What is the Secretome?
The secretome is a term used to refer to all of the genes and their regulatory elements that are involved in regulating gene expression (the actual activity of genes). These elements include transcription factors, DNA methylation sites, histone marks, protein complexes and other molecular components. The secretome comprises ~10% of total genome . The majority of these elements have not been characterized or understood well enough to understand their function. However, it is known that many of them play roles in regulating gene expression. The secretome may also contain non-coding elements such as RNA polymerase II promoters and enhancers .
Genes are the basic units of genetic information; they encode proteins that perform specific biological functions. A protein is made up of amino acids which are chemical building blocks with three carbon atoms each. Amino acids are found in two forms: essential and non-essential. Essential amino acids cannot be synthesized by humans and must come from food sources like meat, milk, eggs or fish. Non-essential amino acids can be produced by humans but require dietary supplements.
There are several types of proteins, some of which are involved in controlling gene expression.
Expression control elements are regulatory regions of DNA that control the rate and timing of gene transcription. These control elements consist of various types of transcription factors that bind to specific sites on the DNA. They are also referred to as enhancers and promoters. Enhancers bind other proteins that recruit RNA polymerase II and allow them to bind to a promoter region. A single gene can have many enhancers and they can work with each other by allowing for complex regulation of a single promoter.
Transcription factors may act as on or off switches that turn expression of a gene on or off. Promoters can also be turned on or off by different proteins or other signaling molecules.
The secretome is involved in the highly complex process of gene expression. When scientists learn more about the secretome, the precise functions of many regulatory elements will be understood in greater detail. This knowledge could lead to the development of better ways to treat various medical conditions and make advances in other life science areas.
Difference Between the Genome and the Secretome
What is the difference between the genome and the secretome?
The genome refers to an organism’s entire DNA sequence, including both coding and non-coding sequences. The secretome refers only to a subset of regulatory elements that do not code for proteins. While DNA encodes the building blocks of life, it is really RNA that carries out most of the important roles in cells. The secretome does not code for the amino acids that make up proteins, but it can regulate genes that do.
The secretome may be able to tell us more about our own natural defenses against diseases such as cancer and other illnesses. For example, there are some recently discovered non-coding RNA transcripts that are directly involved in activating interferon genes. Most of these transcripts are part of the secretome and their roles in gene expression have not yet been fully characterized.
The majority of the human genome (98.5%) does not code for proteins; this portion is referred to as non-coding DNA. Most of it is made up of various types of repetitive sequences. There are also long strings of DNA that do not fit into any category; these are called “junk DNA” and their function is not well understood. All of this DNA makes up the bulk of our genomes but only a very small portion of it actually does something.
Transposons, repetitive sequences and other seemingly useless DNA do nothing except take up space within the genome.
Some non-coding DNA does have a known purpose; it is involved in the regulation of gene expression or the creation of small nucleotide RNAs. The secretome is a small part of this category of non-coding DNA. The existence of the secretome has only been known for a few years but there is a great deal still to be learned about it. This collection of regulatory elements does not code for proteins but they do help control how and when our genes express proteins.
Another less well-known part of the genome is the rest of the non-coding DNA that doesn’t fall under any specific category. There are a few large repetitive sequences, some small ones and some other types of DNA that are not really defined at all. For now these “genomic deserts” remain the least understood parts of our entire genome.
- Senescence-messaging secretome: SMS-ing cellular stress (T Kuilman, DS Peeper – Nature reviews cancer, 2009 – nature.com)
- Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome (S Yoshimoto, TM Loo, K Atarashi, H Kanda, S Sato… – Nature, 2013 – nature.com)
- A catalogue of the effector secretome of plant pathogenic oomycetes (S Kamoun – Annual review of phytopathology, 2006 – annualreviews.org)
- A host-targeting signal in virulence proteins reveals a secretome in malarial infection (NL Hiller, S Bhattacharjee, C van Ooij, K Liolios… – …, 2004 – science.sciencemag.org)
- Secretome proteomics for discovery of cancer biomarkers (M Makridakis, A Vlahou – Journal of proteomics, 2010 – Elsevier)