Monthly Archives: March 2016

Day 60 (3p25.3-3p24.3): the oxytocin receptor

oxytocin2http://blogs.discovermagazine.com/neuroskeptic/2013/12/08/spinal-taps-save-oxytocin-research/#.VtN5-pMrK1u

Day 60 has 85 protein-coding genes (browser view), including OXTR, the gene for the oxytocin receptor.

Oxytocin is used medically to induce childbirth, and stimulates lactation. It has also been attached to more dubious claims. An intronic SNP in the OXTR gene, rs53576, is associated with a number of personality traits.

Click here to see the sequence of Day 60 with the rs53576 variant flashing.

 

 

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Day 61 (3p24.3-3p24.2): a simple repeat

Screen Shot 2016-03-02 at 10.20.00 PM

Day 61 has only 19 protein-coding genes (browser view). Today’s highlight is one of the types of repetitive sequence that makes up over half of the genome: a simple repeat. This particular repeat is over a thousand bases long and consists mostly of As and Ts.

These simple repeats tend to crop up in the genome through a mistake in copying DNA called replication slippage.

Click here to see the sequence of Day 61 with this simple repeat underlined.

 

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Day 62 (3p24.2-3p22.3): a sushi domain protein

glycoproteinhttp://www.wardelab.com/11-1.html

Day 62 has 29 protein-coding genes (browser view), including SUSD5 (sushi domain containing 5). Because there isn’t much known about this gene, it’s simply named after a part of the protein that looks familiar: a sushi domain. The sushi domain is so called because it consists of a loop within another loop.

Click here to see the full sequence of Day 62 with your SUSD5 gene underlined.

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Day 63 (3p22.3-3p22.1): catenin beta, a moonlighting armadillo

Chttp://www.wired.com/2014/01/absurd-creature-of-the-week-pink-fairy-armadillo-crawls-out-of-the-desert-and-into-our-hearts/

Day 63 has 63 protein-coding genes, including CTNNB1 (catenin beta 1), also known as beta-catenin. Beta catenin helps cells stick to each other to form structured tissues, but also moonlights with a radically different role in the nucleus: regulating genes during development.

CTNNB1 is homologous to the armadillo gene in flies. CTNNB1 is shared with animals as distant as worms, meaning it is at least 500 million years old.

Click here to see the sequence of day 63 with your CTNNB1 gene underlined.

 

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Day 64: (3p22.1-3p21.2): CCR5 Δ32, an HIV resistance mutation

HIV_attachmenthttps://en.wikipedia.org/wiki/CCR5#/media/File:HIV_attachment.gif

 

Day 64 has a whopping 154 protein-coding genes (browser view), more than any other day on Chromosome 3 (no other day breaks 90.) It is home to the CCR5 (chemokine C-C motif receptor 5) gene.

The CCR5 protein is expressed on the surface of T-cells, and is required for HIV infection. 10% of European-ancestry people carry a deletion of part of CCR5 (Δ32). These people are partially resistant to HIV; the 1% of people who carry a deletion in both copies of CCR5 are totally resistant. This mutation arose in a single human; the evolutionary reason why it rose to such a high prevalence in only one population has been hotly debated.

Click here to see the sequence of Day 64. The flashing “K” marks the beginning of the 32-base deletion.

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Day 65 (3p21.2-3p14.2): TLR9, detecting invading DNA

http://www.nature.com/ni/journal/v7/n1/fig_tab/ni0106-13_F1.html

 

Day 65 has 85 protein-coding genes (browser view) including the gene for TLR9 (toll-like receptor 9).

Like TLR5 on Day 26, TLR9 is a protein that is primed to detect invading pathogens. TLR9 does this by watching for DNA that looks foreign. Normally, the two letters CG next to each other (aka CpG) are methylated in human DNA. Unmethylated CpGs are the norm in bacteria and viruses. TLR9 watches for DNA with unmethylated CpGs to mount an immune response.

Click here to see the sequence of Day 65, with TLR9 underlined.

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Day 66 (3p14.2-3p14.1): FRA3B, the most fragile spot in the genome

Screen Shot 2016-03-12 at 6.41.14 PMhttp://link.springer.com/referenceworkentry/10.1007%2F978-3-642-16483-5_2262

Day 66 has 20 protein-coding genes (browser view). Inside one of those genes, FHIT, lies FRA3B, a fragile site. FRA3B is the most common place for DNA to physically break from exposure to genotoxic chemicals like those in cigarette smoke, and is frequently found broken in cancer.

Click here to see the sequence of Day 66 with FRA3B underlined.

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Day 67 (3p14.1-3p12.3): a gene from a bornavirus

Borna_1800https://en.wikipedia.org/wiki/Borna,_Leipzig#/media/File:Borna_1800.jpg

 

Day 67 has 21 protein-coding genes (browser view), including EBLN2 (endogenous Bornavirus-like nucleoprotein 2), a gene that hopped from a virus to animal genomes over 40 million years ago.

About 8% of the human genome consists of endogenous retroviruses. Retroviruses – like HIV – carry the ability to reverse transcribe themselves from RNA into DNA, integrating into the host genome. The discovery of EBLN2 in 2010 was surprising, though, because it came from Borna virus, which is not a retrovirus. Borna is an RNA virus that infects the brain and is deadly in sheep and horses (it was named after a German town where an outbreak in horses occurred), but infects humans with no clear effects besides possible correlations with psychiatric disease.

Click here to see the sequence of Day 67 with EBLN2 underlined.

 

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Day 68 (3p12.3-3p12.1): a gene desert with two roundabout genes

lbknews.com_http://blogs.villagegreen.com/detroit/files/2012/08/lbknews.com_.jpg

 

Day 68 is the most gene-poor of any part of Chromosome 3: only four protein-coding genes (browser view). Two are related: ROBO1 and ROBO2 (roundabout homologs 1 and 2).

Roundabout genes were discovered in fly. The roundabout proteins are on the surface of growing axons in the brain, and help them decide whether to cross between the halves of the brain.

Roundabout genes are found as far away as worm, meaning they are at least 550 million years old.

Click here to see the sequence of Day 68 with ROBO1 underlined.

 

 

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Day 69 (3p12.1-3q11.2): a centromere and CGGBP1, a transcription factor

Screen Shot 2016-04-08 at 10.40.09 PM

Day 69 has only 13 protein-coding genes (browser view), and the centromere of Chromosome 3. The genes include CGGBP1 (CGG triplet-repeat binding protein 1.) The gene for CGGBP1 encodes a protein that binds to DNA – as the name suggests, it binds to repeats of “CGG” in DNA, and turns on nearby genes. That makes it a transcription factor.

CGGBP1 is well known because it regulates the region of DNA that causes Fragile X syndrome, but it probably has many other roles as well.

Click here to see Day 69 with CGGBP1 underlined.

 

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