Histones modifications and variants Dr. Institute of Molecular Biology, Johannes Gutenberg University, Mainz www.imb.de
Lecture Objectives 1. Chromatin structure and function Chromatin and cell state Nucleosome 2. Histone variants Classification: genomic organization, transcription, post-translation modifications H3 variants H2A variants Biological functions 3. Histone modifications Histone Code Lysine Acelycation Lysine methylation Regulation of early development by Polycomb proteins Histone modifications in cancer
From epigenetics to regenerative medicine Differentiated cells skin hair Blood Cancer stem cell Adult stem cell bone cartilage muscles epithelium in stomach, intestine, liver? Embryonic progenitor Pluripotent Embryonic stem cell
How can one cell can give rise to different tissues? Cancer stem cell Adult stem cell Embryonic progenitor Pluripotent Embryonic stem cell 1) Non-cell autonomous: Ligands act on the receptor inducers 2) Cell autonomous: factors within the cell - determinants transcription factors
How can one cell can give rise to different tissues? 1) Non-cell autonomous inputs : Ligands act on the receptor inducers 2) Cell autonomous inputs : factors within the cell- determinants transcription factors 3) Possibility for a transcription factor to bind DNA
Chromatin structure DNA + Proteins = Chromatin Chromatin is a feature of eukaryotes
Nucleosome is a primary unit of chromatin 1) Histones are the major protein complexes of chromatin 2) They are small (100-140 aa) and positively charged 3) Histone tails could be modified by Acetylation, Methylation, Ubiquitination, Phosphorylation, etc https://biomoocnews.blogspot.com/2012/10/daily-newsletter-october-22-2012.html
Early thoughts: Chromatin negatively regulates gene expression Heterochromatin formation at the inactive X- chromosome Genes transposed to heterochromatin become inactive Nature Rev Genetics, 2010
Nucleosomes are dynamic 1) Canonical histones are replaced by histone variants 2) Histone tails are modified 3) The histone octamer is moved to a new position along the DNA
Histone variants
Human histone variants
Classification of histones Canonical histones Histone variants Genomic organization Organized in clusters Single genes Trends in Genetics, 2013
Classification of histones Canonical histones Histone variants Transcription Intron-less No polya tail Peak of transcription in S-phase Have introns Have polya tail Constitutive expression through the cell cycle Trends in Genetics, 2013
Classification of histones Canonical histones Histone variants Post-translational modifications Trends in Genetics, 2013
Evolution of H3 histone variants Cell Research, 2011
Chromosomal distribution of histone variants
CENP-A organizes centromeric chromatin 1) Timing of incorporation is species specific 2) Lower evolutionary conservation than for other histones 3) Incorporation is sequence independent 4) Transmitted through generations Essays in Biochemistry, 2010
H3.3 functions 1) At telomeres: silencing of transcription from telomeric repeats 2) At pericentric repeats: establishment of constitutive heterochromatin 3) At repetitive elements: transcriptional silencing 4) At gene promoters: keeps genes poised for activation or active transcription 5) At enhancers: active enhancers
H3.3 chaperons Cell Research, 2011
H2A histone variants Nature Reviews Genetics
H2A variant functions 1) At pericentric repeats: H2A.Z stops spreading of heterochromatin 2) At gene promoters: H2A.Z keeps genes poised for activation or active transcription macroh2a keeps genes silent 3) At enhancers: H2A.Z is associated with active enhancers or poised enhancers
Chromatin reprogramming after fertilization protamine H3.3 Replication independent!!!
Histone mutations in cancer Ann Rev Cancer Biol, 2018
Chromatin Immunoprecipitation assay Wikipedia
Chromatin Immunoprecipitation assay Wikipedia
Histone modifications
Histone code https://commons.wikimedia.org Histone code - combinatorial patterns of histone modifications that specify distinct biological outcomes, in part by the recruitment of downstream effector proteins readers or complexes in trans.
