Scientists Analyze Chromosomes 2 and 4: Discover Largest "Gene Deserts"

National Human Genome Research Institute ^ | 06 April 2005 | Staff

[PatrickHenry]

A detailed analysis of chromosomes 2 and 4 has detected the largest "gene deserts" known in the human genome and uncovered more evidence that human chromosome 2 arose from the fusion of two ancestral ape chromosomes, researchers supported by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported today.

In a study published in the April 7 issue of the journal Nature, a multi-institution team, led by [load of names deleted, but available in the original article].

"This analysis is an impressive achievement that will deepen our understanding of the human genome and speed the discovery of genes related to human health and disease. In addition, these findings provide exciting new insights into the structure and evolution of mammalian genomes," said Francis S. Collins, M.D., Ph.D., director of NHGRI, which led the U.S. component of the Human Genome Project along with the DOE.

Chromosome 4 has long been of interest to the medical community because it holds the gene for Huntington's disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence - a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

One of the central goals of the effort to analyze the human genome is the identification of all genes, which are generally defined as stretches of DNA that code for particular proteins. The new analysis confirmed the existence of 1,346 protein-coding genes on chromosome 2 and 796 protein-coding genes on chromosome 4.

As part of their examination of chromosome 4, the researchers found what are believed to be the largest "gene deserts" yet discovered in the human genome sequence. These regions of the genome are called gene deserts because they are devoid of any protein-coding genes. However, researchers suspect such regions are important to human biology because they have been conserved throughout the evolution of mammals and birds, and work is now underway to figure out their exact functions.

Humans have 23 pairs of chromosomes - one less pair than chimpanzees, gorillas, orangutans and other great apes. For more than two decades, researchers have thought human chromosome 2 was produced as the result of the fusion of two mid-sized ape chromosomes and a Seattle group located the fusion site in 2002.

In the latest analysis, researchers searched the chromosome's DNA sequence for the relics of the center (centromere) of the ape chromosome that was inactivated upon fusion with the other ape chromosome. They subsequently identified a 36,000 base pair stretch of DNA sequence that likely marks the precise location of the inactived centromere. That tract is characterized by a type of DNA duplication, known as alpha satellite repeats, that is a hallmark of centromeres. In addition, the tract is flanked by an unusual abundance of another type of DNA duplication, called a segmental duplication.

"These data raise the possibility of a new tool for studying genome evolution. We may be able to find other chromosomes that have disappeared over the course of time by searching other mammals' DNA for similar patterns of duplication," said Richard K. Wilson, Ph.D., director of the Washington University School of Medicine's Genome Sequencing Center and senior author of the study.

In another intriguing finding, the researchers identified a messenger RNA (mRNA) transcript from a gene on chromosome 2 that possibly may produce a protein unique to humans and chimps. Scientists have tentative evidence that the gene may be used to make a protein in the brain and the testes. The team also identified "hypervariable" regions in which genes contain variations that may lead to the production of altered proteins unique to humans. The functions of the altered proteins are not known, and researchers emphasized that their findings still require "cautious evaluation."

In October 2004, the International Human Genome Sequencing Consortium published its scientific description of the finished human genome sequence in Nature. Detailed annotations and analyses have already been published for chromosomes 5, 6, 7, 9, 10, 13, 14, 16, 19, 20, 21, 22, X and Y. Publications describing the remaining chromosomes are forthcoming.

The sequence of chromosomes 2 and 4, as well as the rest of the human genome sequence, can be accessed through the following public databases: GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of Japan (www.ddbj.nig.ac.jp); and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at EMBL's Nucleotide Sequence Database. [Links in original article.]

NHGRI is one of the 27 institutes and centers at NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.

[AntiGuv]

I realize what you're saying and it's an interesting question that I don't know the answer to (i.e., if, for whatever reason, they exchanged gametes would offspring result?) but all other sources I've seen on the Green Warbler aside from the S.F. Chronicle graphic say they cannot interbreed. This may only be due to them not recognizing the mating calls, but there are other clearly different species that "can" in theory interbreed but never will in practice.

In some ways, and I think you already know this, "species" is an arbitrary, problematic concept - designed to assist in our classification of the natural world. The boundaries are frequently fuzzy as one would expect in a backdrop of common descent.

