Johnstone Lab Index
Genome architecture
Average size of a topologically associated domain in humans1 Mb1
Average size of a TAD in mice880 kb1
Average size of a TAD in fruit flies140 kb1
CTCF binding sites in mammalian genomes55,000–65,0002
CTCF binding sites active in mammalian cells40,000–90,0003
Proportion of CTCF binding sites that are cell-type specific30–60%4
Typical time CTCF is bound at a given site1–10 min5
Typical time cohesin sits on chromatin during G1 loop extrusion20–25 min5
Speed at which cohesin extrudes DNA0.5–2 kb/s6
Mean distance of enhancer–promoter chromatin interactions in humans~173 kb7
The human genome
Size of the human genome3.2 Gb8
Protein-coding genes in the human genome~20,0008
Percentage of the genome consisting of exons1%9
Percentage of the genome consisting of LINE-1 elements17%9
Percentage of the genome consisting of SINEs20%9
Percentage of the genome consisting of ERVs8%9
Percentage of the genome consisting of DNA transposons3%9
Number of CpGs in the human genome28–30 million10
Fraction of CpGs methylated in healthy human tissue~60%10
Fraction of CpGs located in CpG islands~1%10
Number of CpG islands in the human genome~30,00010
Number of transcription factors in humans~1,60011
Percentage of TF binding sites containing CpGs66%11
Percentage of genes expressed in a typical human cell30–60%12
Average number of TSS peaks associated with a gene~413
Comparative genomics
Genome size of E. coli5 Mb8
Genome size of S. cerevisiae12 Mb8
Genome size of C. elegans100 Mb8
Genome size of D. melanogaster140 Mb8
Genome size of zebrafish1.4 Gb8
Genome size of mouse2.8 Gb8
Transcription & RNA
Speed of RNA polymerase II~2–5 kb/min14
Average mRNA molecules per mouse fibroblast cell~174,00015
Average mRNA half-life in mouse fibroblast~11 hours15
Average rRNA molecules per ER-HoxA9 mouse cell~3,410,00016†
Cancer genomics
Median somatic copy number alterations per cancer sample3917
Median focal amplification SCNAs per cancer sample1117
Median focal deletion SCNAs per cancer sample1217
Percentage of primary tumor samples containing ecDNA17.1%18
Percentage of normal tissue containing ecDNA0%18
Percentage of cancer cell lines containing ecDNA24–40%19
DNA methylation & gene expression
Difference in methylation between exons and surrounding introns~5% overall20
Methylation difference for lowly expressed genes (bottom 20%)~10%20
Methylation difference for highly expressed genes (top 20%)~2%20
† preprint, no PMID assigned yet
1. Smirnov et al. (2024). optimalTAD: TAD annotation based on chromatin marks enrichment. bioRxiv. No PMID (preprint).
2. Kim et al. (2015). CTCF as a multifunctional protein in genome regulation and gene expression. Exp Mol Med. PMID: 26045254
3. Hansen et al. (2020). CTCF as a boundary factor for cohesin-mediated loop extrusion. Nucleus. PMID: 32631111
4. Tajmul et al. (2025). CTCF binding landscape is shaped by N-terminal nucleosome epigenetic state. Nucleic Acids Res. No PMID yet (published July 2025).
5. Hansen et al. (2017). CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife. PMID: 28467304
6. Kim et al. (2019). Human cohesin compacts DNA by loop extrusion. Science. PMID: 31780627
7. Dekker et al. (2025). An integrated view of the structure and function of the human 4D nucleome. Nature. PMID: 41407856
8. NCBI genome statistics; Alberts et al., Molecular Biology of the Cell, 7th Ed. (2022).
9. Payer & Burns (2019). Transposable elements in human genetic disease. Nat Rev Genet. PMID: 31515540
10. Edwards et al. (2010); Jeziorska et al. (2017); Bernstein et al. (2016). [Multiple sources — see lab spreadsheet for individual PMIDs.]
11. Yin et al. (2019). Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. PMID: 30890722
12. Alberts et al., Molecular Biology of the Cell, 7th Ed. (2022), p. 399.
13. Xu et al. (2019). PLoS Biol. PMID: 30668580; FANTOM Consortium (2014). Nature. PMID: 24670764
14. Guo & Price (2013). Chem Rev. PMID: 23488757
15. Schwanhäusser et al. (2011). Global quantification of mammalian gene expression control. Nature. PMID: 21593866 [corrigendum PMID: 23407496]
16. biorxiv.org/content/10.1101/2025.08.01.668217v1 — preprint, no PMID.
17. Zack et al. (2013). Pan-cancer patterns of somatic copy number alteration. Nat Genet. PMID: 24071852
18. Bailey et al. (2024). Origins and impact of extrachromosomal DNA. Nature. PMID: 39506150
19. Turner et al. (2017). Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. PMID: 28178237
20. Singer et al. (2015). A diverse epigenetic landscape at human exons with implication for expression. NAR. PMID: 25765649