The importance of detailed epigenomic profiling of different cell types within organs.
The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes.
Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Theresa Ryan
TR
Stueve
Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Crystal N
CN
Marconett
Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Beiyun
B
Zhou
Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Zea
Z
Borok
Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.|Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Ite A
IA
Laird-Offringa
D000818:Animals; D002478:Cells, Cultured; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D014644:Genetic Variation; D006801:Humans; D008168:Lung / Q000378:metabolism; D009928:Organ Specificity; D011401:Promoter Regions, Genetic; D059010:Single-Cell Analysis; D059467:Transcriptome
ChIP-seq; DNA methylation; cell-specific epigenomes; environmental epigenetics; epigenomics; histone modification; lung; organ