Monday, March 06, 2017

What's in Your Genome? Chapter 2: The Big Picture

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! I thought I'd post the TOC for each chapter as I finish the first drafts. Here's chapter 2.

Chapter 2: The Big Picture
  • How much of the genome has been sequenced?
  • Whose genome was sequenced?
  • How many genes?
  • Pseudogenes
  • Regulatory sequences
  • Origins of replication
  • Centromeres
  • Telomeres
  • Scaffold Attachment regions (SARs)
  • Transposons
  • Viruses
  • Mitochondrial DNA (NumtS)
  • How much of our genome is functional?


8 comments :

  1. Why capitalize the "s" in "Numts"? Hey, does the human genome have any tandem repeats of whole mt genomes? I seem to recall that some bird species do.

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    Replies
    1. Are you thinking of the cat?

      JV Lopez, N Yuhki, R Masuda, W Modi, SJ OBrien
      Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat
      J Mol Evol, 39 (1994), pp. 174–190 95018295

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    2. Why capitalize the "s" in "Numts"?

      "Sequences."

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    3. Why capitalize the "s" in "Numts"?

      There are many different ways of writing the term. Do you have a particular reason for preferring NUMTs, Numts, NUMTS, or numts?


      Lang, M., Sazzini, M., Calabrese, F. M., Simone, D., Boattini, A., Romeo, G., ... & Gasparre, G. (2012). Polymorphic NumtS trace human population relationships. Human genetics, 131(5), 757-771.

      Bintz, B. J., Dixon, G. B., & Wilson, M. R. (2014). Simultaneous Detection of Human Mitochondrial DNA and Nuclear‐Inserted Mitochondrial‐origin Sequences (NumtS) using Forensic mtDNA Amplification Strategies and Pyrosequencing Technology. Journal of forensic sciences, 59(4), 1064-1073.

      Calabrese, F. M., Balacco, D. L., Simone, D., & Attimonelli, M. (2012). NumtS footsteps from the past: an interbreed between eukaryotic nucleus and the mitochondrion. EMBnet. journal, 18(A), p-82.

      Calabrese, F. M., Simone, D., & Attimonelli, M. (2012). Primates and mouse NumtS in the UCSC Genome Browser. BMC bioinformatics, 13(4), S15.

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    4. I don't understand the rationale for that particular orthography. I would understand "NuMtS", though I prefer just "numts". And of course the singular is "numt".

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  2. Last time I checked, the largest human Numts were still less than the whole genome. Nothing as wild as the birds...

    (my comment based on this paper).
    https://www.ncbi.nlm.nih.gov/pubmed/22536961

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  3. Looks very interesting!
    I'd add a section "How many proteins?"
    And if I were to write it I would dedicate a section to the "adaptive immunity" against transposons (piRNAs) :-)
    The things that happen to cancer genomes are also of interest to me.

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