User:Seppi333/sandbox6

The common nomenclature of histone modifications is:

• The name of the histone (e.g., H3)
• The single-letter amino acid abbreviation (e.g., K for Lysine) and the amino acid position in the protein
• The type of modification (Me: methyl, P: phosphate, Ac: acetyl, Ub: ubiquitin)
• The number of modifications (only Me is known to occur in more than one copy per residue. 1, 2 or 3 is mono-, di- or tri-methylation)

So H3K4me1 denotes the monomethylation of the 4th residue (a lysine) from the start (i.e., the N-terminal) of the H3 protein.

class="wikitable" style="text-align:center" |+ Examples of histone modifications in transcriptional regulation
rowspan="2" | Type of modification ! colspan="9" | Histone
H3K4 ! H3K9 ! H3K14 ! H3K27 ! H3K79 ! H3K36 ! H4K20 ! H2BK5 ! H2BK20
mono-methylation | activation | activation{{cite journal | vauthors = Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K | title = High-resolution profiling of histone methylations in the human genome | journal = Cell | volume = 129 | issue = 4 | pages = 823–37 | date = May 2007 | pmid = 17512414 | doi = 10.1016/j.cell.2007.05.009 | s2cid = 6326093 }} | | activation | activation | | activation | activation |
di-methylation | |repression{{cite journal | vauthors = Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ | title = Determination of enriched histone modifications in non-genic portions of the human genome | journal = BMC Genomics | volume = 10 | pages = 143 | year = 2009 | pmid = 19335899 | pmc = 2667539 | doi = 10.1186/1471-2164-10-143 }} {{open access}} | | repression | activation | | | |
tri-methylation | activation{{cite journal | vauthors = Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I | title = The landscape of histone modifications across 1% of the human genome in five human cell lines | journal = Genome Research | volume = 17 | issue = 6 | pages = 691–707 | date = June 2007 | pmid = 17567990 | pmc = 1891331 | doi = 10.1101/gr.5704207 }} | repression | | repression | activation, repression | activation | | repression |
acetylation | | activation | activation | activation{{cite journal | vauthors = Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R | title = Histone H3K27ac separates active from poised enhancers and predicts developmental state | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 50 | pages = 21931–6 | date = Dec 2010 | pmid = 21106759 | pmc = 3003124 | doi = 10.1073/pnas.1016071107 | doi-access = free }} | | | | |activation

class="wikitable" style="text-align:center"
rowspan="2" | Type of modification ! colspan="8" | Histone
H3K4 ! H3K9 ! H3K14 ! H3K27 ! H3K79 !H3K122 ! H4K20 ! H2BK5
mono-methylation !style="background: #dedefa;" | activation{{cite journal | author = Benevolenskaya EV | title = Histone H3K4 demethylases are essential in development and differentiation | journal = Biochem. Cell Biol. | volume = 85 | issue = 4 | pages = 435–43 |date=August 2007 | pmid = 17713579 | doi = 10.1139/o07-057 }} !style="background: #dedefa;" | activation | !style="background: #dedefa;" | activation !style="background: #dedefa;" | activation{{cite journal |vauthors=Steger DJ, Lefterova MI, Ying L, Stonestrom AJ, Schupp M, Zhuo D, Vakoc AL, Kim JE, Chen J, Lazar MA, Blobel GA, Vakoc CR | title = DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells | journal = Molecular and Cellular Biology | volume = 28 | issue = 8 | pages = 2825–39 |date=April 2008 | pmid = 18285465 | pmc = 2293113 | doi = 10.1128/MCB.02076-07 }} | !style="background: #dedefa;" | activation !style="background: #dedefa;" | activation
di-methylation !style="background: #dedefa;" | activation !style="background: #ffdead;" |repression | !style="background: #ffdead;" | repression !style="background: #dedefa;" | activation | | |
tri-methylation !style="background: #dedefa;" | activation !style="background: #ffdead;" | repression | !style="background: #ffdead;" | repression !style="background: #ffffa2;" | activation, repression | | !style="background: #ffdead;" | repression
acetylation | !style="background: #dedefa;" | activation !style="background: #dedefa;" | activation !style="background: #dedefa;" | activation{{cite journal|last1=Creyghton|first1=MP|title=Histone H3K27ac separates active from poised enhancers and predicts developmental state|journal=Proc Natl Acad Sci USA|date=Dec 2010|volume=107|issue=50|pages=21931–6|doi=10.1073/pnas.1016071107|pmid=21106759|pmc=3003124|doi-access=free }} | !style="background: #dedefa;" |activation{{Cite journal|last1=Pradeepa|first1=Madapura M.|last2=Grimes|first2=Graeme R.|last3=Kumar|first3=Yatendra|last4=Olley|first4=Gabrielle|last5=Taylor|first5=Gillian C. A.|last6=Schneider|first6=Robert|last7=Bickmore|first7=Wendy A.|date=2016-04-18|title=Histone H3 globular domain acetylation identifies a new class of enhancers|journal=Nature Genetics|language=en|volume=48|issue=6 |doi=10.1038/ng.3550|issn=1546-1718|pages=681–686|pmid=27089178|pmc=4886833}} | |

