Since
the Human Genome Project, our knowledge of the genetic code has
increased beyond that of simple genes. The genome is in fact quite
complex, composed of overlapping gene regions, many stretches of
repeating code, non-coding microRNAs (miRNAs), etc. In addition, despite
every cell containing a complete copy of the genome, proteins are not
identically expressed within different organs. There is inherent protein
"noise" between different cell types. Noise in this case may be defined as
variation in the concentration of a protein across different cel types.
Hoffman and Pilpel (2015) summarize a research paper (Schmiedel et
al., 2015) in which investigators were attempting to create a
reporter method to measure fluctuations in protein noise. It has been
suggested that miRNAs may have a regulatory role in filtering noise across
different tissue types.
miRNAs are short pieces of non-coding RNA; they do not become translated
to a protein product. Many miRNAs assume regulatory roles by binding to
complementary sequence sites on mRNAs to decrease protein expression. If
a miRNA targets an mRNA strand, the mRNA may be degraded, thus lowering
the expression level of the gene that encoded the mRNA. This
paper explores a different kind of regulatory role for miRNAs.
This project was discovery science to try to determine how microRNAs may
cooperate with mRNAs to regulate protein noise. Discovery science may be
defined as those investigations without a defined hypothesis, often
applying to large data-sets. In this case, investigators built a reporter
model in order to understand if miRNAs regulated protein noise. They did
not have a specific example in mind but were analyzing general trends.
Figure
1. When miRNAs are present, mRNA that is expressed at a
lower level fluctuates less, but mRNA that is present in greater
amounts shows more noise. (Taken
from Hoffman and Pilpel, 2015).
Genomic Methodology
In this project, investigators wondered whether organisms had
evolved some sort of biological mechanism to control expression noise and
attempted to attribute a regulatory role to miRNAs. They determined a
model to quantify putative regulation on noise levels. The method consists
of a transgenic fluorescence reporter that will measure gene expression
noise, and enable researchers to modify whether that reporter has miRNA
binding sites in the 3' untranslated region (3' UTR). Fluorescence under
various states of miRNA binding sites was analyzed using flow cytometry
and fluorescence activated cell sorting (FACS), and the data were
incorporated into mathematical models. After modeling and completing their
cell assays, the researchers concluded that miRNAs have a regulatory role
in two different ways. For genes that are lowly expressed, miRNAs reduce
protein noise, but for genes that are highly expressed, miRNAs increase
noise (see Figure 1).
Take-Home Message
The biological phenomenon comes down to two forms of noise: intrinsic
(within the cell, such as biochemical operations) or extrinsic (manifested
in global differences between cells, such as ribosome copy number).
Proteins expressed at low levels fall into the former category whereas
highly expressed proteins are in the latter category. Extrinsic effects on
protein expression would cause varied miRNA expression as well. For
example, different cell types may have different numbers of RNA
polymerases, affecting the number of active miRNA transcripts.
miRNA binding reduces intrinsic protein noise, but any increases in
protein expression noise must be due to extrinsic noise that the miRNA
cannot control. While this appears inconclusive, an analysis of the mouse
genome revealed ~90% of genes could be regulated by miRNAs (Hoffman and
Pilpel, 2015). The implications of this research include providing a
mechanism by which cells reinforce their genomic identities by controlling
unhealthy fluctuations in gene expression (noise) via miRNAs.
Evaluation
The
investigators used a standard cell-assay reporter protocol to determine
the effects of certain miRNA binding targets on protein expression
levels. Their method was simple but elegant, and provided some insight
into yet another layer of complexity regarding the genetic code. Not
only does miRNA regulate the intrinsic levels of mRNAs, but it also
reduces or increases protein noise based on cell type. The
perspectives article successfully broke down the confusing differences
between extrinsic and intrinsic noise, and provided examples of miRNA
mechanisms in each case.
This project opens the doors to further research on miRNA regulation of
specific proteins' noise levels. We now have technology to sequence the
genome of individual cells. With a reporter system based on the one
described in this paper, future scientists may understand the nuances
between the genetic code of a cell, its transcriptome, and maybe even what
makes specific genes noisier than others within a cell type.
References
Hoffman, Yonit and Pilpel Yitzhak. (2015) MicroRNAs silence the noisy
genome. Science 348:41-42.
Schmiedel, Horn M. et al. (2015) MicroRNA control of protein
expression noise. Science 348:128-132.
