Monthly Archives: February 2016

Day 32 (2p24.2-2p23.3): ApoB, one gene that encodes two different cholesterol carriers

Day 32 has 41 protein-coding genes including APOB (apolipoprotein B). The APOB protein is the protein part of LDL (low density lipoprotein, or so-called “bad cholesterol”) particles, which shuttle cholesterol in your bloodstream.

APOB is a good example of a gene that is subject to RNA editing to make two versions of a protein. (This is different than alternative splicing – an actual letter of the RNA is changed rather than splicing different pieces together to make a different RNA.) In the small intestine, only the half of APOB protein is made, and this version makes chylomicrons which carry lipids from food to the blood.

Click here to see Day 32 with your APOB gene.

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Day 33 (2p23.3-2p22.3): proopiomelanocortin, source of the runners’ high

 

"Bechovice Prague CZ memorial of running race" by User:Miaow Miaow - Own work. Licensed under Public Domain via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Bechovice_Prague_CZ_memorial_of_running_race.JPG#/media/File:Bechovice_Prague_CZ_memorial_of_running_race.JPG"Bechovice Prague CZ memorial of running race" by User:Miaow Miaow - Own work. Licensed under Public Domain via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Bechovice_Prague_CZ_memorial_of_running_race.JPG#/media/File:Bechovice_Prague_CZ_memorial_of_running_race.JPG

 

 

Day 33 has 88 protein-coding genes including POMC (proopiomelanocortin.)  POMC is interesting because it is chopped up to make several different hormones with very different roles: from MSH which stimulates skin cells to darken, to beta-endorphin, responsible for improved mood after exercise.

Click here to see your POMC gene on Day 33.

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Day 34 (2p22.3-2p21): EIF2AK2 (PKR), a watchdog for virus genes

| Genome Year

By J Roberto Trujillo – Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=28909393

 

Day 34 has 32 protein-coding genes, including EIF2AK2 (eukaryotic translation initiation factor 2-alpha kinase 2), also known as PKR (protein kinase R). The protein PKR watches for signs of viral invasion – specifically, double-stranded RNA. Although our cells use RNA as a way to xerox copy transcripts of genes, these transcripts are single-stranded. Double-stranded RNA is a hallmark of virus genomes in the cell. When PKR detects virus genomes, it tries to turn off the cell’s translation machinery.

Because EIF2AK2 is so effective, viruses have evolved ways to try to evade it. For example, one of HIV’s genes makes an RNA (Tat) that fools PKR into thinking that it is one of the cell’s translation proteins to turn off. By making enough of this decoy, PKR loses its ability to stop HIV from making its own proteins.

Click here to see your EIF2AK2 gene on Day 34.

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Day 35 (2p21-2p16.3): EPAS1, an ancient echo that persists in the highest mountains

By Stanisław Jaworski – Zbigniew Kowalewski; Andrzej Paczkowski (1986) Mount Everest – Dzieje zdobycia i Podboju, Warsaw: Wydawnictwo Sport i Turystyka, pp. 163 ISBN 83-217-2527-9http://lo-zywiec.pl/~heinrich/foto/fot3.jpg, Public Domain, https://commons.wikimedia.org/w/index.php?curid=3947842

 

Day 35 has 50 protein-coding genes, including EPAS1 (Endothelial PAS domain-containing protein 1).  The EPAS1 protein is a transcription factor that turns on certain genes when oxygen levels are low.

EPAS1 has recently gained fame because it is a beautiful example of local adaptation. When searching for genetic differences between high-altitude and surrounding populations in Tibet, researchers found a whopping mismatch in versions of the EPAS1 gene. The high-altitude version of EPAS1 equips people for low-oxygen conditions. Even more surprising, the actual mutations were not acquired in Tibet, but rather introgressed from an ancient extinct hominin species, the Denisovans.

Click here to see EPAS1 on Day 35.

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Day 36 (2p16.3-2p16.1): RTN4, saying No-go to nerves

Detail of Carswell’s drawing of MS lesions in the brain stem and spinal cord (1838)

 

Day 36 has only 24 protein-coding genes. One of them is RTN4 (reticulon 4), also known as Nogo.

