A Grimson

A Krek

A Stark

AJ Giraldez

AR Soares

AS Flynt

AS Yoo

B John

BP Lewis

C Cheng

C Conaco

CA Logan

CO Gualerzi

Cortemeglia

D Baek

D Kultz

D Zheng

DG Hendrickson

DP Bartel

E Wienholds

EI Boyle

EJ Thatcher

EV Makeyev

GM Schratt

J Dresios

J Li

J Tsang

J Zhang

JA Nielsen

K Chen

K Tu

K Yamaguchi-Shinozaki

KK Biggar

KR Cordes

L Goentoro

L Lopez-Maury

L Vergauwen

Liangbiao Chen

LP Lim

M Hammell

M Kertesz

M Zhao

M Zuker

MR Friedlander

NJ Martinez

NL Simone

P Landgraf

PY Chen

R Li

R Shalgi

R Zhang

RC Lee

RJ Johnston Jr

RL Malek

Ruolin Yang

S Maslov

S Roush

S van Dongen

SA Manakov

Shue Chen

T Hansen

TP Frazier

V Hilgers

VG Tusher

W Qu

X Chen

X Jian

Y Erlich

Y Liang

YJ Hua

Z Dai

Zhonghua Dai

BMC Genomics

English

PubMed

Springer - Publisher Connector

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

Abstract
          
            Background
            MicroRNAs (miRNAs) play important roles in regulating the expression of protein-coding genes by directing the degradation and/or repression of the translation of gene transcripts. Growing evidence shows that miRNAs are indispensable player in organismal development with its regulatory role in the growth and differentiation of cell lineages. However, the roles of miRNA-mediated regulation in environmental adaptation of organisms are largely unknown. To examine this potential regulatory capability, we characterized microRNAomes from the brain of zebrafish raised under normal (28°C) and cold-acclimated (10°C, 10 days) conditions using Solexa sequencing. We then examined the expression pattern of the protein-coding genes under these two conditions with Affymetrix Zebrafish Genome Array profiling. The potential roles of the microRNAome in the transcriptomic cold regulation in the zebrafish brain were investigated by various statistical analyses.
          
          
            Results
            Among the total 214 unique, mature zebrafish miRNAs deposited on the miRBase website (release 16), 175 were recovered in this study. In addition, we identified 399 novel, mature miRNAs using multiple miRNA prediction methods. We defined a set of 25 miRNAs differentially expressed under the cold and normal conditions and predicted the molecular functions and biological processes that they involve through Gene Ontology (GO) annotation of their target genes. On the other hand, microarray analysis showed that genes related to mRNA processing and response to stress were overrepresented among the up-regulated genes in cold-stress, but are not directly corresponding to any of the GO molecular functions and biological processes predicted from the differential miRNAs. Using several statistical models including a novel, network-based approach, we found that miRNAs identified in this study, either individually or together, and either directly or indirectly (i.e., mediated by transcription factors), only make minor contribution to the change in gene expression patterns under the low-temperature condition.
          
          
            Conclusions
            Our results suggest that the cold-stress response of mRNA expression may be governed mainly through regulatory modes other than miRNA-mediated regulation. MiRNAs in animal brains might act more as developmental regulators than thermal adaptability regulators.
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Crossref

A mammalian microRNA expression atlas based on small RNA library sequencing. Cell

AF: MicroRNAs regulate brain morphogenesis in zebrafish. Science

Agartz I, et al: Brain expressed Yang et al.

al: Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol

al: The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev

B: Salt and Drought Stresses Induce the Aberrant Expression of microRNA Genes in Tobacco.

Burge CB: Prediction of mammalian microRNA targets. Cell

Characterization of microRNA expression profiles in normal human tissues.

Chong K: Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response.

CL: Transcriptional and posttranscriptional control of cold-shock genes.

Crabtree GR: MicroRNA-mediated switching of chromatin-remodelling complexes in neural development.

D: miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature

DP: MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell

DP: The impact of microRNAs on protein output. Nature

Efficient frequency-based de novo shortread clustering for error trimming in next-generation sequencing. Genome Res

Enright AJ: Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods

Enright AJ: miRBase: tools for microRNA genomics.

Enright AJ: Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.

et al: Combinatorial microRNA target predictions. Nat Genet

F: Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics

Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput Biol

GN: Transcriptional responses to thermal acclimation in the eurythermal fish Gillichthys mirabilis (Cooper 1864).

GO:: TermFinder–open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics

Greenberg ME: A brain-specific microRNA regulates dendritic spine development. Nature

GS: The effects of temperature reduction on gene expression and oxidative stress in skeletal muscle from adult zebrafish. Comp Biochem Physiol C Toxicol Pharmacol

Hannon GJ: Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods

Hogstrand C: Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion.

HS: Identification and target prediction of miRNAs specifically expressed in rat neural tissue.

Human MicroRNA targets. PLoS Biol

JB: Ionizing radiation-induced oxidative stress alters miRNA expression. PLoS One

JG: Genomic organization of zebrafish microRNAs.

JG: miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos.

JG: Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet

KB: The emerging roles of microRNAs in the molecular responses of metabolic rate depression.

L: Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol Dev

LD: Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis.

Li WX: Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis. New Phytol

Long-term warm or cold acclimation elicits a specific transcriptional response and affects energy metabolism in zebrafish. Comp Biochem Physiol A Mol Integr Physiol

Long-term warm or cold acclimation elicits a specific transcriptional response and affects energy metabolism in zebrafish. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology

M: mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptorpositive and estrogen receptor-negative breast cancer. Genome Biol

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs.

MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl Acad Sci USA

MicroRNAs: target recognition and regulatory functions. Cell

MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.

Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol

Molecular evolution of a primate-specific microRNA family. Mol Biol Evol

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res

Oudenaarden A: MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell

Parallel DNA pyrosequencing unveils new zebrafish microRNAs.

Plasterk RH: MicroRNA expression in zebrafish embryonic development. Science

PO: Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol

Rajewsky N: Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol

Rajewsky N: The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet

Reciprocal actions of REST and a microRNA promote neuronal identity.

Segal E: The role of site accessibility in microRNA target recognition. Nat Genet

Shinozaki K: Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol

Significance analysis of microarrays applied to the ionizing radiation response.

Slack FJ: The let-7 family of microRNAs. Trends Cell Biol

SM: Drosophila microRNAs 263a/b confer robustness during development by protecting nascent sense organs from apoptosis. PLoS Biol

SM: MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems.

SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics

Specificity and stability in topology of protein networks. Science

Sunkar R: Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNAstars during silkworm development.

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res

Tanavde V: Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha.

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell

The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell

The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell

Thomas LG: Temperature tolerances of wild-type and red transgenic zebra danios.

V: mirWIP: microRNA target prediction based on microRNAcontaining ribonucleoprotein-enriched transcripts. Nat Methods

VP: Cold stress-induced protein Rbm3 binds 60S ribosomal subunits, alters microRNA levels, and enhances global protein synthesis.

Walhout AJ: A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev

XJ: Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer’s disease cortex reveals altered miRNA regulation.

YX: Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res

Zhang Z: Evolution of an X-linked primate-specific microRNA cluster. Mol Biol Evol

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

Abstract

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