Biomedical Engineering Reference
In-Depth Information
7.7
Analyzing genomic organization and
variations in genomic copy number
The human genome has more than 3 billion bases in the haploid comple-
ment and it soon became apparent in studying the genome that only a small
percentage of the genetic material (about 1%) encoded information for
protein synthesis. The remainder of this material was sometimes referred
to as 'junk DNA' - perhaps remnants of our evolutionary past fi lled with
pseudo-genes that have once been original genes, now replaced by more
modern copies, or maybe mutated viral sequences that just stayed within
our genome and were there for a free ride. However, it is becoming more
apparent that this so-called junk DNA is no such thing and that it may play
important roles in cell development.
This non-coding DNA is often placed into different classifi cations based
on the type and number of repetitive sequences that one fi nds. Two of the
main classes of these repeats are:
SINES; and
LINES.
SINES
refers to short interspersed repeated sequences. In humans, the most
often seen SINE is the Alu family DNA sequence, which has a 300 base con-
sensus sequence, that is repeated between 300,000 and 900,000 times in the
human genome. A consensus sequence is an idealized nucleotide sequence
in which each base is most often found at a given particular position, when
the actual sequences of different individuals are compared. The reason
for the existence of these repeats and their function in the genome is not
known.
The second large class of repeated sequence seen in humans is called
LINES
, referring to long interspersed repeated sequences. The 3' end of this
6,400 base pair consensus sequence is repeated between 50,000 and 100,000
times and the 5' end is repeated 4,000 to 20,000 times in the human genome.
As with the Alu sequence, the purpose of this long repeat is a mystery.
The unique sequences that contain the code for the genes and are tran-
scribed into mRNA for protein synthesis are usually found once in the
haploid genome, and diploid cells will contain two copies of each unique
sequence with each member of the pair coming from a different parent.
However, there are also in the genome - often closely linked to functioning
genes -
pseudo-genes
, which are inexact copies of a gene sequence having
some minor changes that make them non-functional. These pseudo-genes
are possible ancestral genes that became modifi ed to the present gene by
mutations that gave the modern gene a selective advantage and the one that
persists today.
