MicroRNA-mediated gene regulation plays a minor role in the transcriptomic plasticity of cold-acclimated Zebrafish brain tissue

Yang, Ruolin; Dai, Zhendong; Chen, Shue; Chen, Liangbiao

doi:10.1186/1471-2164-12-605

Cited by 38 publications

(25 citation statements)

References 73 publications

(76 reference statements)

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“…However, Yang et al previously reported that cold acclimation trigger changes in some miRNA profiles in adult zebrafish brains and those miRNAs have poor associations to the affected genes. They concluded that microRNAs play a minor role in mediating transcriptome plasticity during cold stress [30]. It appears to be contradictory to our finding that the affected miRNAs have predicted target genes involved in cold-inducible biological processes, including melanogenesis, GnRH signaling pathway and circadian rhythm.…”

Section: Discussioncontrasting

confidence: 99%

“…As miRNAs accumulate over time, miRNAs exert their suppressive effect on the mRNA targets, causing a decrease in mRNA target expression. The poor correlation between cold-affected miRNAs and mRNAs observed previously [30] might be due to the time of sample collection or the use of different tissues (brain tissue vs. whole larvae used here). The duration of stress also determines if cells can re-establish homeostasis or initiate the mechanism to acclimate to the new environment [57].…”

Section: Discussionmentioning

confidence: 79%

“…Yang et al claimed that miRNAs may have a minor role in regulating transcriptome plasticity in cold acclimated zebrafish brains based on the poor correlations between cold-induced transcriptomic and miRNAtome profiles [30]. This is in clear contrast to our previous understanding observed in other organisms [31, 32].…”

Section: Introductionmentioning

confidence: 92%

“…miR-8 and miR-429 have been reported to be involved in the osmotic stress response in zebrafish [28, 29]. In contrast, high-throughput miRNAtomes analysis revealed no significant impact by miRNA-mediated gene regulation in the cold - acclimated adult zebrafish brains [30]. This result is puzzling, but we reasoned that the cold-induced responses might be different in organisms or tissues used.…”

Section: Introductionmentioning

confidence: 97%

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MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

et al. 2016

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BackgroundMicroRNAs (miRNAs) are critical regulators responding to acute environmental stresses in both plants and animals. By modulating gene expression, miRNAs either restore or reconstitute a new expression program to enhance cell tolerance to stresses. Cold shock is one of the stresses that can induce acute physiological responses and transcriptional changes in aquatic creatures. Previous genomic studies have revealed many cold-affected genes in fish larvae and adults, however, the role of miRNAs in acute cold response is still ambiguous. To elucidate the regulatory roles of miRNAs in the cold-inducible responses, we performed small RNA-seq and RNA-seq analyses and found potential cold regulatory miRNAs and genes. We further investigated their interactions and involvements in cold tolerance.ResultsSmall RNA-seq and RNA-seq identified 29 up-/26 down-regulated miRNAs and 908 up-/468 down-regulated genes, respectively, in responding to cold shock for 4 h at 18 °C. miRNA and transcriptomic analyses showed these miRNAs and mRNAs are involved in similar biological processes and pathways. Gene ontology enrichment analyses revealed the cold-induced genes were enriched in pathways, including melanogenesis, GnRH pathway, circadian rhythm, etc. We were particularly interested in the changes in circadian clock genes that affect daily metabolism. The enrichment of circadian clock genes was also observed in previous fish cold acclimation studies, but have not been characterized. To characterize the functional roles of circadian clock genes in cold tolerance, we individually overexpressed selected clock genes in zebrafish larvae and found one of the core clock genes per2 resulted in better recovery from cold shock. In addition, we validated the interaction of per2 with its associate miRNA, dre-mir-29b, which is also cold-inducible. It suggests the transcription of per2 can be modulated by miRNA upon cold shock.ConclusionsCollectively, our observations suggest that miRNAs are fine turners for regulating genomic plasticity against cold shock. We further showed that the fine tuning of core clock gene per2 via its associated miRNA, dre-mir-29b, can enhance the cold tolerance of zebrafish larvae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3239-4) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 92%

