Astonishing DNA complexity update
by Alex Williams
Image istockphoto.com
Published: 3 July 2007 (GMT+10)
Recently we reported astonishing new discoveries about the complexity of the information
content stored in the DNA molecule.1
Notably, the 97% of the human DNA that does not code for protein is not leftover
‘junk DNA’ from our evolutionary past, as previously thought, but is
virtually all being actively used right now in our cells.
Here are a few more exciting details from the ENCODE (Encyclopedia of DNA Elements)
pilot project report.2 As
a help in understanding this, DNA is a very stable molecule ideal for storing information.
In contrast, RNA is a very active (and unstable) molecule and does lots of work
in our cells. To use the stored information on our DNA, our cells copy the information
onto RNA transcripts that then do the work as instructed by that information.
- Traditional ‘beads-on-a-string’ type genes do form the basis of the
protein-producing code, even though much greater complexity has now been uncovered.
Genes found in the ENCODE project differ only about 2% from the existing catalogue
of known protein-coding genes.
- We reported previously that the transcripts overlap the gene regions, but the overlaps
are huge compared to the size of the genes. On average, the transcripts
are 10 to 50 times the size of the gene region, overlapping on both sides. And as
many as 20% of transcripts range up to more than 100 times the size of
the gene region. This would be like photocopying a page in a book and having to
get information from 10, 50 or even 100 other pages in order to use the information
on that page.
that makes the ‘junk’ about 50 times more active
than the genes
- The untranslated regions (now called UTRs, rather than ‘junk’) are far
more important than the translated regions (the genes), as measured by
the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed
on average in five different overlapping and interleaved ways,
while UTRs are transcribed on average in seven different overlapping
and interleaved ways. Since there are about 33 times as many bases in UTRs than
in genic regions, that makes the ‘junk’ about 50 times
more active than the genes.
- Transcription activity can best be predicted by just one factor, the way that the
DNA is packaged into chromosomes. The DNA is coiled around protein globules called
histones, then coiled again into a rope-like structure, then super-coiled in two
stages around scaffold proteins to produce the thick chromosomes that we see under
the microscope. This suggests that DNA information normally exists in a form similar
to a closed book—all the coiling prevents the coded information from coming
into contact with the translation machinery. When the cell wants some information
it opens a particular page, ‘photocopies’ the information, then closes
the book again. Recent other work3
shows that this is physically accomplished as follows:
- The chromosomes in each cell are stored in the membrane-bound nucleus. The nuclear
membrane has about 2000 pores in it, through which molecules can be passed in and
out. The required chromosome is brought near to one of these nuclear pores.
- The section of DNA to be transcribed is placed in front of the pore.
- The supercoil is unwound to expose the transcription region.
- The histone coils are twisted so as to expose the required copying site.
- The double-helix of the DNA is unzipped to expose the coded information.
- The DNA is grasped into a loop by the enzymes that do the copying, and this loop
is copied onto an RNA transcript. The transcript is then checked for accuracy (and
is degraded and recycled if it is faulty). The RNA transcript is then specially
tagged for export, and is exported through the pore and carried to wherever it is
needed in the cell.
- The ‘book’ of DNA information is then closed by a reversal of the coiling
process and movement of the chromosome away from the nuclear pore region.
- The most surprising result, according to the ENCODE authors, is that 95% of the
functional transcripts (genic and UTR transcripts with at least one known function)
show no sign of selection pressure (i.e. they are not noticeably conserved and are
mutating at the average rate). This contradicts Charles Darwin’s theory that
natural selection is the major cause of our evolution. It also creates an interesting
paradox: cell architecture, machinery and metabolic cycles are all highly conserved
(e.g. the human insulin gene has been put into bacteria to produce human insulin
on an industrial scale), while most of the chromosomal information is freely mutating.
How could this state of affairs be maintained for the supposed 3.8 billion years
since bacteria first evolved? A better answer might be that life is only thousands,
not billions of years old. It also looks like cells, not genes, are in
control of life—the direct opposite of what neo-Darwinists have long assumed.
Related articles
References
- Alex Williams, Astonishing DNA complexity uncovered.
Return to Text.
- Ewan Birney, et. al., Identification and analysis of functional
elements in 1% of the human genome by the ENCODE pilot project, Nature
447: 799-816, 2007. Return to Text.
- Asifa Akhtar & Susan M. Gasser, The nuclear envelope and
transcriptional control, Nature Reviews Genetics 8:507–517,
2007. Return to Text.
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