs and their target genes, which can be computationally predicted in plants, are expressed in developing and germinating seeds as in other plant tissues, suggesting that miRNAs may be involved in the regulation of gene expression in seeds. Profiling multiple miRNAs expressed in developing and germinating seeds, characterizing their expression patterns in a spatio-temporal manner, and elucidating their biological functions will provide information essential for understanding the mechanisms of seed development and germination. In this review, an overview of the recent technical advances in seed miRNA research and their potential applications for plant, specifically seed, research are presented.

Cooperative signaling between cytokine receptors and the glucocorticoid receptor in the expansion of erythroid progenitors: molecular analysis by expression profiling

Blood ◽  
2003 ◽  
Vol 102 (9) ◽  
pp. 3136-3146 ◽  
Author(s):  
Andrea Kolbus ◽  
Montserrat Blázquez-Domingo ◽  
Sebastian Carotta ◽  
Walbert Bakker ◽  
Susanna Luedemann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Glucocorticoid Receptor ◽  
Large Scale ◽  
Target Genes ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Gene Profiling ◽  
Erythroid Progenitors ◽  
Erythroid Progenitor ◽  
Synergistic Interactions

AbstractErythroid progenitors undergo renewal (proliferation without apparent differentiation) in response to erythropoietin (Epo), stem cell factor (SCF), and glucocorticoids (dexamethasone) (Dex). SCF and Dex cooperate with Epo to promote proliferation and inhibit differentiation of erythroid progenitors, while Epo alone is required to protect erythroid cells from apoptosis during terminal red cell maturation. To examine the mechanism of the synergistic interactions of Epo, SCF, and Dex, we analyzed gene expression patterns using DNA chip–based large-scale comparative gene profiling using microarrays enriched in hematopoietic transcripts or containing randomly selected genes. Differentially regulated genes were validated by real-time reverse transcription–polymerase chain reaction (RT-PCR). The results reveal cooperative regulation of gene expression by glucocorticoids and Epo/SCF on a number of genes, such as CIS, BTG1, VDUP1, CXCR4, GILZ, and RIKEN29300106B05. While Epo and SCF never showed opposite effects on gene expression, Dex either enhanced or attenuated the effect of Epo and/or SCF. Several glucocorticoid receptor (GR)–target genes were regulated by Dex only in the presence of Epo and/or SCF, suggesting that the GR functions in the context of a larger transactivation complex to regulate these genes. The data also suggest that modulation of cytokine-induced signals by the GR is an important mechanism in erythroid progenitor renewal.

scholarly journals Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1059
Author(s):  
Alice Shwe ◽  
Tone-Kari Knutsdatter Østbye ◽  
Aleksei Krasnov ◽  
Sigmund Ramberg ◽  
Rune Andreassen
Keyword(s):  
Gene Expression ◽  
Atlantic Salmon ◽  
Target Genes ◽  
Sea Water ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Head Kidney ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.

scholarly journals Non-monotonic regulation of gene expression, neural progenitor fate and brain growth by the chromatin remodeller CHD8

2018 ◽  
Author(s):  
Shaun Hurley ◽  
Conor Mohan ◽  
Philipp Suetterlin ◽  
Jacob Ellegood ◽  
Fabrizio Rudari ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Development ◽  
Protein Function ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Neural Progenitor ◽  
Dominant Negative ◽  
Brain Growth ◽  
Loss Of Function ◽  
Altered Expression

SummaryHeterozygous CHD8 mutations are associated with autism and macrocephaly with high penetrance in the human population. The reported mutations may have loss-of-function (haploinsufficient), hypomorphic or dominant negative effects on protein function. To determine the effects of reducing CHD8 protein function below haploinsufficient levels on brain development, we established a Chd8 allelic series in the mouse. Chd8 heterozygous mice exhibited relatively subtle brain overgrowth and little gene expression changes in the embryonic neocortex. In comparison, mild Chd8 hypomorphs displayed significant postnatal lethality, with surviving animals exhibiting more pronounced brain hyperplasia, and significantly altered expression of over 2000 genes. Autism-associated genes were downregulated and neural progenitor proliferation genes upregulated. Severe Chd8 hypomorphs displayed even greater transcriptional dysregulation, affecting genes and pathways that largely overlapped with those dysregulated in the mild hypomorphs. By contrast, homozygous, conditional deletion of Chd8 in early neuronal progenitors resulted in the induction of p53 target genes, cell cycle exit, apoptosis and pronounced brain hypoplasia. Intriguingly, increased progenitor proliferation in hypomorphs was primarily restricted to TBR2+ intermediate progenitors, suggesting critical roles for CHD8 in regulating the expansion of this population. Given the importance of these progenitors in human cortical growth, this observation suggests that human brain development might be more sensitive to CHD8 deficiency than the mouse. We conclude that brain development is acutely sensitive to CHD8 dosage and that the varying sensitivities of different progenitor populations and cellular processes to CHD8 dosage can result in non-linear effects on gene transcription and brain growth.

scholarly journals Macromolecule biosynthesis: a key function of sleep

2007 ◽  
Vol 31 (3) ◽  
pp. 441-457 ◽  
Author(s):  
Miroslaw Mackiewicz ◽  
Keith R. Shockley ◽  
Micah A. Romer ◽  
Raymond J. Galante ◽  
John E. Zimmerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Sleep Deprivation ◽  
Expression Patterns ◽  
State Level ◽  
Altered Expression ◽  
Mouse Cerebral Cortex ◽  
Genes Encoding ◽  
Function Of Sleep ◽  
Cellular Components

