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Lectures 5, 6, 7.docx

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BIOL 3110
Michael Gadsden

Lecture 5 May 23 (after test 1) Protein Scaffold- with respect to protein scaffolding, there is a specific complementary sequence required for binding to DNA while there is no specific sequence needed for histone binding to DNA. The sequence specificity of protein scaffolds may lead to different sized loops in DNA. This may indicate different expression units Position Effect Variegation Epigenetic inheritance = inheritance of protein structure rather than from a DNA sequence. A form of inheritance superimposed on the genetic inheritance based on DNA. position effects- the activity of a gene depends on its position relative to a nearby region of heterochromatin on a chromosome. In drosophila, chromosome breakage events that directly connect a region of heterochromatin to a region of euchromatin tend to inactivate the nearby euchromatin genes. the zone of inactivation spreads a different distance in different early cells in the embryo but once the heterochromatic condition is established on a gene, it tends to be stably inherited by all of the cells progeny. ie. picture of red eye of drosophila-one eye is wild type (normal) where the heterochromatin and euchromatin are separated by a barrier protein/DNA sequence and the patchy red spots where different cells early in embryo had different amount of silenced genes by the neighbouring heterochomatin ( this would happen if the barrier protein between the hetero and euchromatin was lost) Lysine is present in high concentrations in histones when lysine is methylated, there is an increase in hydrophobic interactions which leads to the formation of euchromatin in embryos there is a competition between enzymes that methylate or acetylate lysine ie. H3, lysine 9 (K9) (H3K9 binding proteins). If it is acetylated, it becomes euchromatin, if methylated it becomes heterochromatin if H3 K9 position methylated, it attracts chromatin remodelling proteins with chromodomains (repress transcription) chromatin remodelling complexes with bromodomains lead to activate transcription there are approximately 30 different of these types of proteins in humans remodelling: reposition, eject or replace modification: cis vs. trans modifications just by binding the modifier, there is a direct effect on the structure Wrapped neucleosomes last for 250 msec while unwrapped neucleosomes last for 10-50 msec. During this unwrapped phase, sequence specific DNA binding proteins can bind to binding sites on DNA. This means that chromatin structure can effect gene expression. both remodelling and modification can occur together and they can respond to environmental cues such as hormones or temperature. change of expression allows repair of dna Chromatin remodelling complexes bind to both protein core of nucleosomes and the ds. DNA and uses ATP hydrolysis to move the DNA relative to the core. This changes the structure of the nucleosome temporarily making DNA less tightly bound to the histone core. As genes are turned on and off, chromatin remodelling complexes are brought to specific regions of DNA where they act locally to influence chromatin structure. mutations in these chromatin remodelling complexes and histone modification enzymes associated with some cancers Transcription activators-transcription requires promoters and enhancer sequences in DNA binding proteins to these sites leads to altered DNA structure and this allows transcription factors to bind to DNA. SWI/SNF is a chromatin remodelling complex which has a bromodomain, thus is leads to activation of transcription because they position the nucleosome in such a way that the promoter regions on the DNA are exposed. ChIP-Seq experiment Lecture 6 May 28 off-topic lampbrush found in cells who are replicating a lot to make a lot of product (ie. oocytes in amphibians) loops are regions of high transcription, one gene (mainly) per loop the transcripts contains information for the gene and RNA made from the 3 UTR usually the extra 3 UTR region called microsatellite DNA and it contains regions of repeated sequences often used in forensics in oocyte, most DNA not in lampbrush form andis highliy condensed, only areas where a lot of expression required do lampbrush loops form loops in humans- not the lampbrush type (loops in humans not that high in transcription) but it is looped this was proven by an experiment which cross-linked protein DNA creates covalent bond cut loop of DNA with restriction enzymes (cut DNA at specific palindromic sequences) ie. EcoRI cuts d.s. DNA. So DNA cut into random fragments. The parts of DNA left on the loop can be ligated with DNA ligase which attaches sticky ends which are complementary to each other. (see notes for diagram). Once DNA ligated back into loop, you can add primers and put DNA under PCR and remove proteins. When you sequence the PCR product, you can identify 2 sequences of DNA that were originally far apart but had come together to form the loop. Polytene: multiple rounds of DNA replication without cell division which results in polyploid state BUT they dont separate so chromatids attached side by side. this is found in larva of insects. Banded dark regions are heterochromatin (95%) while the lighter regions are euchromatin (5%). Back to slides Transcription activators (A transcriptional activator is a protein that increases gene transcription of a gene or set of genes.) SWI/SNF is a remodelling complex which has a bromodomainthe bromodomain is a structure on the remodelling complex that leads to activation of transcription lucine zippers? chromodomains- deactivate transcription ChIP seq experiment- uses micrococcal endonuclease to randomly cut DNA it removes all DNA that is not bound by protein. (exonucleases can also do this: Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain.) Histone Varients Histones which differ mainly in tail region from there original form and therefore affects modification. (varients of each type ie. H3.3 etc) H3.3 replaces H3 in areas of active transcription CENPA- replaces H3 at centromere H2AX associated with DNA repair when double stranded breaks in DNA occur. The serine on the C terminus of H2 and is phosphorylated. the phosphorylated serine attracts DNA repair enzymes MacroH2A associated with chromosome inactivation particularly of the X chromosome. In females it happens around 2-4 cell embry0 (very early in embryo development). paternally derived X inactivated first by increased condensation of the chromosome. then, both activated later in embryo stage. After both are activated, 1 randomly chosen X is inactivated. Therefore, depending on development, different cells in same organ/tissue can express different alleles. ie. red/green colour blindness in retinal cells of heterozygotes. has a large c terminus tail which is thought to bind RNA called XIST. (side point- ubiquitin is a highly conserved in eukaryotes, attaches covalently to lysine which destines that protein to be destroyed by preteosomes macro-DNA - X inactivation associated with MacroH2. in diagram, used antibodies to label macroH2 DNA on x chromosome. XIST RNA- condenses X-chromosome. associates with macroH2A. Also inactivates x that is highly methylated. ( CpG =cytosine phosphate Guanine so its CG, not GC) [The levels of X-linked gene expression between male and female mammals are normalized by rendering all but one X chromosome largely transcriptionally silent in female cells (1). X chromosome inactivation occurs early in development and the choice of which chromosome to inactivate is random (2). The inactive X chromosome (Xi) is heterochromatic and can be observed as a staining mass (Barr body) at the periphery of interphase nuclei (3). Several general features of gene silencing characterize the Xi, including DNA hypermethylation (4,5), histone H3 and H4 hypoacetylation (68) and late replication in S phase (9,10). In addition, chromatin of the Xi demonstrates a number of unique features that distinguish it from other regions of heterochromatin. One such feature is the colocalization with the Xi of a large untranslated RNA, the X inactive specific transcript (XIST) (1113). XIST is expressed exclusively from the Xi and associates in cis along the length of the chromosome. Another characteristic of the Xi is its distinct nucleosome composition. Four variants of the core histone H2A have a differential distribution in chromatin of the Xi. Two variants, macroH2A1 and macroH2A2, are enriched on the Xi (1416), while the variants H2A-Bbd, and to a lesser extent H2A.Z, are deficient on the Xi (15,17). MacroH2A1 and macroH2A2 are unusual histone H2A variants that have an extensive C- terminal tail that comprises nearly two-thirds of the protein. Originally identified through its association with the nucleosome (18), macroH2A is highly localized in female cells as a distinct nuclear body, referred to as a macro chromatin body (MCB), which is coincident with the Xi and the Barr body (14). Two distinct macroH2A genes encode the macroH2A1 and ma
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