What is in a genome?

English language svg version of Image:Plasmid ...
English language svg version of Image:Plasmid (numbers).svg Description : This image shows a line drawing of a bacterium with its chromosomal DNA and several plasmids within it. The bacterium is drawn as a large oval. Within the bacterium, small to medium size circles illustrate the plasmids, and one long thin closed line that intersects itself repeatedly illustrates the chromosomal DNA. (Photo credit: Wikipedia)

I first have to apologize. The mission of this blog is to inform those who are curious about science and nature. My ADD gets the best of me sometimes and I digress towards more policy and advocation.

So…what is in a genome? A broad question with lots of answers. Let’s start with the ‘simple’ example of a genome; bacteria. Unlike humans, and other animals, bacteria have only one true chromosome which is circular. Many bacteria, however, have extra DNA not on the chromosome. This extra DNA is also circular and usually called a plasmid. Many bacteria have several plasmids, and some even have very large plasmids called cosmids.

There is not a lot of room within a bacterial cell, so there is not a lot of ‘junk’ DNA in its chromosome. If an average gene is 1000 base pairs (bp), then a 7 Mbp (7,000,000 bp) genome usually has about 6500 genes. This means bacteria pack a big punch in a small size cellular blueprint. Other than genes, bacteria contain DNA elements that help regulate what and when genes are actively transcribed into RNA to produce functional proteins. Promoters are areas of DNA upstream of genes that are attractive places for some proteins to interact with. Some proteins activate gene transcription while other repress transcription. This ensures only the proteins needed by the cell are being produced since making and degrading unneeded proteins costs energy.

What about plants and animals?

I’ll leave plants out since I’m not knowledgeable enough to write about them. Animals have very elaborate genomes. The number of chromosomes vary for each organism and are not circular. For simplicity, I will discuss humans. Humans have pairs of each chromosome that are identical except for the pair that determine a persons sex. Even identical chromosomes are essentially different in the characteristics of individual genes (see dominant and recessive alleles). Strands of DNA are wrapped around proteins known as histones which interact to compact the size of the chromosome.

The major chromatin structures.
The major chromatin structures. (Photo credit: Wikipedia)

Human genes have MANY ways of being regulated. The histones themselves can undergo modification by enzymes that affects how compact they are and how attractive they are to proteins regulating gene transcription. Like bacteria, human gene transcription can be regulated by promoters. However, unlike bacteria, these genes will not totally be used to make a protein. Human genes are composed of introns, regions not translated into a protein, and exons, regions that are translated into protein. Human messenger RNA is processed after transcription which removes intron sequences leaving only exons that will be shuttled out of the nucleus for protein synthesis. To make this more complicated, during processing, many genes can undergo something called alternative splicing. This means as mRNA is being processed, even some exons can be removed resulting in different versions of a protein! 

Other elements can regulate gene transcription besides promoters. Animals have DNA elements called enhancers and insulators that may or may not be located close to actual genes. Enhancers and insulators can intricately interact to regulate gene expression.

Français : Organisation de l'ADN en chromosome...
Français : Organisation de l’ADN en chromosome National Human Genome Research (USA) (Photo credit: Wikipedia)


I will leave it at this. I hope you enjoyed my little ramble about genomes. Let me know what you think…please…

The Human Genome Project: Thank you, Department of Energy!

Some of you may not know (or care) about the origination of the Human Genome Project. I just left a meeting discussing the archiving of HGP documents within our group in DOE (Biological and Environmental Research Information System group, formerly the Human Genome Management Information System) with members of DOE’s Office of Scientific & Technical Information (OSTI). It was interesting, being a history buff, the inner workings as described by my fearless leader who was there from the beginning in the mid 1980s, yes the ’80s. Not many people know that the NIH was very hesitant to fund some of the approaches used in the project. However, DOE saw a great opportunity and took a chance. After these projects were successful, NIH was glad to throw tons of money into projects. Even Jim Watson (of Watson and Crick fame) was very hesitant at first. If DOE had not had the vision to proceed in unfamiliar directions, perhaps the Human Genome Project would not have turned out as it did. Some of the technologies that came from the Project now enable for cheaper and better analysis of genomes. 2013 marks the 10 year anniversary of the completion of the HGP. I am glad the documents stemming from meetings in the initial planning of the HGP will be preserved.

When the HGP was completed, it was a huge accomplishment for mankind. Without it, progress in human genetics would not be possible (see ENCODE). I personally want to thank the vision within DOE.