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BME 130 – Genomes Lecture 14 Chromatin, Gene expression, and splicing Nuclear organization Common translocations Chromatin domains H3 H4 H2A H2B Histone modifications DNA Methylation at CpG sites CHiP-Seq DNA DNA-binding proteins (histones, e.g) crosslink Immuno-precipitate and fragment DNA Immuno-precipitate and fragment DNA Reverse cross-links and sequence ChIP-Seq and ChIP-chip comparison of two histone marks trxG (activation) PcG (repression) Lower background & tighter peaks in ChIP-Seq (better contrast) Highly dynamic histone modification during differentiation Housekeeping Neural txn factor Neurogenesis txn factor adipose txn factor Neural progenitor marker Brain & lung txn factor Promoter classes high CpG gene CpG intermediate CpG gene low CpG gene Highly expressed, housekeeping genes; other genes N=11,410 Mixture of genes N=3,338 Genes with high tissue-specificity N=3,014 ES = embryonic stem cells NPC=neural progenitor cells MEF=embryonic fibroblasts H3K36me3 marks gene bodies (may prevent aberrant transcriptional initiation) Imprinting is reflected in H3K36me3 state Nucleosome positioning and gene structure Histone modification in cell division Haspin P H3 H3 P H3 H3 Eukaryotic pre-mRNA expression Eukaryotic RNAPol II transcripts have a 7-methyl-G cap Eukaryotic 3’ end processing Splicing Intron flavors Intron content varies widely SR proteins are trans-acting splicing factors Trans-splicing (C. elegans) RNA editing Eukaryotic mRNA degradation Nonsense-meditaed mRNA decay Alternative splicing and NMD to control gene expression Alternative splicing and NMD to control gene expression
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