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Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

Nature Ecology & Evolution volume 2, pages 537–548 (2018)Cite this article

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Abstract

How evolutionary changes at enhancers affect the transcription of target genes remains an important open question. Previous comparative studies of gene expression have largely measured the abundance of messenger RNA, which is affected by post-transcriptional regulatory processes, hence limiting inferences about the mechanisms underlying expression differences. Here, we directly measured nascent transcription in primate species, allowing us to separate transcription from post-transcriptional regulation. We used precision run-on and sequencing to map RNA polymerases in resting and activated CD4+ T cells in multiple human, chimpanzee and rhesus macaque individuals, with rodents as outgroups. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. Genes regulated by larger numbers of enhancers are more frequently transcribed at evolutionarily stable levels, despite reduced conservation at individual enhancers. Adaptive nucleotide substitutions are associated with lineage-specific transcription and at one locus, SGPP2, we predict and experimentally validate that multiple substitutions contribute to human-specific transcription. Collectively, our findings suggest a pervasive role for evolutionary compensation across ensembles of enhancers that jointly regulate target genes.

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Fig. 1: Maps of primary transcription in CD4+ T cells.
Fig. 2: Frequency of changes in TRE transcription.
Fig. 3: Evolutionary changes in TRE transcription correlate with DNA sequence conservation.
Fig. 4: Changes in non-coding RNA transcription predict changes in gene transcription.
Fig. 5: TRE conservation correlates with loop interactions and distance to gene promoters.
Fig. 6: Stabilizing selection on protein-coding gene transcription.

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Acknowledgements

We thank M. Jin for assistance in establishing the magnetic separation of CD4+ T cells, J. Rogers for help establishing contacts with primate centres, L. Core, H. Kwak, N. Fuda and I. Jonkers for assistance troubleshooting the PRO-Seq library prep, and A. Wetterau for preparing nuclei for mouse and rat CD4+ T cells. This work was supported by generous seed grants from the Cornell University Center for Vertebrate Genomics, Center for Comparative and Population Genetics, National Human Genome Research Institute grant HG009309 to C.G.D., National Heart, Lung, and Blood Institute grant UHL129958A to C.G.D. and J.T.L., National Institute of General Medical Sciences grant GM102192 to A.S., National Human Genome Research Institute grant HG0070707 to A.S. and J.T.L., National Institute of Diabetes and Digestive and Kidney Diseases DK058110 to W.L.K. and Cancer Prevention and Research Institute of Texas RP160319 to W.L.K. The content is solely the responsibility of the authors and does not necessarily represent the official views of the US National Institutes of Health. Finally, we would like to thank the anonymous human and non-human primate donors who gave blood in support of this study.

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Authors and Affiliations

  1. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

    Charles G. Danko, Lauren A. Choate, Brooke A. Marks, Edward J. Rice, Zhong Wang, Tinyi Chu, Andre L. Martins, Scott A. Coonrod & Elia D. Tait Wojno

  2. Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

    Charles G. Danko & Scott A. Coonrod

  3. Graduate Field of Computational Biology, Cornell University, Ithaca, NY, USA

    Tinyi Chu & Andre L. Martins

  4. Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Noah Dukler & Adam Siepel

  5. Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA

    Noah Dukler

  6. Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA

    Elia D. Tait Wojno

  7. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA

    John T. Lis

  8. Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA

    W. Lee Kraus

  9. Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA

    W. Lee Kraus

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  1. Charles G. Danko
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Contributions

L.A.C., B.A.M., C.G.D., E.J.R. and E.D.T.W. performed the CD4+ T cell extraction, validation and PRO-Seq experiments. C.G.D., Z.W., T.C., A.L.M., L.A.C. and N.D. analysed the data. C.G.D., A.S., J.T.L., W.L.K. and S.A.C. supervised the data collection and analysis. C.G.D. and A.S. wrote the paper with input from the other authors.

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Correspondence to Charles G. Danko or Adam Siepel.

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Supplementary Notes 1–3, Supplementary Figures 1–15, Supplementary Tables 1–3.

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Danko, C.G., Choate, L.A., Marks, B.A. et al. Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nat Ecol Evol 2, 537–548 (2018). https://doi.org/10.1038/s41559-017-0447-5

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