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Comparison of Nuclear Gene Content

-genomes of diverse organisms can harbor very different numbers of genes
-idea that more complex organisms would have dramatically higher numbers of genes than simple organisms is not true in all circumstances
-Craig Venter and Francis Collins leaders of private and public efforts sequence human genome


Gene Duplication (What?)

-one path to acquiring new genes
-some cases individual genes are duplicated while in other situations large segments of chromosomes can be duplicated
-often occur as result of error in homologous recombination or from movement of transposable element
-rare cases entire chromosome or genome is duplicated which result from errors in chromosome segregation and cell division


Gene Duplication (When?)

-can occur during formation of gametes during meiosis as well as mitosis
-several cancers are due to gene duplications in isolated tissues


Gene Duplication (Happens? sub-functionalization)

-immediately after, both daughter genes are identical in sequence, structure and function
-as time proceeds random mutations knock out complementary functions in two daughter genes thereby leaving each daughter gene to execute subset of tasks that were controlled by ancestral gene


Gene Duplication (Happens? neo-functioanlization)

-random mutations alter function of only one of two daughter genes.
-results in one daughter carrying out all ancestral functions while other daughter gene acquires new functions


Mutatioin That Lead to Neo-functionalization

-can affect regulatory models or coding sequences
-note: in hypothetical example in note two daughter genes carrying out same function (coding sequence not altered) but they are doing it indifferent tissues.
-If coding sequence is changed then the actual function of the encoded protein will diverge


Gene Gain and Loss

-can have profound influence-->lead to evolution of bacterial pathogens and marine phytoplankton from putative brown algae


Comparison of Modern Primates

-indicates 100's of genes that have been lost and gained over last 48 million years
-losses and gains could be underlying causes for some of difference that are observed between various primates
-differences between the species can also be cause by differences in DNA sequences of common genes, expression patterns, transcriptional levels and protein modifications


Organization of Human Genome

-contains approximately 30,000 genes (note each gene found in two copies)
-only 1.5% is taken up by coding portion (exons) of genes
-rest made up of non-coding segments like introns, regulatory and untranslated sequences, intergenic DNA, pseudogenes, gene fragments and satellite sequences.
-last category is made up by remnants of transposable elements
-simpler organisms have higher gene density and thus fewer stretches of non-coding DNA
-also contains mitochondrial genome


Mitochondrial Genome

-portion of genome is efficiently organized. Contributes 37 genes and almost no non-coding DNA


DNA Organization: Sea Urchin

-discovered that mRNA transcripts contained only a fraction of the sequences that were found within genomic DNA
-for the first time showed that the nuclear genome contained a significant portion of non-coding sequences
-presaged several discoveries including the identification of exons and introns and the process of RNA splicing
-- Sequencing of the Drosophila, mouse, and human genomes confirmed that similar relationships existed in other complex organisms


Non-coding DNA

-the vast majority of the human genome is comprised of non-coding DNA
-this is true of nearly all eukaryotic organisms
-exception:yeast which is a single celled eukaryote
-yeast genome has high gene density and fewer non-coding DNA segments than other eukaryotes
-Bacterial genomes are even more compact: their genomes are fairly devoid of introns, transposable elements, pseudogenes and repetitive sequences



-inactive genes that are either no longer expressed due to a mutation in regulatory element or is dysfunctional due to a mutation within coding sequences
-can be recognized since they contain sequences that are similar to functional gene
-formation is very common after gene duplication and significant portion of eukaryotic genomes is comprised of inactive pseudogenes
-arise from duplications located relatively close to sister genes while those born from retrotransposition can be located at considerable distances


Psudeogene: mutation in regulatory element

-duplication event takes place which is then followed by accumulation of deleterious mutations in one of daughter genes


Psudeogene: mutation within coding sequence

-messenger RNA is converted into cDNA clone by the reverse transcriptase enzyme.
-this DNA copy inserted into genome via retrotransposition.
-original mRNA lacks enhancer and promoter elements, newly integrated cDNA copy cannot be transcribed and is inactive in genome


Example of Pseudogenes

-analysis of hemoglobin genes
-during evolution globin genes have been duplicated several times
-some genes transcribed during fetal development while others expressed only in adulthood.
-few globin genes expressed during both phases.
-in addition to these active genes several of duplication products have been inactivated by random mutations.
-sit idle within genome on chromosome 11 and 16


Transposable Elements

-makeup significant portion of eukaryotic genomes
-ancestors of bacteriophages and viruses
-continue to exist and infect both prokaryotic and eukaryotic cells
-bacterial genomes contain very few transposbale elements
-yeast contains a few more but overall number still small
-in genomes of higher organisms (humans and maize) percentage of genome comprised by these elements increases significantly


Varigated Coloration of Corn

-due to localized movement of transposable elements around genome
some instances the element will insert itself into gene that is required for normal color of kernel
-inactivation of these genes which happens on a cell by cell basis results in the variegated pattern.