Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics Oxford Academic. 2018;17:116–37.

Article  CAS  Google Scholar 

Villar D, Flicek P, Odom DT. Evolution of transcription factor binding in metazoans — mechanisms and functional implications. Nat Rev Genet. 2014;15:221–33.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515:355–64.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ballester B, MedinaRivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. eLife Sci. 2014;3:e02626.

Article  Google Scholar 

Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, et al. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet. 2007;39:730–2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, et al. Ten things you should know about transposable elements. Genome Biol. 2018;19:199.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014;24:1963–76.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Trizzino M, Park Y, Holsbach-Beltrame M, Aracena K, Mika K, Caliskan M, et al. Transposable elements are the primary source of novelty in primate gene regulation. Genome Res. 2017;27:1623–33.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, et al. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018;28:448–59.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, et al. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding. Science. 2010;328:1036–40.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, et al. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell. 2013;154:530–40.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng Y, Ma Z, Kim B-H, Wu W, Cayting P, Boyle AP, et al. Principles of regulatory information conservation between mouse and human. Nature. 2014;515:371–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cardoso-Moreira M, Halbert J, Valloton D, Velten B, Chen C, Shao Y, et al. Gene expression across mammalian organ development. Nature. 2019;571:505–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature. 2011;478:343–8.

Article  CAS  PubMed  Google Scholar 

Deplancke B, Alpern D, Gardeux V. The genetics of transcription factor DNA binding variation. Cell. 2016;166:538–54.

Article  CAS  PubMed  Google Scholar 

Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression. Nat Ecol Evol. 2018;2:152.

Article  PubMed  Google Scholar 

Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, et al. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol. 2020;21:5.

Article  PubMed  PubMed Central  Google Scholar 

Rauluseviciute I, Drabløs F, Rye MB. DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis. Clin Epigenetics. 2019;11:193.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li E, Zhang Y. DNA Methylation in Mammals. Cold Spring Harb Perspect Biol. 2014;6:a019133.

Article  PubMed  PubMed Central  Google Scholar 

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011 Available from: http://www.nature.com/doifinder/10.1038/nature10716 Cited 2018 Jun 25

Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, et al. DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma. Nat Med. 2017;23:386–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schwartzman O, Tanay A. Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet. 2015;16:716–26.

Article  CAS  PubMed  Google Scholar 

Hernando-Herraez I, Evano B, Stubbs T, Commere P-H, Jan Bonder M, Clark S, et al. Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells. Nat Commun. 2019;10:4361.

Article  PubMed  PubMed Central  Google Scholar 

Zhang L, Xie WJ, Liu S, Meng L, Gu C, Gao YQ. DNA methylation landscape reflects the spatial organization of chromatin in different cells. Biophys J. 2017;113:1395–404.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jansz N. DNA methylation dynamics at transposable elements in mammals. Essays Biochem. 2019;63:677–89.

Article  CAS  PubMed  Google Scholar 

Greenberg MVC, Bourchis D. The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol. 2019;20:590–607.

Article  CAS  PubMed  Google Scholar 

Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92.

Article  CAS  PubMed  Google Scholar 

Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465–76.

Article  CAS  PubMed  Google Scholar 

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun. 2015;6:6363.

Article  CAS  PubMed  Google Scholar 

Ginno PA, Gaidatzis D, Feldmann A, Hoerner L, Imanci D, Burger L, et al. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity Nature Communications. Nat Publishing Group. 2020;11:2680.

CAS  Google Scholar 

Burger L, Gaidatzis D, Schübeler D, Stadler MB. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 2013;41:e155–e155.