Gene Regulation. Sonja J. Prohaska WS 2017/18. Computational EvoDevo, University of Leipzig Santa Fe Institute, Santa Fe, NM, U.S.

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1 Computational EvoDevo, University of Leipzig Santa Fe Institute, Santa Fe, NM, U.S. WS 2017/18

2 The structural definition: What does that mean? used by the molecular biology community: Chemical modification of DNA or chromatin-associated proteins that are added or removed by modification enzymes. DNA methylation histone modification nuclear organization (in 3D)

3 Eukaryotic Chromatin Structure chromatin: complex of protein and DNA like beeds on a string nucleosome (i.e. the beads ) protein component: 8 histone molecules, i.e. the histone complex DNA component: 146bp of DNA wrappend around the histone complex in 1.67 left-handed turns linker DNA between nucleosomes can be of variable length (10-80bp) role in DNA packaging and genome/gene regulation

4 Euchromatin and Heterochromatin Euchromatin: loosely packed DNA, higher histone acetylation, H3K4 methylation, R-banding Heterochromatin: densely packed DNA, lower histone acentylation, H3K9 methylation and HP1, C/G-banding

5 The Human Histone Modification System Steffen PA and Ringrose L (2014) What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory Nature Reviews Mol. Cell Biol. 15, (2014)

6 Components of the Histone Modification System ChAPs/NAPs, proteins substrate to modification histones modifications acetylation, methylation, phosphorylation, ubiquitination, a.o. writer, modification enzymes histone acetylase, histone methyltransferase, kinase, a.o. eraser, demodification enzymes histone deacetylase, histone demethylase, phosphatase, a.o. reader, protein domain recognizing a specific modification e.g. bromo, chromo,

7 ChAPs: Histones and Nucleosome Assembly histones are small, positively charged proteins interact with the negatively charged DNA backbone require histone chaperons to assemble canonical histones H3, H4, H2A, H2B two H3-H4 heterodimers form the histone core wrap DNA once two H2A-H2B heterodimers on top and bottom causing the second DNA turn

8 ChAPs: Nucleosome Assembly (Dynamics) DNA chromatin ChAPs histones H3 H4 H2A H2B two nucleosomes nucleosome with histone tails video:

9 ChAPs: Generating Variation histone variants for special purposes H3: H3.1, H3.2 replication-dependent expression (in S-phase) H3: H3.3 replication-independet (inserted during transcription) H3: CENP-A centromeric region H2A: H2A.Z modulator of nucleosome positioning promoter stability/mobility H2A: H2A.X DNA double strands break marker Serin at 139 is phosphorylated, recruits double strand breaks repair H2A: macroh2a, H2A.Bbd (Barr body-deficient) relevant for X chromosome inactivation Histone assembly and exchange require histone chaperones.

10 ChAPs: Histone Tails are Traget Sites for Modification unstructured N-terminal domains ( tails ) protrude from the histone core numbering of amino acids from N- to C-terminus e.g. amino acid 4 of H3 is a Lysine (K) Histone tails are subject to chemical modification.

11 Modifications: Histone Modification chemical groups being added to histones acetylation (ac): lysine (K) methylation (me): lysine (K), arginine (R) phosphorylation (ph): Serine (S), Threonine (T), Tyrosine (Y) ubiquitination (ub): lysine (K) more: biotinylation, ribosylation, glycosylation, deimination, a.o. tri-methylation at lysine (K) at position 4 of histone H3 H3K4me3

12 Modifications: Chemistry

13 before we continue on a molecular level on how these modifications are set... What do histone modifications do? general aspects creat variants that have slightly different physico-chemical properties in a more efficient way cost-efficiency: less histones to compose and decompose for a change time-efficiency: less time required for modification than expression of a different variant direct physico-chemical aspects example: DNA-backbone is negatively charged, histone are positively charged good binding adding negative charges, e.g. by acetylation, to histone less well binding information theoretic aspects variant are bound by differend modification reader, writer, and eraser enzymes high combinatorial complexity (the rise of the histone code) neutral and highly dynamical (i.e. temporal?) storage of information (on a lifetime scale) for comparison: mutantion and selection act on evolutionary time scale (very slow)

14 Histone code (classical view, classical example) H3K4me3: activating mark H3K27me3: repressive mark H3K4me3 AND H3K27me3: poised state

15 WRITING/adding histone modification Histone modifying enzymes called writer histone acetyltransferase (HAT) ac e.g. GNAT family, MYST family, p300/cbp histone methyltransferase (HMT) me e.g. Lysine methylation: SET-domain containing proteins, Dot1 e.g. Arginine methylation: PRMTs kinase ph e.g. Aurora, MSK, JAK, Mst1 ubiquitination enzymes ub multi-step process involving E1, E2, E3

16 EREASING/removing histone modification (part 1) acetylation (ac) histone deacetylase (HDAC) e.g. Sir family, Rpd3 methylation (me) histone demethylase (HDM) e.g. lysine demethylation : LSD1, JmjC e.g. arginine dementylation: PAD4, JmjC phosphorylation (ph) phosphatase e.g. S/T-phosphatases, Y-phosphatases I/II ubiquitination (ub) de-ubiquitination enzymes e.g. JAMM, UCH, OTU, ULP, UCH-L3

17 EREASING/removing histone modification (part 2) other means to remove histone modifications spontaneous de-modification tail clipping histone replacement/exchange histone octamer eviction

18 READING/recognition of histone modification Musselman et al. 2012; Taverna et al. 2007

19 Combining Functional Protein Domains two functional domains combined in a single protein two functional domains combined in a protein complexes

20 Histone Marks and Cell Differentiation

21 Histone Marks Across Cell Cycle

22 Histone Marks During Development

23 Histone Marks During the Circadian Cycle