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Genome
The genome is all the DNA in a cell.
All the DNA on all the chromosomes Includes genes, intergenic sequences, repeats
Specifically, it is all the DNA in an organelle. Eukaryotes can have 2-3 genomes
Nuclear genome Mitochondrial genome Plastid genome
Genomics
Genomics is the study of genomes, including large chromosomal segments containing many genes. The initial phase of genomics aims to map and sequence an initial set of entire genomes. Functional genomics aims to deduce information about the function of DNA sequences.
Should continue long after the initial genome sequences have been completed.
Human genome
22 autosome pairs + 2 sex chromosomes 3 billion base pairs in the haploid genome Where and what are the 30,000 to 40,000 genes? Is there anything else From NCBI web site, photo from T. Ried, Natl Human Genome Research Institute, NIH interesting/important?
Genome Structure
Distinct components of genomes Abundance and complexity of mRNA Normalized cDNA libraries and ESTs Genome sequences: gene numbers Comparative genomics
|___________|__|__|__|__|__|
L = length = 1000 bp = a + 5b N = complexity = 600 bp = a + b
ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab ab etc.
i zyajczkbl qfreig httrai nrun ni nsofa stel i zab ethco tton qwf tzxvbi fyou don tb el ie vei ml eavin gyo uj ustcoun tthed aysi mgo nerxcvwp owe ntdown to th ecrossroa dstri edtocatch ari derob ertj ohn so npzvmwcomeo nho mei ntomykitche ntrad
cdefghijklm nopqr stuv cdefghijklm nopqr stuv cdefghijklm nopqr stuv cdefghijklm nopqr stuv
1.5 microM
dC kC2 dt
t t
or
dC kdt 2 C
C t 1 1 kt C 1 kC 0 t 00 C 0
t
For a renaturation measurement, one usually shears DNA to a constant fragment length L (e.g. 400 bp). Then L is no longer a variable, and
C0 t 1 2 N
unknown
(5)
N standard standard N C0 t 1 2
E.g. E. coli N = 4.639 x 106 bp
C0 t 1 2 unknown
(6)
Fig. 1.7.5
fraction reassociated
0.25
0.50
About 50,000 copies of L1 repeats (0.2 to 7 kb in length), plus 1000 to 10,000 copies of at least 10 other f amiles of inters persed middle repetitiv e DNA (e.g. THE LTR repeats) Thousands of copies of rRNA genes
0.75
1.00 10
-6
10
-5
10
-4
10
-3
10
-2
10
-1
10
10
10
10
10
105
Co t
Almost all transposable elements in mammals fall into one of four classes
Retrotransposons
Encode reverse transcriptase and other enzymes required for transposition No long terminal repeats (LTRs)
Cause new mutations in humans Homologous repeats found in all mammals and many other animals
Finding repeats
Compare a sequence to a database of known repeat sequences from the organism of interest RepeatMasker Arian Smit and P. Green, U. Wash. http://ftp.genome.washington.edu/cgibin/RepeatMasker Try it on INS gene sequence