Landscapes of Human cis-regulatory Elements and Transcription Factor Binding Sites...

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" summary

Built a registry of nearly 1 million candidate cis‑regulatory elements from ENCODE data, then aligns them with a 240‑mammal CACTUS alignment and mammal PhyloP scores to find three conservation classes: deeply conserved, mixed, and primate‑specific. Curated 367 TFs and 15.6M TF binding sites reveal primate clusters are largely transposon‑derived (≈86% for group III) and about 20% of regulatory elements are primate innovations while ~12% (≈1/8) are deeply conserved and explain most trait heritability via LD score regression.

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" chapters (24)

1. 0:00Intro
2. 0:551.5% of the human genome encode proteins
3. 1:41candidate Cis-Regulatory Elements (CCREs)
4. 2:51The Encyclopedia of DNA Elements (ENCODE) Project (2003-2022)
5. 5:08ENCODE experiments
6. 6:12CCREs at the SP1 locus
7. 6:51ENCODE3 publications in 2020
8. 7:37Only a subset of CREs is conserved
9. 9:24Stronger conservation is detected using 240 placental mammals than 100 vertebrates
10. 10:52Roughly half of CCREs are highly conserved across mammals
11. 14:585% CREs are conserved beyond mammals
12. 16:51Landscape of cСREs across placental mammals
13. 20:04CCRE landscape reflects genome function
14. 21:14Factorbook integrates 2,409 TF CHIP-seq experiments with regulatory elements
15. 21:57Landscape of HNF4A-bound sites across placental mammals
16. 25:09Group 3 sites are derived from transposable elements
17. 26:1886.1% G3 sites are derived from transposable elements
18. 26:53Landscape of FOXA1-bound sites across placental mammals
19. 27:26Large clusters of FOXA1-bound sites reflect gains and losses
20. 28:02Constrained sites are more likely to be functional
21. 28:34Constrained sites are more likely to be bound
22. 28:48Constrained sites drive diverse human traits
23. 29:30GWAS variants are especially enriched in conserved CCREs and transcription factor binding sites
24. 29:50Conclusions

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