[Stultis]

called gene deserts because they are devoid of any protein-coding genes. However, researchers suspect such regions are important to human biology because they have been conserved throughout the evolution of mammals and birds

Anybody know? Does this mean that the nucleotide sequences in the regions are conserved (wrt what would be expected from selectively neutral evolution) or does it just mean that the size and position of these regions, and/or some other characteristic beyond the primary sequence structure, is conserved?

[balrog666]

I must say, at least, I admire you for your self-admission. The fact that you blatantly admit it, reinforces its validity.

You missed the point again. Somehow I just can't seem to underestimate you.

[dread78645]

Nanobot placemark

[jennyp]

creationist-equivalent-of-corporal-queball PLACEMARKER.

[AndrewC]

You missed the point again.

No. You are validating your self-description even more. I ignored your attempted point and highlighted your trolling nature. Or are you going to provide yet even more evidence by trying to defend your comment as a relevant contribution to this thread?

[balrog666]

Now you're about 0-for-200,000. Go troll somewhere else.

[AndyTheBear]

"This analysis is an impressive achievement that will deepen our understanding of the human genome and speed the discovery of genes related to human health and disease. In addition, these findings provide exciting new insights into the structure and evolution of mammalian genomes,"

Ahh, how refreshing. Nice repeatable scientific experimentation with respect to the human genome As a side effect of this science we gain insight into the historical model of the evolution of species. Too bad the later is beyond the scope of the scientific method - and too bad this latter fact is too offensive to the sensibilities of some who like to think they are objective.

[AndrewC]

Now you're about 0-for-200,000. Go troll somewhere else.

Don't say I didn't warn you.

[balrog666]

Here's a clue:

Don't post to me. Ever.

[microgood]

OK. What process would create apes, then a couple millions of years later, humans with similar genes?

Assuming that your statement about the timing of apes and man is correct, I do not know. But it might be the same process that allowed creatures with arms and legs and brains to come into existence where they previously did not exist (of course I am just speculating here).

[microgood]

The problem with convergence theory in this sense is that these features that are deemed emblematic of common ancestry are to a degree arbitrary. There is no reason for them to have emerged independently with precisely this arrangement (or even close to it, in the traits discussed above).

Except for the fact that it could have just happened that way. I understand that the historical information may bolster the assumption of common ancestry, but it certainly does not prove the assumption nor is it a testable assumption.

[AntiGuv]

Well that's true, in much that same way that, while the odds that you just so happen for no apparent reason to share many of your father's traits are infinitesimal, they aren't nonexistent.

[AndrewC]

I expect the same behavior from the individual who posted the order to me and alerted you. Finally, he should consider contributing to the discussion rather than the typical "BWAAHHHHHHAAAAHHHAAHAA" comments and other belittling comments he makes.

[PatrickHenry]

For those who care about the ever-growing List-O-Links, here are a few of the changes made recently:

13Apr: Added section on Eugenics, with three new links
12Apr: Added section on the Cambrian Explosion with three new links
10Apr: Added "Neither intelligent nor designed" to Isn't ID Superseding Evolution? section
01Apr: Added "The Evolution of Man Scientifically Disproved" from 1928 to THEORY IN CRISIS section
31Mar: Noted Link not working for Gould's "Evolution as Fact and Theory"
27Mar: Added section SOME LINKS DEBUNKING "YOUNG EARTH" BELIEFS with three links
26Mar: Added "The Pocket Darwin" to What is Evolution? section
24Mar: Added "Timeline of Evolutionary Thought" to What is Evolution? section
24Mar: Added "History of Science" to Essential Information section
24Mar: Added "The omphalos hypothesis" to section on Epistemological Issues (it's "Last-Thursdayism")

[Chaguito]

I'm no "evo" but the discovery of the fusion was discovered three years ago. So that indeed is "years" of assurance, if the discovery means what the discoverers say it means.

[Chaguito]

Yikes! That was the most poorly worded sentence of my career. To many "discover" words. Sorry.

[JusPasenThru]

Saving for later. Too long and lots of big words.

[microgood]

Well that's true, in much that same way that, while the odds that you just so happen for no apparent reason to share many of your father's traits are infinitesimal, they aren't nonexistent.

You can make a lot more assumptions about observable events in that you can test your theories. Saying an offspring has the traits of its parent is a little different than saying apes and man share a common ancestor.

[VadeRetro]

I'm cool, I reckon he looks stupider than me to the lurkers.

If he doesn't look stupider than dirt, something's wrong.