Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning MA et al (2015) De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay. Am J Hum Genet 96(3):498–506

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA (2014) Minfi: a flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays. Bioinformatics 30(10):1363–1369

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aslam M, Ullah A, Paramasivam N, Kandasamy N, Naureen S, Badshah M, Khan K et al (2019) Segregation and potential functional impact of a rare stop-gain PABPC4L variant in familial atypical parkinsonism. Sci Rep 9(1):13576

Article  PubMed  PubMed Central  Google Scholar 

Awamleh Z, Chater-Diehl E, Choufani S, Wei E, Kianmahd RR, Yu A, Chad L et al (2022) DNA methylation signature associated with bohring-opitz syndrome: a new tool for functional classification of variants in ASXL genes. Eur J Hum Genet EJHG. https://doi.org/10.1038/s41431-022-01083-0

Article  PubMed  Google Scholar 

Ball MP, Li JB, Gao Y, Lee J-H, LeProust EM, Park I-H, Xie B, Daley GQ, Church GM (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27(4):361–368

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bjarnegård M, Enge M, Norlin J, Gustafsdottir S, Fredriksson S, Abramsson A, Takemoto M, Gustafsson E, Fässler R, Betsholtz C (2004) Endothelium-specific ablation of PDGFB leads to pericyte loss and glomerular, cardiac and placental abnormalities. Development 131(8):1847–1857

Article  PubMed  Google Scholar 

Bondhus L, Wei A, Arboleda VA (2022) DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. BMC Bioinformatics 23(1):364

Article  CAS  PubMed  PubMed Central  Google Scholar 

Boulet AM, Capecchi MR (2002) Duplication of the Hoxd11 gene causes alterations in the axial and appendicular skeleton of the mouse. Dev Biol 249(1):96–107

Article  CAS  PubMed  Google Scholar 

Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT et al (2017) An improved ATAC-Seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14(10):959–962

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dasen JS, Jessell TM (2009) Hox networks and the origins of motor neuron diversity. Curr Top Dev Biol 88:169–200

Article  CAS  PubMed  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-Seq aligner. Bioinformatics 29(1):15–21

Article  CAS  PubMed  Google Scholar 

Dreveny I, Deeves SE, Fulton J, Yue B, Messmer M, Bhattacharya A, Collins HM, Heery DM (2014) The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification. Nucleic Acids Res 42(2):822–835

Article  CAS  PubMed  Google Scholar 

Fang J, Wang J, Liangliang Yu, Wenxia Xu (2021) Role of HOXC10 in cancer. Front Oncol 11(May):684021

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fang L, Chen D, Zhang J, Li H, Bradford B, Jin C (2022) Potential functions of histone H3.3 lysine 56 acetylation in mammals. Epigenetics 17(5):498–517

Article  PubMed  Google Scholar 

Forte E, Ramialison M, Nim HT, Mara M, Li JY, Cohn R, Daigle SL et al (2022) Adult mouse fibroblasts retain organ-specific transcriptomic identity. Elife. https://doi.org/10.7554/eLife.71008

Article  PubMed  PubMed Central  Google Scholar 

Fortin J-P, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD (2014) Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol 15(12):503

Article  PubMed  PubMed Central  Google Scholar 

Gaspar JM (2018) Improved peak-calling with MACS2. bioRxiv. https://doi.org/10.1101/496521

Article  Google Scholar 

Genais T, Gigan D, Augé B, Moussalem D, Waltzer L, Haenlin M, Gobert V (2020) The drosophila MOZ homolog enok controls notch-dependent induction of the RUNX gene lozenge independently of its histone-acetyl transferase activity. bioRxiv. https://doi.org/10.1101/2020.07.27.222620

Article  Google Scholar 

Hellman A, Chess A (2007) Gene body-specific methylation on the active X chromosome. Science 315(5815):1141–1143

