Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

Guimbellot, Jennifer S.; Erickson, Stephen W.; Mehta, Tapan; Wen, Hui; Page, Grier P.; Sorscher, Eric J.; Hong, Jeong S.

doi:10.1186/1755-8794-2-15

Cited by 67 publications

(60 citation statements)

References 46 publications

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“…In most cases, the number of induced DEGs exceeded the number of reduced DEGs; however, the number of reduced DEGs was greater when treatment duration was extended. Most animal data sets identified fewer than 100 DEGs, with the exception of stagnant human cell cultures (more than 1,000 DEGs; Guimbellot et al, 2009). DEG numbers in microorganisms were similar to those of animals, despite their lower gene contents.…”

Section: Data Collection and Identification Of Differentially Expressmentioning

confidence: 99%

“…Low-oxygen response expression data were obtained for 21 organisms from databases and publications: Arabidopsis (Arabidopsis thaliana; BrancoPrice et al, 2008;van Dongen et al, 2009;Mustroph et al, 2009), rice (Oryza sativa; Lasanthi- Kudahettige et al, 2007;Narsai et al, 2009), poplar (Populus trichocarpa; Kreuzwieser et al, 2009), Chlamydomonas reinhardtii (Mus et al, 2007), Homo sapiens (Kim et al, 2006;Chen et al, 2008;Guimbellot et al, 2009), Mus musculus (Greijer et al, 2005;Allen et al, 2006;Hu et al, 2006), Danio rerio (van der Meer et al, 2005;Marques et al, 2008), Drosophila melanogaster (Liu et al, 2006;Azad et al, 2009), Caenorhabditis elegans (Shen et al, 2005), Trichoderma reesei (Bonaccorsi et al, 2006), Saccharomyces cerevisiae (Linde et al, 1999;Lai et al, 2005;Protchenko et al, 2008), Schizosaccharomyces pombe (Todd et al, 2006), Candida albicans (Setiadi et al, 2006), Cryptococcus neoformans (Chun et al, 2007), Escherichia coli (Salmon et al, 2003;Kang et al, 2005;Covert et al, 2008), Mycobacterium tuberculosis (Park et al, 2003), Pseudomonas aeruginosa (Alvarez-Ortega and Harwood, 2007), Pseudomonas stutzeri (Dou et al, 2008), Sinorhizobium meliloti (Becker et al, 2004), Synechocystis species PCC 6803 (Summerfield et al, 2008), and Zymomonas mobilis (Yang et al, 2009). Additional Arabidopsis and human data sets evaluated responses across experimental conditions and cell types (Arabidopsis, …”

Section: Data Set Collection and Analysismentioning

confidence: 99%

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Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

et al. 2010

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High-throughput technology has facilitated genome-scale analyses of transcriptomic adjustments in response to environmental perturbations with an oxygen deprivation component, such as transient hypoxia or anoxia, root waterlogging, or complete submergence. We showed previously that Arabidopsis (Arabidopsis thaliana) seedlings elevate the levels of hundreds of transcripts, including a core group of 49 genes that are prioritized for translation across cell types of both shoots and roots. To recognize low-oxygen responses that are evolutionarily conserved versus species specific, we compared the transcriptomic reconfiguration in 21 organisms from four kingdoms (Plantae, Animalia, Fungi, and Bacteria). Sorting of organism proteomes into clusters of putative orthologs identified broadly conserved responses associated with glycolysis, fermentation, alternative respiration, metabolite transport, reactive oxygen species amelioration, chaperone activity, and ribosome biogenesis. Differentially regulated genes involved in signaling and transcriptional regulation were poorly conserved across kingdoms. Strikingly, nearly half of the induced mRNAs of Arabidopsis seedlings encode proteins of unknown function, of which over 40% had up-regulated orthologs in poplar (Populus trichocarpa), rice (Oryza sativa), or Chlamydomonas reinhardtii. Sixteen HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes, including four that are Arabidopsis specific, were ectopically overexpressed and evaluated for their effect on seedling tolerance to oxygen deprivation. This allowed the identification of HUPs coregulated with genes associated with anaerobic metabolism and other processes that significantly enhance or reduce stress survival when ectopically overexpressed. These findings illuminate both broadly conserved and plant-specific lowoxygen stress responses and confirm that plant-specific HUPs with limited phylogenetic distribution influence low-oxygen stress endurance.Oxygen is required for the efficient production of ATP by plants and other aerobes. Despite the extremely high affinities for oxygen of the oxidases involved in aerobic respiration (K m of 0.08-1 mM; Hoshi et al., 1993), obligate and facultative aerobes regularly experience oxygen deprivation for myriad reasons. Although oxygen is a by-product of photosynthesis, plants lack a circulatory system to mobilize oxygen to heterotrophic roots, tubers, meristems, germinating pollen, and developing seeds. These and flooded organs are vulnerable to oxygen deficiency. In mammals, intermittent tissue or cellular hypoxia can occur due to inhibition of pulmonary respiration (i.e. sleep apnea; Azad et al., 2009) and blood flow (i.e. stroke; Mense et al., 2006), a low-oxygen environment (i.e. high altitude), or high cellular density and metabolic activity (i.e. tumor cells and ischemia [Fang et al., 2009]). In the case of microbes, oxygen availability is influenced by the density and identity of surrounding organisms and can be modulated over the course of a day or season, as observed in the microb...

