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References from Chromatin dynamics and cellular energy homeostasis. Local targets link to admitted publications; unresolved targets remain external evidence.
Clinical review: oxygen as a signaling molecule
10.1186/cc9185 · 2010 · External reference
Cell energy metabolism: an update
10.1016/j.bbabio.2020.148276 · 2020 · External reference
Chromatin and metabolism
10.1146/annurev-biochem-062917-012634 · 2018 · External reference
The multifaceted contributions of mitochondria to cellular metabolism
10.1038/s41556-018-0124-1 · 2018 · External reference
Chromatin balances cell redox and energy homeostasis
10.1186/s13072-023-00520-8 · 2023 · External reference
Free radicals and antioxidants in normal physiological functions and human disease
10.1016/j.biocel.2006.07.001 · 2007 · External reference
Histone H3 threonine 11 phosphorylation by Sch9 and CK2 regulates chronological lifespan by controlling the nutritional stress response
10.7554/elife.36157 · 2018 · External reference
Oxidative stress: harms and benefits for human health
10.1155/2017/8416763 · 2017 · External reference
Thriving in oxygen while preventing ROS overproduction: no two systems are created equal
10.3389/fphys.2022.874321 · 2022 · External reference
A functional account of stimulation-based aerobic glycolysis and its role in interpreting BOLD signal intensity increases in neuroimaging experiments
10.1016/j.neubiorev.2023.105373 · 2023 · External reference
Macrophages, metabolites, and nucleosomes: chromatin at the intersection between aging and inflammation
10.3390/ijms221910274 · 2021 · External reference
Nutriepigenomics in environmental-associated oxidative stress
10.3390/antiox12030771 · 2023 · External reference
Altered transposon element-derived genes distort oxygen-free radical scavenger systems in FXD
10.1093/narmme/ugag010 · 2026 · External reference
Variants of core histones and their roles in cell fate decisions, development and cancer
10.1038/nrm.2016.166 · 2017 · External reference
Metabolism and regulation of canonical histone mRNAs: life without a poly(a) tail
10.1038/nrg2438 · 2008 · External reference
Chromatin challenges during DNA replication and repair
10.1016/j.cell.2007.01.030 · 2007 · External reference
ATP-dependent chromatin remodeling shapes the DNA replication landscape
10.1038/nsmb.1419 · 2008 · External reference
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
10.1038/nrm.2017.26 · 2017 · External reference
Regulating the chromatin landscape: structural and mechanistic perspectives
10.1146/annurev-biochem-051810-093157 · 2014 · External reference
Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes
10.1016/j.cell.2013.07.011 · 2013 · External reference
Nucleosome remodeling and epigenetics
10.1101/cshperspect.a017905 · 2013 · External reference
Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex
10.1126/science.273.5274.513 · 1996 · External reference
Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex
10.1126/science.8016655 · 1994 · External reference
Structure and mechanism of the chromatin remodelling factor ISW1a
10.1038/nature09947 · 2011 · External reference
ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps
10.1016/j.cell.2012.12.040 · 2013 · External reference
Yeast Isw1p forms two separable complexes in vivo
10.1128/mcb.23.1.80-91.2003 · 2003 · External reference
Histone octamer structure is altered early in ISW2 ATP-dependent nucleosome remodeling
10.1016/j.celrep.2019.05.106 · 2019 · External reference
Chromatin remodeling through directional DNA translocation from an internal nucleosomal site
10.1038/nsmb973 · 2005 · External reference
Regulation of DNA translocation efficiency within the chromatin remodeler RSC/Sth1 potentiates nucleosome sliding and ejection
10.1016/j.molcel.2016.03.032 · 2016 · External reference
ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding
10.1038/nsmb.1397 · 2008 · External reference
CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion
10.1038/s41586-023-05961-5 · 2023 · External reference
Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
10.1016/j.cell.2017.05.004 · 2017 · External reference
Human Condensin I and II drive extensive ATP-dependent compaction of nucleosome-bound DNA
10.1016/j.molcel.2020.04.026 · 2020 · External reference
Topological domains in mammalian genomes identified by analysis of chromatin interactions
10.1038/nature11082 · 2012 · External reference
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