Article  CAS  PubMed  Google Scholar 

Hibiya K, Katsumoto T, Kondo T, Kitabayashi I, Kudo A (2009) Brpf1, a subunit of the MOZ histone acetyl transferase complex, maintains expression of anterior and posterior hox genes for proper patterning of craniofacial and caudal skeletons. Dev Biol 329(2):176–190

Article  CAS  PubMed  Google Scholar 

Hostikka SL, Capecchi MR (1998) The mouse Hoxc11 gene: genomic structure and expression pattern. Mech Dev 70(1–2):133–145

Article  CAS  PubMed  Google Scholar 

Huang Fu, Paulson A, Dutta A, Venkatesh S, Smolle M, Abmayr SM, Workman JL (2014) Histone acetyltransferase enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire. Genes Dev 28(24):2750–2763

Article  PubMed  PubMed Central  Google Scholar 

Hubert KA, Wellik DM (2023) Hox genes in development and beyond. Development. https://doi.org/10.1242/dev.192476

Article  PubMed  Google Scholar 

Imoto I, Sonoda I, Yuki Y, Inazawa J (2001) Identification and characterization of human PKNOX2, a novel homeobox-containing gene. Biochem Biophys Res Commun 287(1):270–276

Article  CAS  PubMed  Google Scholar 

Jones MJ, Goodman SJ, Kobor MS (2015) DNA methylation and healthy human aging. Aging Cell 14(6):924–932

Article  CAS  PubMed  PubMed Central  Google Scholar 

Katsumoto T, Aikawa Y, Iwama A, Ueda S, Ichikawa H, Ochiya T, Kitabayashi I (2006) MOZ is essential for maintenance of hematopoietic stem cells. Genes Dev 20(10):1321–1330

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kennedy J, Goudie D, Blair E, Chandler K, Joss S, McKay V, Green A et al (2019) KAT6A syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants. Genet Med 21(4):850–860

Article  CAS  PubMed  Google Scholar 

Khan S, Mishra RK, Srivastava S (2023) Chapter 3–Epigenetic regulation of cis-regulatory elements and transcription factors during development. In: Singh G (ed) Perinatal and developmental epigenetics. Translational epigenetics, vol 32. Academic Press, Cambridge, pp 71–113. https://doi.org/10.1016/B978-0-12-821785-6.00004-9

Kim J, Bae D-H, Kim JH, Song K-S, Kim YS, Kim S-Y (2019) HOXC10 overexpression promotes cell proliferation and migration in gastric cancer. Oncol Rep 42(1):202–212

CAS  PubMed  PubMed Central  Google Scholar 

Kirk T, Ahmed A, Rognoni E (2021) Fibroblast memory in development, homeostasis and disease. Cells 10(11):2840. https://doi.org/10.3390/cells10112840

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klopocki E, Kähler C, Foulds N, Shah H, Joseph B, Vogel H, Lüttgen S et al (2012) Deletions in PITX1 cause a spectrum of lower-limb malformations including mirror-image polydactyly. Eur J Hum Genet EJHG 20(6):705–708

Article  CAS  PubMed  Google Scholar 

Kmita M, Duboule D (2003) Organizing axes in time and space; 25 years of colinear tinkering. Science 301(5631):331–333

Article  CAS  PubMed  Google Scholar 

Kolde R (2015) Pheatmap: pretty heatmaps. R package version 1.0. 8

Kong Y, Grimaldi M, Curtin E, Dougherty M, Kaufman C, White RM, Zon LI, Liao EC (2014) Neural crest development and craniofacial morphogenesis is coordinated by nitric oxide and histone acetylation. Chem Biol 21(4):488–501

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20(3):320–331

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee G, Lee M (2017) Classification of genes based on age-related differential expression in breast cancer. Genom Inform 15(4):156–161

Article  Google Scholar 

Levéen P, Pekny M, Gebre-Medhin S, Swolin B, Larsson E, Betsholtz C (1994) Mice deficient for PDGF B show renal, cardiovascular, and hematological abnormalities. Genes Dev 8(16):1875–1887

Article  PubMed  Google Scholar 

Li H (2013) Aligning sequence reads, clone sequences and ass