Eukaryotic Genome & Gene Regulation

• The entire genome of the eukaryotic organism is present in every cell of the organism. Although all genes are present, the numbers and types that are actively transcribed can be managed through the processing and packaging of the DNA.

DNA packing• histones

– 1st level of packaging – are strongly positively charged to

attract the negatively charged phosphate groups of the DNA

– coiling of the DNA around spherical proteins creates a nucleosome • groups of nucleosomes are connected

together by short segments of DNA called linker DNA

• made of a complex of 4 protein subunits: H2A, H2B, H3, H4

• chains of nucleosomes resemble "beads on a string"

• a 5th protein H1 is located on the end of the bead to help with the next level of packaging

• strings of nucleosomes coil to form chromatin – 2nd level of packaging

• the chromatin form looped domains – 3rd level of packaging – highly specific with the same regions being looped in similar cells

• the chromatin can condense more to form the metaphase chromosome – 4th level of packaging – some DNA remains condensed in interphase and is called heterochromatin – less condensed DNA is called euchromatin

Regulation of Gene Expression• As a multicellular embryo develops cells undergo cell

differentiation to form ~200 different types of cells in the human body.– This feat is accomplished through the process of differential gene

expression.

Regulation of Gene Expression• Regulation of Chromatin Structure - genes within heterochromatin

regions are not transcribed – histone modifications

• acetylation (-COOH3) of the histone tails makes the chromatin to be less dense and promotes transcription – inhibits binding of the histone to neighboring histone complexes – deacetlyation inactivates a region and promotes tighter packing

– DNA methylation • addition of a methyl group (-CH3) to DNA (mostly cytosine) inactivates the DNA • method for inactivating the extra X chromosomes in females • methylation patterns are passed with each cell division

– called genomic imprinting

– Epigenetic Inheritance - traits inherited not related to nucleotide sequence • example: enzymes that modify nucleotide structure

Regulation of Transcription Initiation • control elements - proteins that bind to DNA prior to the promoter

region – upstream of the promoter region - can be proximal or distal (enhancer

region) • transcription factors - proteins that bind to the promoter region to

enhance attachment of RNA Pol II – general transcription factors speed up a little - bind to all promoters – specific transcription factors

• activators - bind to the enhancer region upstream of the promoter to make it more accessible

• repressors - block attachment of activators to inhibit transcription or bind to a repressor region to turn off transcription

Post Transcription Regulation • RNA Processing

– alternative splicing - forming multiple transcripts from the same primary transcript

• mRNA Degradation – modification of the 3' end of the transcript can change the

amount of time the RNA transcript – microRNAs (miRNA) attach to complementary mRNA sequences

and block its translation until it is degraded - or cut it up into small pieces (dicers)

– small interference RNAs (siRNA) work by the same function as miRNA through a process of RNA interference (RNAi) • may have evolved as a defense mechanism to RNA viruses

Post Transcription Regulation • Initiation of Translation

– regulatory proteins bind to the 5' region inhibiting translation – can later be removed to initiate translation

• Protein processing and Degradation – post translation modification – addition of -PO4 – addition of sugars and lipids (membrane) – truncation (shortening) – degradation

• addition of ubiquitin signals the protein for destruction by large complexes called proteosomes