The function(s) of sleep remains a major unanswered question in biology. We assessed changes in gene expression in the mouse cerebral cortex and hypothalamus following different durations of sleep and periods of sleep deprivation. There were significant differences in gene expression between behavioral states; we identified 3,988 genes in the cerebral cortex and 823 genes in the hypothalamus with altered expression patterns between sleep and sleep deprivation. Changes in the steady-state level of transcripts for various genes are remarkably common during sleep, as 2,090 genes in the cerebral cortex and 409 genes in the hypothalamus were defined as sleep specific and changed (increased or decreased) their expression during sleep. The largest categories of overrepresented genes increasing expression with sleep were those involved in biosynthesis and transport. In both the cerebral cortex and hypothalamus, during sleep there was upregulation of multiple genes encoding various enzymes involved in cholesterol synthesis, as well as proteins for lipid transport. There was also upregulation during sleep of genes involved in synthesis of proteins, heme, and maintenance of vesicle pools, as well as antioxidant enzymes and genes encoding proteins of energy-regulating pathways. We postulate that during sleep there is a rebuilding of multiple key cellular components in preparation for subsequent wakefulness.

scholarly journals Temporal Regulation of Gene Expression of the Escherichia coli Bacteriophage phiEco32

2012 ◽  
Vol 416 (3) ◽  
pp. 389-399 ◽  
Author(s):  
Olga Pavlova ◽  
Daria Lavysh ◽  
Evgeny Klimuk ◽  
Marko Djordjevic ◽  
Dmitry A. Ravcheev ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulation Of Gene Expression ◽  
Temporal Regulation

A TRIPARTITE CLUSTERING ANALYSIS ON MICRORNA, GENE AND DISEASE MODEL

2012 ◽  
Vol 10 (01) ◽  
pp. 1240007 ◽  
Author(s):  
CHENGCHENG SHEN ◽  
YING LIU
Keyword(s):  
Gene Expression ◽  
Clustering Algorithm ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Disease Model ◽  
Relational Information ◽  
Microrna Gene ◽  
Research Findings ◽  
Family Based

Alteration of gene expression in response to regulatory molecules or mutations could lead to different diseases. MicroRNAs (miRNAs) have been discovered to be involved in regulation of gene expression and a wide variety of diseases. In a tripartite biological network of human miRNAs, their predicted target genes and the diseases caused by altered expressions of these genes, valuable knowledge about the pathogenicity of miRNAs, involved genes and related disease classes can be revealed by co-clustering miRNAs, target genes and diseases simultaneously. Tripartite co-clustering can lead to more informative results than traditional co-clustering with only two kinds of members and pass the hidden relational information along the relation chain by considering multi-type members. Here we report a spectral co-clustering algorithm for k-partite graph to find clusters with heterogeneous members. We use the method to explore the potential relationships among miRNAs, genes and diseases. The clusters obtained from the algorithm have significantly higher density than randomly selected clusters, which means members in the same cluster are more likely to have common connections. Results also show that miRNAs in the same family based on the hairpin sequences tend to belong to the same cluster. We also validate the clustering results by checking the correlation of enriched gene functions and disease classes in the same cluster. Finally, widely studied miR-17-92 and its paralogs are analyzed as a case study to reveal that genes and diseases co-clustered with the miRNAs are in accordance with current research findings.

scholarly journals Alterations of Growth and Focal Adhesion Molecules in Human Breast Cancer Cells Exposed to the Random Positioning Machine

2021 ◽  
Vol 9 ◽  
Author(s):  
Jayashree Sahana ◽  
Thomas J. Corydon ◽  
Markus Wehland ◽  
Marcus Krüger ◽  
Sascha Kopp ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Target Genes ◽  
Interaction Analysis ◽  
Expression Patterns ◽  
Focal Adhesions ◽  
Multicellular Spheroids ◽  
Down Regulation ◽  
Random Positioning Machine ◽  
Mcf 7

In this study, we evaluated changes in focal adhesions (FAs) in two types of breast cancer cell (BCC) lines (differentiated MCF-7 and the triple-negative MDA-MB-231 cell line) exposed to simulated microgravity (s-μg) created by a random positioning machine (RPM) for 24 h. After exposure, the BCC changed their growth behavior and exhibited two phenotypes in RPM samples: one portion of the cells grew as a normal two-dimensional monolayer [adherent (AD) BCC], while the other portion formed three-dimensional (3D) multicellular spheroids (MCS). After 1 h and 30 min (MDA-MB-231) and 1 h 40 min (MCF-7), the MCS adhered completely to the slide flask bottom. After 2 h, MDA-MB-231 MCS cells started to migrate, and after 6 h, a large number of the cells had left the MCS and continued to grow in a scattered pattern, whereas MCF-7 cells were growing as a confluent monolayer after 6 h and 24 h. We investigated the genes associated with the cytoskeleton, the extracellular matrix and FAs. ACTB, TUBB, FN1, FAK1, and PXN gene expression patterns were not significantly changed in MDA-MB-231 cells, but we observed a down-regulation of LAMA3, ITGB1 mRNAs in AD cells and of ITGB1, TLN1 and VCL mRNAs in MDA-MB-231 MCS. RPM-exposed MCF-7 cells revealed a down-regulation in the gene expression of FAK1, PXN, TLN1, VCL and CDH1 in AD cells and PXN, TLN and CDH1 in MCS. An interaction analysis of the examined genes involved in 3D growth and adhesion indicated a central role of fibronectin, vinculin, and E-cadherin. Live cell imaging of eGFP-vinculin in MCF-7 cells confirmed these findings. β-catenin-transfected MCF-7 cells revealed a nuclear expression in 1g and RPM-AD cells. The target genes BCL9, MYC and JUN of the Wnt/β-catenin signaling pathway were differentially expressed in RPM-exposed MCF-7 cells. These findings suggest that vinculin and β-catenin are key mediators of BCC to form MCS during 24 h of RPM-exposure.

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