10.1016/j.cell.2025.10.013 · 2025 · External reference
CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming
10.1016/j.celrep.2022.110626 · 2022 · External reference
CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development
10.1073/pnas.2416384122 · 2025 · External reference
The protein CTCF is required for the enhancer blocking activity of vertebrate insulators
10.1016/s0092-8674(00)81967-4 · 1999 · External reference
ISW1a modulates cohesin distribution in centromeric and pericentromeric regions
10.1093/nar/gkad612 · 2023 · External reference
Variations in flanking or less conserved positions of Reb1 and Abf1 consensus binding sites lead to major changes in their ability to modulate nucleosome sliding activity
10.1186/s40659-025-00627-0 · 2025 · External reference
Poly(dA:dT) tracts differentially modulate nucleosome remodeling activity of RSC and ISW1a complexes, exerting tract orientation-dependent and -independent effects
10.3390/ijms242015245 · 2023 · External reference
The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription factors
10.1371/journal.pgen.1005940 · 2016 · External reference
Exploring the interaction between the SWI/SNF chromatin remodeling complex and the zinc finger factor CTCF
10.3390/ijms21238950 · 2020 · External reference
Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging
10.1101/gad.233221.113 · 2014 · External reference
Ageing-associated changes in transcriptional elongation influence longevity
10.1038/s41586-023-05922-y · 2023 · External reference
H3K36 methylation promotes longevity by enhancing transcriptional fidelity
10.1101/gad.263707.115 · 2015 · External reference
Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes
10.1038/nature11326 · 2012 · External reference
Nucleosome displacement in transcription
10.1101/gad.1435706 · 2006 · External reference
Selective suppression of antisense transcription by Set2-mediated H3K36 methylation
10.1038/ncomms13610 · 2016 · External reference
Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription
10.1016/j.cell.2005.10.023 · 2005 · External reference
Regulation of DNA alkylation damage repair: lessons and therapeutic opportunities
10.1016/j.tibs.2016.10.001 · 2017 · External reference
Phosphorylated hMSH6: DNA mismatch versus DNA damage recognition
2011 · External reference
MPTAC links alkylation damage signaling to sterol biosynthesis
10.1016/j.redox.2022.102270 · 2022 · External reference
MPTAC determines APP fragmentation via sensing sulfur amino acid catabolism
10.1016/j.celrep.2018.07.013 · 2018 · External reference
ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding
10.1038/nsmb.1397 · 2008 · External reference
C G composition in transposon-derived genes is increased in FXD with perturbed immune system
10.1093/narmme/ugae015 · 2024 · External reference
Trinucleotide repeat disorders
10.1146/annurev.neuro.29.051605.113042 · 2007 · External reference
Base editing of trinucleotide repeats that cause Huntington's disease and Friedreich's ataxia reduces somatic repeat expansions in patient cells and in mice
10.1038/s41588-025-02172-8 · 2025 · External reference
Insights into DNA repeat expansions among 900,000 biobank participants
10.1038/s41586-025-09886-z · 2026 · External reference
Nucleosome remodeling by hMSH2-hMSH6
10.1016/j.molcel.2009.12.010 · 2009 · External reference
GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7
10.1016/j.molcel.2005.02.013 · 2005 · External reference
Nucleotide biosynthetic enzyme GMP synthase is a TRIM21-controlled relay of p53 stabilization
10.1016/j.molcel.2013.12.017 · 2014 · External reference
SAICAR stimulates pyruvate kinase isoform M2 and promotes cancer cell survival in glucose-limited conditions
10.1126/science.1224409 · 2012 · External reference
Nucleotide metabolism behind epigenetics
10.3389/fendo.2021.731648 · 2021 · External reference
Crosstalk among histone modifications
10.1016/j.cell.2008.10.036 · 2008 · External reference
Signals and combinatorial functions of histone modifications
10.1146/annurev-biochem-061809-175347 · 2011 · External reference
Diverse activities of histone acylations connect metabolism to chromatin function
10.1016/j.molcel.2016.06.038 · 2016 · External reference
Serine and SAM responsive complex SESAME regulates histone modification crosstalk by sensing cellular metabolism
10.1016/j.molcel.2015.09.024 · 2015 · External reference
Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation
10.1038/emboj.2011.193 · 2011 · External reference
Transcriptional activators direct histone acetyltransferase complexes to nucleosomes
10.1038/28886 · 1998 · External reference
A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation
10.1016/s0092-8674(00)81220-9 · 1998 · External reference
Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions
10.1126/science.1103455 · 2004 · External reference
Interplay between metabolism and epigenetics: a nuclear adaptation to environmental changes
10.1016/j.molcel.2016.05.029 · 2016 · External reference
Acetyl-CoA and the regulation of metabolism: mechanisms and consequences
10.1016/j.ceb.2015.02.003 · 2015 · External reference
Histone acetyltransferase complexes: one size doesn't fit all
10.1038/nrm2145 · 2007 · External reference
Glucose starvation induces a switch in the histone acetylome for activation of gluconeogenic and fat metabolism genes
10.1016/j.molcel.2021.12.015 · 2022 · External reference
Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex
10.1101/gad.11.13.1640 · 1997 · External reference
Sirtuin chemical mechanisms
10.1016/j.bbapap.2010.01.021 · 2010 · External reference
Nicotinamide riboside promotes Sir2 silencing and extends lifespan via Nrk and Urh1/Pnp1/Meu1 pathways to NAD+
10.1016/j.cell.2007.03.024 · 2007 · External reference
Evolution of distinct responses to low NAD(+) stress by rewiring the Sir2 deacetylase network in yeasts
10.1534/genetics.120.303087 · 2020 · External reference
Metabolic regulation of gene expression through histone acylations
10.1038/nrm.2016.140 · 2017 · External reference
Histone acylation beyond acetylation: terra incognita in chromatin biology
2015 · External reference
A subset of human bromodomains recognizes butyryllysine and crotonyllysine histone peptide modifications
10.1016/j.str.2015.08.004 · 2015 · External reference
Dynamic competing histone H4 K5K8 acetylation and butyrylation are hallmarks of highly active gene promoters
10.1016/j.molcel.2016.03.014 · 2016 · External reference
Bromodomain-dependent stage-specific male genome programming by Brdt
10.1038/emboj.2012.233 · 2012 · External reference
Metabolic regulation of gene expression by histone lysine beta-hydroxybutyrylation
10.1016/j.molcel.2016.03.036 · 2016 · External reference
Short- and medium-chain fatty acids in energy metabolism: the cellular perspective
10.1194/jlr.r067629 · 2016 · External reference
One-carbon metabolism and nucleotide biosynthesis as attractive targets for anticancer therapy
10.18632/oncotarget.15053 · 2017 · External reference
Histidine Nτ-methylation identified as a new posttranslational modification in histone H2A at His-82 and H3 at His-39
10.1016/j.jbc.2023.105131 · 2023 · External reference
3-methylhistidine in actin and other muscle proteins
10.1042/bj1050361 · 1967 · External reference
The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyltransferase
10.1074/jbc.271.25.15034 · 1996 · External reference
SETD3 protein is the actin-specific histidine N-methyltransferase
10.7554/elife.37921 · 2018 · External reference
A novel 3-methylhistidine modification of yeast ribosomal protein Rpl3 is dependent upon the YIL110W methyltransferase
10.1074/jbc.m110.170787 · 2010 · External reference
Arginine methylation: the coming of age
10.1016/j.molcel.2016.11.003 · 2017 · External reference
Histone-binding domains: strategies for discovery and characterization
10.1016/j.bbagrm.2014.01.007 · 2014 · External reference
Readers of histone methylarginine marks
10.1016/j.bbagrm.2014.02.015 · 2014 · External reference
A metabolic function for phospholipid and histone methylation
10.1016/j.molcel.2017.02.026 · 2017 · External reference
The Swi-Snf chromatin remodeling complex mediates gene repression through metabolic control
10.1093/nar/gkad711 · 2023 · External reference
Methionine adenosyltransferase II-dependent histone H3K9 methylation at the COX-2 gene locus
10.1074/jbc.m112.429738 · 2013 · External reference
Methionine metabolism in health and cancer: a nexus of diet and precision medicine
10.1038/s41568-019-0187-8 · 2019 · External reference
Methionine adenosyltransferase II serves as a transcriptional corepressor of Maf oncoprotein
10.1016/j.molcel.2011.02.018 · 2011 · External reference
Histone H3 glutathionylation in proliferating mammalian cells destabilizes nucleosomal structure
10.1089/ars.2012.5021 · 2013 · External reference
Critical roles of the cysteine-glutathione axis in the production of gamma-glutamyl peptides in the nervous system