During development, growing nerves need help knowing exactly where to branch and connect. They hear a cocktail of chemical signals from the body – some of them saying grow in a certain direction, and some of them staying stop. Nogo is one of the stop signals. It is also thought to be one of the reasons that nerves don’t regenerate after injury. Nogo levels also seem to be associated with plasticity (learning and rewiring) in the brain, and Nogo may be one of the links between exercise and improved mental function.

Click here to see your RTN4 gene that makes Nogo, on Day 36.

 

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Day 37 (2p16.1-2p15): A copper-handling gene discovered using dogs

https://commons.wikimedia.org/wiki/File:Diego_juillet2009_014.JPG

https://commons.wikimedia.org/wiki/File:Diego_juillet2009_014.JPG

Day 37 has 34 genes, including COMMD1 (copper metabolism domain containing 1).  This gene helps cells use copper, an essential nutrient used by some enzymes.

COMMD1 was discovered by looking at Bedlington Terriers, a dog breed with a predisposition to copper toxicosis. Because purebred dogs are so genetically similar to each other, figuring out the genetic differences between dogs with and without copper toxicosis was easier than it would have been in humans.

Click here to see your COMMD1 gene on Day 37.

 

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Day 38 (2p14-2p12): The anthrax receptor

Day 38 has 97 protein-coding genes, including ANTXR1 (anthrax toxin receptor 1). The anthrax bacteria smuggles two toxins into cells using the ANTXR1 protein.

Of course, ANTXR1 is not in your genome with the purpose of letting anthrax in; it has some normal role in cell function that just hasn’t been figured out. Its previous name, TEM8 (tumor endothelial marker 8), also came from studying disease: it was turned on in tumors and not in surrounding normal cells.

Click here to see your ANTXR1 gene which will hopefully never perform its named function.

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Day 39 (2p12-2p11.2): a cluster of regeneration genes

Screen Shot 2016-02-14 at 11.10.46 AM

Day 39 has only 11 protein-coding genes, but it has four of the five genes for regeneration proteins.  REG1A, for example, is a protein originally found by studying kidney stones. Pancreatic cells secrete REG1A as they are undergoing programmed cell death – it’s a signal to create more cells to replace them.

Click here to see your REG1A gene on Day 39. Notice that it is a very short coding sequence, and that it has two neighboring REG genes.

 

 

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Day 40 (2p11.2-2p11.1): The IGK@ locus, an incredible card-shuffling act

| Genome Year

Day 40 has 49 protein-coding genes. Click here for a genome browser view and notice all of the IGK (immunoglobulin kappa) genes at the end of the day: this huge cluster is known as the IGK@ locus.

Our adaptive immune systems are able to produce antibodies against billions of potential germs, but we only have a relative handful of genes that encode antibodies. These presented a paradox that was solved by Susumu Tonegawa, who discovered that our B and T cells edit their genomes to shuffle together different antibody subunit genes to create 3×1011 possible antibodies. IGK@ is one of the special places in the genome where this shuffling happens.

The systems for immune gene recombination are shared among jawed vertebrates, but the process happens differently in different species.

Click here to see the sequence of Day 40, jumping to a typical IGK@ gene, IGKV1-17.

 

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Day 41 (2p11.1-2q11.2): ADRA2B, a gene involved with emotional memory

 

Rwandan_Genocide_Murambi_skulls

 

Day 41 starts with the centromere of Chromosome 2, then the long (q) arm starts with 60 protein-coding genes, including the gene for ADRA2B (alpha-2b adrenergic receptor), which plays a part in neurotransmitter release in the brain.

A deletion of three amino acids in ADRA2B is very common. Researchers have found that people with this mutation have enhanced emotional memory. This effect was found to hold true in two very different contexts: volunteers remembering images presented during an experiment, and refugees of the Rwandan genocide remembering trauma.

Click here to see the sequence of your ADRA2B gene on Day 41. (The reference genome happens to have the less-common version with the deletion.) Click here to see Day 41 in a genome browser.

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