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Section: Data Collection and Identification Of Differentially Expressmentioning

confidence: 99%

Section: Data Set Collection and Analysismentioning

confidence: 99%

Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

et al. 2010

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“…For example, as discussed above, several reports have shown the link between upregulation of miR-23b and hypoxia [167,185,186]. As miR-23b and miR-23b* share the same precursor, miR-23b* could also be regulated by HIF.…”

Section: Mir-23b* Regulation By Other Factorsmentioning

confidence: 89%

MiRNA and Proline Metabolism in Cancer

Liu¹,

Phang²

2013

Oncogene and Cancer - From Bench to Clinic

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“…A study in humans found that hypoxic events altered the expression of several miRNAs (eg, miR-152) in colonic cells. 41 An animal study screening for lung miRNA profiles in rats after chronic hypoxia showed aberrant expression of several miRNA markers, including miR-30. 42 It is possible that the aberrant expression of miRNAs might relate to hypoxic or hyperoxic insults from ventilator and oxygen use.…”

Section: Discussionmentioning

confidence: 99%

MicroRNA Expression Aberration Associated with Bronchopulmonary Dysplasia in Preterm Infants: A Preliminary Study

Wu¹,

Chen²,

Hsieh³

et al. 2013

Respir Care

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BACKGROUND: Because environmental insults and genetic factors account for the variance in the risk of bronchopulmonary dysplasia (BPD) in very low birth weight (VLBW, birth weight < 1,500 g) preterm infants, the search for BPD biomarkers has begun to focus on the regulators of non-coding RNA such as microRNAs (miRNAs). Therefore, this study aimed to identify potential miRNAs involved in the pathogenesis of BPD in VLBW preterm infants. METHODS: A case-control study (15 subjects with BPD and 15 sex-matched control subjects without BPD) was conducted to investigate the expression profiles of 365 miRNAs in the peripheral blood of VLBW preterm infants at 36 weeks post-menstrual age (called the older-age set). The expression levels of identified miRNAs were further evaluated in a subsample of blood collected during the first 2 weeks post-natal age (called the younger-age set). Possible biological functions and pathways implicated in the target genes regulated by the miRNAs were explored using database predictions. RESULTS: A 4-miRNA signature (miR-152, miR-30a-3p, miR-133b, and miR-7) with aberrant expression levels at 36 weeks, derived from a supervised classification with internal cross-validation, discriminated the subjects with BPD from those without BPD with an accuracy of 0.91. The discriminative accuracy of the 4 miRNAs was supported by random permutations of either the disease status or the number of miRNAs selected (both P < .001). A down-regulation change of miR-152 and miR-30a-3p expression levels and an up-regulation change of miR-133b and miR-7 expression levels were found in the older-age set, compared to the younger-age set. CONCLUSIONS: This is the first study to identify blood-based miRNAs associated with BPD. The findings provide information regarding the roles of these biomarkers in the development of BPD in VLBW preterm infants.

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Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis

Cited by 67 publications

References 46 publications

Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

Cross-Kingdom Comparison of Transcriptomic Adjustments to Low-Oxygen Stress Highlights Conserved and Plant-Specific Responses

MiRNA and Proline Metabolism in Cancer

MicroRNA Expression Aberration Associated with Bronchopulmonary Dysplasia in Preterm Infants: A Preliminary Study

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