10.3390/ijms24098044 · 2023 · External reference
Histone demethylation by a family of JmjC domain-containing proteins
10.1038/nature04433 · 2006 · External reference
The activity of JmjC histone lysine demethylase KDM4A is highly sensitive to oxygen concentrations
10.1021/acschembio.6b00958 · 2017 · External reference
Roles of HIF and 2-oxoglutarate-dependent dioxygenases in controlling gene expression in hypoxia
10.3390/cancers13020350 · 2021 · External reference
Investigations on the oxygen dependence of a 2-oxoglutarate histone demethylase
10.1042/bj20121155 · 2013 · External reference
Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase
10.1038/nsmb1273 · 2007 · External reference
Hypoxia induces rapid changes to histone methylation and reprograms chromatin
10.1126/science.aau5870 · 2019 · External reference
Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate
10.1126/science.aaw1026 · 2019 · External reference
2-oxoglutarate-dependent dioxygenases in cancer
10.1038/s41568-020-00303-3 · 2020 · External reference
2-oxoglutarate derivatives can selectively enhance or inhibit the activity of human oxygenases
10.1038/s41467-021-26673-2 · 2021 · External reference
Mitochondrial protein lipoylation and the 2-oxoglutarate dehydrogenase complex controls HIF1α stability in aerobic conditions
10.1016/j.cmet.2016.09.015 · 2016 · External reference
JMJD family proteins in cancer and inflammation
10.1038/s41392-022-01145-1 · 2022 · External reference
Engineering biological C-H functionalization leads to allele-specific regulation of histone demethylases
10.1021/jacs.6b08653 · 2016 · External reference
The solid and liquid states of chromatin
10.1186/s13072-021-00424-5 · 2021 · External reference
Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs
10.1073/pnas.1424028112 · 2015 · External reference
Putting the squeeze on phase separation
10.1021/jacsau.1c00443 · 2022 · External reference
Spatially non-uniform condensates emerge from dynamically arrested phase separation
10.1038/s41467-023-36059-1 · 2023 · External reference
Viscoelastic phase separation in biological cells
10.1038/s42005-022-00947-7 · 2022 · External reference
A phase separation model for transcriptional control
10.1016/j.cell.2017.02.007 · 2017 · External reference
A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells
10.1016/j.cell.2011.03.042 · 2011 · External reference
Enhancer RNA (eRNA) in human diseases
10.3390/ijms231911582 · 2022 · External reference
The Mediator complex: a central integrator of transcription
10.1038/nrm3951 · 2015 · External reference
NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis
10.1016/j.molcel.2014.08.024 · 2014 · External reference
The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis
10.1073/pnas.1433065100 · 2003 · External reference
Affinity map of bromodomain protein 4 (BRD4) interactions with the histone H4 tail and the small molecule inhibitor JQ1
10.1074/jbc.m113.523019 · 2014 · External reference
The BRD4-nucleosome interaction is enhanced modestly and non-selectively by histone acetylation
10.1093/nar/gkaf1406 · 2025 · External reference
Brd4 coactivates transcriptional activation of NF-κB via specific binding to acetylated RelA
10.1128/mcb.01365-08 · 2009 · External reference
The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer
10.1038/ng.403 · 2009 · External reference
Chromosome 8q24-associated cancers and MYC
10.1177/1947601910381380 · 2010 · External reference
MYC acetylated lysine residues drive oncogenic cell transformation and regulate select genetic programs for cell adhesion-independent growth and survival
10.1101/gad.350736.123 · 2023 · External reference
RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation
10.1038/s41594-018-0102-0 · 2018 · External reference
The molecular basis for cellular function of intrinsically disordered protein regions
10.1038/s41580-023-00673-0 · 2024 · External reference
Structural insights into p300 regulation and acetylation-dependent genome organisation
10.1038/s41467-022-35375-2 · 2022 · External reference
NF-κB regulation: lessons from structures
10.1111/j.1600-065x.2012.01097.x · 2012 · External reference
Structural basis of the nucleosome transition during RNA polymerase II passage
10.1126/science.aau9904 · 2018 · External reference
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors
10.1126/science.aav8912 · 2019 · External reference
The regulation and functions of DNA and RNA G-quadruplexes
10.1038/s41580-020-0236-x · 2020 · External reference