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Translatomics

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Translatomics

Translatomics is the study of all open reading frames (ORFs) that are being actively translated in a cell or organism. This collection of ORFs is called the translatome. Characterizing a cell's translatome can give insight into the array of biological pathways that are active in the cell. According to the central dogma of molecular biology, the DNA in a cell is transcribed to produce RNA, which is then translated to produce a protein. Thousands of proteins are encoded in an organism's genome, and the proteins present in a cell cooperatively carry out many functions to support the life of the cell. Under various conditions, such as during stress or specific timepoints in development, the cell may require different biological pathways to be active, and therefore require a different collection of proteins. Depending on intrinsic and environmental conditions, the collection of proteins being made at one time varies. Translatomic techniques can be used to take a "snapshot" of this collection of actively translating ORFs, which can give information about which biological pathways the cell is activating under the present conditions.

Usually, the ribosome profiling technique is used to acquire the translatome information. Recent advancements, including single-cell ribosome profiling, have significantly improved the resolution of these studies, allowing researchers to gain insights into translation at the level of individual cells. This is particularly important for heterogeneous cell populations, where overall bulk measurements may mask important cell-to-cell differences in protein synthesis. Other methods are polysome profiling, full-length translating mRNA profiling (RNC-seq), and translating ribosome affinity purification (TRAP-seq). Unlike the transcriptome, the translatome is a more accurate approximation for estimating the expression level of some genes, since the correlation between the proteome and translatome is higher than the correlation between the transcriptome and proteome.

Nearing the completion of the Human Genome Project the field of genetics was shifting its focus toward determining the functions of genes. This involved cataloguing other collections of biological materials, like RNA and proteins in cells. These collections of materials were called -omes, evoking the widespread excitement surrounding the sequencing of the human genome. The term translatome was first proposed in 2001 by Greenbaum et al. The translatome was intended to describe the relative quantities of proteins in a proteome. The term translatome now generally refers to the collection of proteins actively being created in a cell. Translatomics, in combination with degradomics, aims to describe the net change to the proteome under different conditions.

The aim of genomics is to study the genome, or the collection of genetic material in an organism. Genomics subfields, or other -omics, such as Transcriptomics and proteomics aim to characterize genome function by quantifying products of the genome (such as RNA and proteins) under different conditions. In doing so, omics gain insight into different levels of regulation of gene expression and therefore genome function. However, these fields characterize biomolecules that have already been formed. In some cases, RNA or protein abundance does not reflect function because these biomolecules may be degraded rapidly, or they may remain in a cell long after they are initially synthesized. When using proteomics techniques to study the proteome, regulation of protein abundance at the level of post-translational modification and protein degradation may obscure earlier regulatory processes. Because cellular functions are often regulated at the level of translation, meaning the transcriptome does not always reflect genome function, using translatomics techniques to study the translatome may allow one to observe regulation of genome function that would be obscured in transcriptomics or proteomics studies.

Most translatomics techniques focus on characterizing the mRNAs that are complexed with ribosomes and therefore being translated.

Polysome profiling is a technique used to characterize the degree of translation of one or more mRNAs. A highly translated mRNA exists as a polysome, meaning it is complexed with multiple ribosomes. mRNAs translated at lower levels are complexed with fewer ribosomes. In polysome profiling, a sucrose gradient is used to separate molecular complexes in a cell lysate based on size. The fractions from the column are analyzed by sequencing or other methods. The translation rate of mRNAs is determined based on its detection and abundance in the fractions of lower and higher molecular weight.

The full length translating mRNA (RNC-seq) involves centrifugation of lysated sample on a sucrose cushion. This allows separation of the Ribosome-nascent chain complex(RNC) from free mRNAs and other cell components. The RNCs form a pellet in the centrifugation that is collected for further analysis. The mRNA being translated in these RNCs can be sequenced, allowing identification and quantification of the mRNAs being translated at the time. However, RNC-mRNA complexes are fragile which can lead to ribosomes to dissociate from the mRNAs and degradation of mRNAs, potentially biasing the collected results.

In Ribosome profiling, cellular mRNA including polysomes is subjected to ribonucleases, enzymes that cleave RNA. Those positions in the RNA molecules that are bound by ribosomes are protected against digestion. After cessation of ribonuclease activity, these protected sites can be recovered and sequenced. The sequences obtained from ribo-seq therefore represent fragments of mRNAs that were being actively translated.

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