• H3K4me3 is enriched in transcriptionally active promoters.{{cite journal|last1=Liang|first1=G|title=Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome|journal=Proc. Natl Acad. Sci. USA|date=2004|volume=101|issue=19|pages=7357–7362|doi=10.1073/pnas.0401866101|pmid=15123803|pmc=409923|doi-access=free}}
• H3K9me3 is found in constitutively repressed genes.
• H3K27me3 is found in facultatively repressed genes.
• H3K36me3 is found in actively transcribed gene bodies.
• H3K9ac is found in actively transcribed promoters.
• H3K14ac is found in actively transcribed promoters.
• H3K27ac distinguishes active enhancers from poised enhancers.
• H3K122ac is enriched in poised promoters and also found in a different type of putative enhancer that lacks H3K27ac.

class="wikitable"

+Legend: | {{col-list|colwidth=30em| su: sumoylation ub: ubiquitination ph: phosphorylation ac: acetylation me1: mono-methylation me2: di-methylation me3: tri-methylation }}

;Humans

H2A

• H2AK5ac - Transcriptional activation (Hs){{cite journal | vauthors = Zhao Y, Garcia BA | title = Comprehensive Catalog of Currently Documented Histone Modifications | journal = Cold Spring Harbor Perspectives in Biology | volume = 7 | issue = 9 | pages = a025064 | date = September 2015 | pmid = 26330523 | pmc = 4563710 | doi = 10.1101/cshperspect.a025064 | url = }}

H2B

• H2BK5ac - Transcriptional activation (Hs)

H3

• Lysine residue 4:
• H3K4me1 - Transcriptional activation (Hs)
• H3K4me2 - Transcriptional activation (Hs)
• H3K4me3 - Transcriptional activation (Hs)
• Lysine residue 9:
• H3K9me1 - Transcriptional repression (Hs) via G9a and G9a-like protein
• H3K9me2 - Transcriptional repression (Hs) via G9a, G9a-like protein, and SETDB1
• H3K9me3 - Transcriptional repression (Hs) via SETDB1
• H3K9ac - Transcriptional activation (Saccharomyces cerevisiae)/Nuclear receptor coactivation (Hs) via SETDB1
• Lysine residue 27:
• H3K27me1 - ...
• H3K27me2 - ...
• H3K27me3 - ...
• Quote from a source on H3K4, H3K9, and H3K27 mono/di/tri-methylation states: {{tq|It needs to be kept in mind that methylation of histone H3K4 is generally associated with increased transcriptional activity [45] whereas methylation of H3K9 and H3K27 is associated with repression of gene expression [44, 46].}}{{cite journal | vauthors = Cadet JL | title = Epigenetics of Stress, Addiction, and Resilience: Therapeutic Implications | journal = Molecular Neurobiology | volume = 53 | issue = 1 | pages = 545–560 | date = January 2016 | pmid = 25502297 | pmc = 4703633 | doi = 10.1007/s12035-014-9040-y | url = }}
• H3K27ac-See "Other organisms"
• Lysine residue 14:
• H3K14ac - Transcriptional activation (Hs)
• Lysine residue 36:
• H3K36me1 - Transcription activation (Hs)
• H3K36me2 - Transcription activation (Hs) {{a note}} in Saccharomyces cerevisiae, H3K36me2 is associated with gene repression
• H3K36me3 - Transcription activation (Hs)
• Arginine residue 8:
• H3R8me1 - Transcriptional repression (Hs) via PRMT5
• H3R8me2s (symmetric dimethylation) - Transcriptional repression (Hs) via PRMT5

