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

@article{Lim2005MicroarrayAS,
  title={Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs},
  author={Lee P. Lim and Nelson C. Lau and Philip W. Garrett-engele and Andrew Grimson and Janell M. Schelter and John C. Castle and David P. Bartel and Peter S. Linsley and Jason M. Johnson},
  journal={Nature},
  year={2005},
  volume={433},
  pages={769-773}
}
MicroRNAs (miRNAs) are a class of noncoding RNAs that post-transcriptionally regulate gene expression in plants and animals. To investigate the influence of miRNAs on transcript levels, we transfected miRNAs into human cells and used microarrays to examine changes in the messenger RNA profile. Here we show that delivering miR-124 causes the expression profile to shift towards that of brain, the organ in which miR-124 is preferentially expressed, whereas delivering miR-1 shifts the profile… 
View on Springer
bartellab.wi.mit.edu
4,770 Citations
Highly Influential Citations
153
Background Citations
2,024
Methods Citations
190
Results Citations
66

4,770 Citations

RNA world: The wide reach of microRNAs
TLDR
The authors reasoned that, for genuine targets, sites of interaction with the regulatory miRNA would be preserved in orthologous genes from other vertebrates much more frequently than similarly abundant sites that lack complementarity to the miRNA.
Coherent but overlapping expression of microRNAs and their targets during vertebrate development.
MicroRNAs (miRNAs) are small noncoding RNAs that direct post-transcriptional repression of protein-coding genes. In vertebrates, each highly conserved miRNA typically regulates hundreds of target…
How Do MicroRNAs Regulate Gene Expression?
TLDR
An miRNA can decrease the intracellular concentration of its target mRNAs by accelerating the normal process of mRNA degradation and can inhibit the translation or decoding of the target mRNA, with the relative importance of these two mechanisms differing between different miRNA-mRNA pairs.
Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos
TLDR
It is found that the expression levels of miRNA targets are lower in all mouse and Drosophila tissues than in the embryos, and miRNAs are more preferentially target ubiquitously expressed genes than tissue-specifically expressed genes.
Exploring the regulatory roles of microRNAs in mammalian development
TLDR
A method to explore the impact of species-specific miRNAs on the evolution of 3′ UTRs was developed, and it was found that target sites of many mi RNAs show positive selection.
Global analysis of microRNA target gene expression reveals the potential roles of microRNAs in maintaining tissue identity
TLDR
The results strongly suggest that the global functions of microRNAs are largely involved in driving tissue differentiation and maintaining tissue identity rather than in tissue-specific physiological functions, and imply that disruption of microRNA functions might cause delineation of differentiated cells, a crucial step towards carcinogenesis.
Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs
TLDR
Sufficient information exists within a set of tumor samples to detect endogenous correlations between miRNA and mRNA levels, and a tumor suppression pathway linked to miR-181c is inferred and validated.
The impact of microRNAs on protein output
TLDR
The impact of micro RNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output.
Systems Biology Reveals MicroRNA-Mediated Gene Regulation
TLDR
Several systems-level approaches that have been applied to miRNA research are introduced and discussed, and their potential to reveal miRNA-guided gene regulatory systems and their impacts on biological functions are discussed.
MicroRNAs indirectly regulate other microRNAs in ovarian cancer cells.
TLDR
Using miRNA microarray analysis, it is shown that over 70 different miRNAs are differentially expressed in human ovarian cancer cells after transfection with a single miRNA (miR-7).
...
...

References

SHOWING 1-10 OF 41 REFERENCES
Prediction of Mammalian MicroRNA Targets
Human MicroRNA Targets
TLDR
This work has predicted target sites on the 3′ untranslated regions of human gene transcripts for all currently known 218 mammalian miRNAs to facilitate focused experiments and suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of allhuman genes.
Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation
TLDR
The identification of a subset of brain-expressedMiRNAs whose expression behavior is conserved in both mouse and human differentiating neurons implicates these miRNAs in mammalian neuronal development or function.
MicroRNA-Directed Cleavage of HOXB8 mRNA
TLDR
Results point to a miRNA-mediated mechanism for the posttranscriptional restriction of HOX gene expression during vertebrate development and demonstrate that metazoan miRNAs can repress expression of their natural targets through mRNA cleavage in addition to inhibiting productive translation.
Identification of Tissue-Specific MicroRNAs from Mouse
Specificity of microRNA target selection in translational repression.
TLDR
The ability of an miRNA to translationally repress a target mRNA is largely dictated by the free energy of binding of the first eight nucleotides in the 5' region of the miRNA, however, G:U wobble base-pairing in this region interferes with activity beyond that predicted on the basis of thermodynamic stability.
MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms
  • Yan ZengR. YiB. Cullen
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
It is demonstrated that an endogenously encoded human miRNA is able to cleave an mRNA bearing fully complementary target sites, whereas an exogenously supplied siRNA can inhibit the expression of an RNA bearing partially complementary sequences without inducing detectable RNA cleavage.
Functional siRNAs and miRNAs Exhibit Strand Bias
siRNAs can function as miRNAs.
TLDR
It is shown that a short interfering RNA (siRNA) can repress expression of a target mRNA with partially complementary binding sites in its 3' UTR, much like the demonstrated function of endogenously encoded microRNAs (miRNAs).
The microRNAs of Caenorhabditis elegans.
TLDR
The census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.
...
...