Histone code Writers enzymes that add covalent modifications to histone tails Erasers enzymes that eliminate covalent modifications from histone tails Readers proteins that bind to a certain modification on a histone tail Histone modifications are dynamic! Immunology and Cell Biology, 2015
Histone tail modifications Cell, 2014
Genome-wide distribution of histone marks H3K27Ac H3K4me1 H2A.Z H3K9/K14/K27Ac H3K4me3/2 H3K9me3/2/1 H3K27me3 H2A.Z H3K27me3 H3K36me3 H3K79me1 H2AK119Ub Enhancer Promoter Gene body
Histone tail modifications associated with active transcription 1) Acetylation of histones at the promoters and enhancers 2) At the promoters: Tri and di-methylation of H3K4 Mono-methylation of H3K9 Acetylation of H2A.Z 3) At the gene bodies: Tri-methylation of H3K36 Mono-methylation of H3K79 H3K27Ac H3K4me1 H2A.Z H3K9/K14/K27Ac H3K4me3/2 H3K9me1 H2A.Z H3K36me3 H3K79me1 Enhancer Promoter Gene body
Histone acylations Nat Rev Mol Cel Biol, 2017
Writers and erasers of Lysine acylations Nat Rev Mol Cel Biol, 2017
Metabolic regulation of histone acylation Nat Rev Mol Cel Biol, 2017
Histone methylation 1) Methylation of histone tails is associated with both transcriptional activation and repression 2) Methyltransferases are SET-domain containing proteins that act in large complexes together with histone acetyltransferases/ deacetylases and DNA methyltransferases 3) Methylation of histones is reversible H3K4me1 H3K4me3/2 H3K9me3/2 H3K27me3 H3K27me3 H3K36me3 H3K79me1 Enhancer Promoter Gene body
H3K9 methylation is required for heterochromatin formation 1) Pericentric heterochromatin 2) Long interspersed repetitive elements and transposons 3) Imprinted genes 4) Zink Finger Protein and Olfactory receptor encoded genes wt Prmd3/Prdm16 ko Cell, 2012
Identification of Polycomb Repressive Complex members Gene X Activation of the posterior Hox gene Anterior-to-Posterior transformation
H3K27me3 is required for facultative gene silencing Nature, 2011
H3K27me3 is required for facultative gene silencing 1) H3K27me3 anti-correlates with DNA methylation and found at CpG containing promoters 2) H3K27me3 is found at the promoters of genes regulating development. Many transcription factors containing homeodomains, signalling molecules, receptors are the targets of PRC2. 3) PRC2 functions are required for cell type specific lineage commitment and differentiation. 4) PRC1 might be associated or not with PRC2 5) PRC1 is required for H2A K119 ubiquitination and chromatin compaction
Functions of H3K4me3 1) H3K4me3 is found at CpG containing promoters independent from their transcriptional status 2) H3K4me3 keeps CpG-rich promoters free from DNA methylation 3) H3K4me3 facilitates transcriptional activation
Recruitment of PRC2/Trx complexes to the target genes 1) In Drosophila: Polycomb/ Trithorax Response Elements 2) In mammals: CpG islands
Histone demethylases
Methylated histones are transmitted through generations Nucleosomes localized at the promoters of many genes retain histones B. Cairns Lab & AH Peters Lab
Histone mutations in cancer H3.3 K27M mutation in gliomas Nature Reviews Genetics
Blocking demethylase activity in cancer
Blocking demethylase activity in cancer
Histone fragments as antimicrobial peptides
Literature 1. Metabolic regulation of gene expression through histone acylations. Sabari BR, Zhang D, Allis CD, Zhao Y. Nat Rev Mol Cell Biol. 2017 Feb;18(2):90-101. 2. Oncogenic Mechanisms of Histone H3 Mutations. Weinberg DN, Allis CD, Lu C. Cold Spring Harb Perspect Med. 2017 Jan 3;7(1). 3. The molecular hallmarks of epigenetic control. Allis CD, Jenuwein T. Nat Rev Genet. 2016 Aug;17(8):487-500. 4. Chromatin plasticity: A versatile landscape that underlies cell fate and identity. Yadav T, Quivy JP, Almouzni G. Science. 2018 Sep 28;361(6409):1332-1336. 5. Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Cell. 2017 Sep 21;171(1):34-57. 6. Histone variants on the move: substrates for chromatin dynamics. Talbert PB, Henikoff S. Nat Rev Mol Cell Biol. 2017 Feb;18(2):115-126.