Section: Introductionmentioning

confidence: 97%

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MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

et al. 2016

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“…Several previous studies have analyzed global microRNA expression in zebrafish embryos using microarrays (Thatcher et al, 2007; Zhang et al, 2011; Tal et al, 2012; Wu et al, 2012) and deep sequencing (Soares et al, 2009; Cifuentes et al, 2010; Yang et al, 2011; Wei et al, 2012). Some of these studies have also used real-time RT-PCR to confirm their results.…”

Section: Discussionmentioning

confidence: 99%

Effects of short-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos

Jenny

Aluru

Hahn

2012

Toxicology and Applied Pharmacology

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Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. MicroRNAs, single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. Recent studies have demonstrated that exposure to xenobiotics can alter microRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. In this study we tested the hypothesis that developmental exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), a well-known teratogen, alters microRNA expression during zebrafish development. We exposed zebrafish embryos to DMSO (0.1%) or TCDD (5 nM) for 1 hr at 30 hours post fertilization (hpf) and measured microRNA expression using several methods at 36 and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf (62-fold) and 60 hpf (135-fold) as determined by real-time RT-PCR, verifying the effectiveness of the exposure. MicroRNA expression profiles were determined using microarrays (Agilent and Exiqon), next-generation sequencing (SOLiD), and real-time RT-PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR-451, 23a, 23b, 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 microRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However, miR-27e was the only microRNA to be identified as differentially expressed by all three methods (both microarrays, SOLiD sequencing, and real-time RT-PCR). These results suggest that TCDD exposure causes modest changes in expression of microRNAs, including some (miR-451, 23a, 23b, 24 and 27e) that are critical for hematopoiesis and cardiovascular development.

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Objective review of de novo stand‐alone error correction methods for NGS data

Alic

Ruzafa

Dopazo

et al. 2016

WIREs Comput Mol Sci

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The sequencing market has increased steadily over the last years, with different approaches to read DNA information, prone to different types of errors. Multiple studies demonstrated the impact of sequencing errors on different applications of Next Generation Sequencing (NGS), making error correction a fundamental initial step. Different methods in the literature use different approaches and fit different types of problems. We analysed a number of 50 methods divided into five main approaches (k-spectrum, suffix arrays, multiple sequence alignment, read clustering and probabilistic models). They are not published as a part of a suite (stand-alone) and target raw, unprocessed data without an existing reference genome (de Novo). These correctors handle one or more sequencing 1 Correspondence to: asalic@posgrado.upv.es 1 technologies using the same or different approaches. They face general challenges (sometimes with specific traits for specific technologies) such as repetitive regions, uncalled bases and ploidy. Even assessing their performance is a challenge in itself because of the approach taken by various authors, the unknown factor (de Novo) and the behaviour of the third party tools employed in the benchmarks. This work aims at helping the researcher in the field to advance the state-of-the-art, the educator to have a brief but comprehensive companion and the bioinformatician to choose the right tool for the right job.The Next Generation Sequencing (NGS) appeared in 2005 and since then its market has increased steadily, with various technologies being developed. The NGS has evolved faster than the the Moore's law in Computer Science, allowing us to sequence and assemble large genomes like the Loblolly Pine with 22 Gb 1 or the Norway Spruce with 20 Gb 2 for a reasonable cost in time and resources. However, there are many other species (e.g. the Amoeba Dubia with a 670 Gb estimated genome size 3 , 200x human genome's size) that are still challenging to assemble. The errors introduced by the sequencing process are one of the main reasons NGS data has to be corrected before any further use. Multiple studies have demonstrated the impact of sequencing errors on different applications of NGS, making error correction a fundamental initial step. [4][5][6][7] There are many error correction tools in the literature that cope with different technologies and error types. However, to our knowledge, there is no complete, objective review of the modern methods that could help researchers, educators and users at the same time. There are benchmarks summarizing a number of methods, but there is none extensively focusing on the implementation, features and the overall domain (including challenges). Our work synthesises 50 de Novo stand-alone error-correction software. The Supplementary Material includes the description of the approach used to search the literature along with the inclusion criteria.The article continues with the motivation (also containing a brief description of the sequencing technologies and various err...

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MicroRNA-mediated gene regulation plays a minor role in the transcriptomic plasticity of cold-acclimated Zebrafish brain tissue

Cited by 38 publications

References 73 publications

MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae

Effects of short-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos

Objective review of de novo stand‐alone error correction methods for NGS data

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