LSM1102 CA1 Reference Paper summary1. This paper is about how chromosomal structure (especially heterochromatic regions) , transposable elements and epigenetics, relate to aging2. Termsa. Deleterious effectsi. Harmful effects to healthb. Histone methylation/ acetylationi. Changes to histone that can either increase or decreases access depending on amino acid affected3. How heterochromatin damage affects ageinga. Deleterious effects on cellular homeostasisi. Aberrant expression of normally repressed genes Transcriptional noise may cause cumulative harm by using up cellular factors needed for transcribing normal genes Genes no longer repressed may express genes that cause aging phenotypesii. Redirection of limited energy towards repair/ maintenance of damaged genes4. Epigenetics also affect aginga. Histone modification (acetylation, methylation etc)i. In yeast, as H4K16 acetylation increases, Sir2 levels decreases Sir2 is a deacetylase, thus genes are less expressedii. In worms Knockdown of H3K4 methyltransferase increases lifespan Knockdown of H3K4 demethylase decreases lifespan Thus excessive H3K4 trimethylation is detrimental to lifespan It is a hallmark of actively transcribed chromatin So the genes transcribed cause aging phenotype Such knockdown is heritable Other knockdown of H3K27me3 demethylase UTX-1 increases lifespan H3K27me3 marks increases Thus less transcription Contrasts with the other demethylase knockdowniii. In drosophila Marks, H3K4me3 and H3K36me3, indicating active chromatin decrease with age Decreased HP1 expression correlates with shortened lifespan Has premature muscle degeneration Has large increase in rRNA transcripts Sign of large volume of transcrtption Increased HP1 expression correlated with increased lifespan Has increased muscle structure and function Has less rRNA transcripts Decrease in H3K27 methylation increase lifespan Contrasts with effect in worm Chromatin marks may be processed differently in different tissues or species, thus affecting aging differently.iv. In mouse As mouse age, there is a general decrease in histone acetylation and increase in histone methylation Hypoacetylation of H4K12 lead to concomitant failure to express a gene necessary for memory consolidation Treatment with histone deacetylatase inhibitors restored gene expression profile and learning behaviour Reduced acetylation of H3K9 and H4K12 also led to reduced gene expression important for long-term potentiation Treatment with histone histone deacetylatase inhibitors also raised acetylation levels and reduced LTP decline Changes in DNA methylation patters are consistent over several tissue types EE paradigm increases learning and memory Correlates to increase in histone acetylation and methylation on different residues on H3 and H4 Histone deacetylase inhibitor also benefits Mouse modules for Alzheimers showed a decrease in H4 acetylation, correlated with defective LTP and memory formation Again, inhibitor treatment helps Mouse module for Hutchinson-Gilford progeria (rapid aging) has hypoacetylated H4K16, correlates to defective lamin A processing and short lifespan Treatments include overexpression of histone acetyltransferace Mof or chemical inhibition of deactylase Contrasts with yeast where acetylation increases with ageb. Loss of histones in heterochromatic regioni. Decrease in silencing, problems abovec. Loss of histone chaperonei. Chaperones binds to histone and regulate nucleosome assembly Affects gene expressiond. In yeast, countering a natural decrease in histone protein levels, led to longer lifei. Knock out HIR1, a histone transcription repressorii. Overexpress H3 and H4 histone genes5. Replicative senescence are correlated witha. Decrease in histone levelsb. Locations of histone methylation an acetylation are redistributedc. Formation of dense non-pericentromeric (not near centromere) heterochromatini. Aka DNA bunches up at locations not near centromereii. Detected by higher levels of methylated histones H3K9me3, H3K27me3d. Weaker DNA packingi. Regions of open and closed chromatin are less distinct and look more similare. Reversal of gene expressioni. Promoters and enhancers of active genes become more closedii. Normally silent heterochromatic regions become more open6. Chromatin position also affects aginga. In yeasti. Heterochromatic telomere regions are near the nuclear envelopii. Silencing of chromatin occurs when it is closer to the nuclear periphery and vice versab. In higher eukaryotesi. Heterochromatic regions usually contain Lamin-associated domains that bind to the nuclear lamina Correlation of poor gene transcription with proximity to laminaii. Transcriptionally active euchromatin regions are found in distinct areas inside the nucleus, caked transcription factoriesiii. The mutation of lamin A can lead to misshapen nuclei that changes heterochromatin organisation, leading to defects in DNA replication and transcriptioniv. Lamin B1 expression naturally decreases with age Knocking down the expression causes early entry into senescence and reorganisation of LAD chromatin structure.7. Transposable elements can have deleterious effects when expresseda. They are widely transcriptionally expressed and can regulate nearby genesb. Types of transposonsi. Retrotransposons gets transcribed, encodes its own reverse transcriptase, gets reverse transcribed and then integrated into a new location Copy and pasteii. DNA transposons are flanked by inverted repeats that act as limits for excision and integration by transposase Transposase are frequently encoded by the transposons Cut and paste May be imperfect and leave behind partial sequencesc. Most TEs are transposition inactive as mutations have silenced the mechanismi. May still be transcribed by promoters within itselfii. Becomes transcriptionally active in response to stress DNA damage Radiation Reactive oxygen species UV radiation Temperature Wounds Infectionsiii. Expressions are affected by histone modifications too In rats, during stress, H3K9me3 levels rise, while expression of certain TEs decreaseiv. Can have numerous regulatory effects Sense/ antisense transcriptional activation Induction of heterochromatic silencing Small RNA targeting Alternative splicingd. Active, mobile TEs can be highly mutagenic and cause genomic instabilityi. Movement activity is supressed by cellular RNAi machineryii. Targeted dsRNA is processed by Dicer enzymes to produce short endogenous small interfering RNAs (esiRNAs), which is loaded into RNA-induced Silencing Complex (RISC) RISC binds to chromatin and catalyses formation and spreading of silencing heterochromatin, repressing transcription Recruits heterochromatin proteins and histone methyltransferase RISC also recognises and hydrolyses target RNA transcripts Post-transcriptional silencing