15.7: Ome-Sweet-Ome
- Page ID
- 88999
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Early technologies like the ones described in this chapter were applied to understanding the structure, function, and regulation of specific genes. Some more recent technologies (e.g., microarrays) are well adapted to a more holistic approach to studying cell function. Terms we have already seen (e.g., genome, epigenome, transcriptome) were coined in an effort to define different objects of study whose underlying network of molecular interactions can more accurately explain cell function. These objects of study often overlap and can be confusing.
Here is a short compendium of -omes, with an attempt at clarification:
- Genome: total DNA content of a cell, identical in every cell of an organism
- Proteome: a cell’s protein profile and steady state at any given moment
- Exome: A cell’s total coding DNA (excluding noncoding DNA)
- Epigenome: A cell’s total DNA-modification/chromatin topography
- Methylome: The pattern of methylation of DNA in the genome
- Paleoproteome: Profile of proteins found in ancient remains by mass spectroscopy
- Transcriptome: A cell’s RNA-transcript profile and steady state at any given moment
- Epitranscriptome: A map of chemical modifications of RNAs that inform their function
- Metabolome: All of the small metabolites in a defined sample (cell, organelle, tissue, etc.)
- Mechanobiome: the molecular network cells use to generate, sense and respond to intraand extracellular forces
- Regulome: a cell’s regulatory components, including metabolites, proteins, mRNAs, genes, cis DNA elements.
One might be excused for assuming that such cellular profiles would be the same for all cells in a tissue, only changing as gene expression is regulated during development or when signaled by extracellular events or chemical signals. But even genomic and exomic profiles can change! Recall somatic mutations in dividing cells, and genome loss in some cells (e.g., erythrocytes that emerge from our reticulocytes). Studies of large numbers of individual cells suggest profile variation even in cells of the same tissue or cell culture. How and why this is so is a rapidly growing new area of study, made possible by new tools for studying DNA, RNA and proteins molecules in single cells (see Mapping Protein Networks, The Dark Proteome, What on Earth is Paleoproteomics? A Human Transcriptome Study, Nature vs Nurture: Diet, Behavior, & the Epigenome, Epitranscriptomics-Functional Modification of RNAs, Sex-Specific Human Transcriptomes ( Sex-Specific Human Transcriptomes-full article. Can you name the next…-ome? Maybe the chondrome (see Mining Mitochondrial Transcriptomes).
Consider the axolotl (a salamander) genome, 10 times bigger than our own ( The HUGE Axolotl Genome, or Axolotl Genome-full article), or the lungfish genome, 14 times the size of ours (The World Record Lungfish Genome!). What do they do with all that DNA? Can our current technologies figure it out? And what’s a lungfish anyway!!?