BME 130 – Genomes Lecture 14 Chromatin, Gene expression, and splicing

Nuclear organization Nucleolus Cajal bodies speckles

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 Lower background & tighter peaks in ChIP-Seq (better contrast) trxG (activation) PcG (repression)

Highly dynamic histone modification during differentiation Neural txn factor House- keeping Neuro- genesis txn factor adipose txn factor Neural progenitor marker Brain & lung txn factor

Promoter classes high CpG gene low CpG intermediate CpG CpG Highly expressed, housekeeping genes; other genes N=11,410 Genes with high tissue-specificity N=3,014 Mixture of genes N=3,338

NPC=neural progenitor cellsMEF=embryonic fibroblastsES = embryonic stem cells

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 H3 P P Survivin Chromosomal passenger complex AuroraB (kinase)

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