Arginine residue 17:

• H3R17me1 - Transcriptional activation (Hs)
• H3R17me2a (w/ H3K18ac and H3K23ac) - Transcriptional activation (Hs) (I'm assuming me2a means dimethyl-acetylation)
• H3K18ac (via p300, w/o other marks) - Transcriptional activation (Hs)
• H3K18ac (via CBP, with H3R17me2 and H3K23ac) - Transcriptional activation (Hs)
• H3K23ac (via CBP, with H3R17me2 and H3K18ac) - Transcriptional activation (Hs)

:Serine residue 10 phosphorylation:

• H3S10ph - Transcriptional activation (in general in Sc, of IEGs in Hs) / upregulation (Hs)
• quote from another source: {{tq|One of the best-characterized histone phosphorylation sites is serine 10 on histone H3 (H3S10).This modification stabilizes the HAT, GCN5, on associated gene promoters while antagonizing the repressive modification - methylation of lysine 9 on histone H3 (H3K9) and its subsequent recruitment of HP1 (heterochromatin protein 1, see below).6 Since phosphorylation at H3S10 recruits a HAT, the neighboring lysine residue at H3K9 is often acetylated in concert with phosphorylation, a process called phosphoacetylation that further potentiates gene activation.}}{{cite journal | author = Renthal W, Nestler EJ | title = Chromatin regulation in drug addiction and depression | journal = Dialogues Clin. Neurosci. | volume = 11 | issue = 3 | pages = 257–268 | date = September 2009 | pmid = 19877494 | pmc = 2834246 | doi = 10.31887/DCNS.2009.11.3/wrenthal| url = | quote= [Psychostimulants] increase cAMP levels in striatum, which activates protein kinase A (PKA) and leads to phosphorylation of its targets. This includes the cAMP response element binding protein (CREB), the phosphorylation of which induces its association with the histone acetyltransferase, CREB binding protein (CBP) to acetylate histones and facilitate gene activation. This is known to occur on many genes including fosB and c-fos in response to psychostimulant exposure. ΔFosB is also upregulated by chronic psychostimulant treatments, and is known to activate certain genes (eg, cdk5) and repress others (eg, c-fos) where it recruits HDAC1 as a corepressor. ... Chronic exposure to psychostimulants increases glutamatergic [signaling] from the prefrontal cortex to the NAc. Glutamatergic signaling elevates Ca2+ levels in NAc postsynaptic elements where it activates CaMK (calcium/calmodulin protein kinases) signaling, which, in addition to phosphorylating CREB, also phosphorylates HDAC5.}}
  [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2834246/figure/DialoguesClinNeurosci-11-257-g002/ Figure 2: Psychostimulant-induced signaling events]

;Other organisms

H2A

• H2AK7ac - Transcriptional activation (Saccharomyces cerevisiae)
• H2AK126su - Transcriptional repression; Blocks Histone acetylation and histone ubiquitination (Saccharomyces cerevisiae) (su: sumoylation)

H2B

• H2BK16su - Gene repression (Saccharomyces cerevisiae)
• H2BK17su - Gene repression (Saccharomyces cerevisiae)
• H2BK34ub - Transcriptional activation (Saccharomyces cerevisiae) (ub: ubiquitination)

H3

• H3K4ac - Transcription activation at some promoters (Saccharomyces cerevisiae)
• H3K27ac - "Enhancer function, gene expression" (Saccharomyces cerevisiae, Drosophila melanogaster) (I guess this essentially means transcriptional activation)

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November 05, 2019 18:30:29 (UTC)