TY - JOUR
T1 - The epigenomic landscape of transposable elements across normal human development and anatomy
AU - Pehrsson, Erica C.
AU - Choudhary, Mayank N.K.
AU - Sundaram, Vasavi
AU - Wang, Ting
N1 - Funding Information:
We thank the Roadmap Epigenomics Project and ENCODE Consortium for generating and processing the data. In particular, we thank Zhiping Weng and Arjan van der Velde for their assistance with the mm10 chromHMM annotations and the mouseENCODE consortium for generating the raw data. We also thank Xiaoyu Zhuo for his advice on TE evolution. E.C.P. is supported by a Postdoctoral Fellowship, PF-17-201-01, from the American Cancer Society. E.C.P., M.N.K.C., and T.W. are also supported by NIH grants R01HG007354, R01HG007175, R01ES024992, U01CA200060, U24ES026699, U01HG009391, and American Cancer Society RSG-14-049-01-DMC. V.S. was partially supported by the Cancer Biology Pathway, Washington University, and is currently supported by a fellowship from the EMBL Interdisciplinary Postdoc (EIPOD) programme under Marie Skłodowska-Curie actions COFUND (grant number 664726).
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome. Although most are silenced, certain TEs have been co-opted by the host. However, a comprehensive, multidimensional picture of the contribution of TEs to normal human gene regulation is still lacking. Here, we quantify the epigenomic status of TEs across human anatomy and development using data from the Roadmap Epigenomics Project. We find that TEs encompass a quarter of the human regulatory epigenome, and 47% of elements can be in an active regulatory state. We demonstrate that SINEs are enriched relative to other classes for active and transcribed marks, that TEs encompass a higher proportion of enhancer states in the hematopoietic lineage, and that DNA methylation of Alu elements decreases with age, corresponding with a loss of CpG islands. Finally, we identify TEs that may perform an evolutionarily conserved regulatory function, providing a systematic profile of TE activity in normal human tissue.
AB - Transposable elements (TEs) have deposited functional regulatory elements throughout the human genome. Although most are silenced, certain TEs have been co-opted by the host. However, a comprehensive, multidimensional picture of the contribution of TEs to normal human gene regulation is still lacking. Here, we quantify the epigenomic status of TEs across human anatomy and development using data from the Roadmap Epigenomics Project. We find that TEs encompass a quarter of the human regulatory epigenome, and 47% of elements can be in an active regulatory state. We demonstrate that SINEs are enriched relative to other classes for active and transcribed marks, that TEs encompass a higher proportion of enhancer states in the hematopoietic lineage, and that DNA methylation of Alu elements decreases with age, corresponding with a loss of CpG islands. Finally, we identify TEs that may perform an evolutionarily conserved regulatory function, providing a systematic profile of TE activity in normal human tissue.
UR - http://www.scopus.com/inward/record.url?scp=85076356478&partnerID=8YFLogxK
U2 - 10.1038/s41467-019-13555-x
DO - 10.1038/s41467-019-13555-x
M3 - Article
C2 - 31822674
AN - SCOPUS:85076356478
SN - 2041-1723
VL - 10
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 5640
ER -