title: Low-Cell-Number Epigenome Profiling Aids the Study of Lens Aging and Hematopoiesis.
abstract: Understanding how chromatin modification regulates development and disease can be limited by available material. Despite recent progress, balancing high-quality and reliable mapping using chromatin-immunoprecipitation-based deep sequencing (ChIP-seq) remains a challenge. We report two techniques, recovery via protection (RP)-ChIP-seq and favored amplification RP-ChIP-seq (FARP-ChIP-seq), that provide reproducible mapping in as few as 500 cells. RP-ChIP-seq allows detection of age-associated epigenetic changes in a single mouse lens, whereas FARP-ChIP-seq accurately maps histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in long-term hematopoietic stem cells (LT-HSCs), short-term HSCs (ST-HSCs), and multi-potent progenitors (MPPs) from one mouse. These datasets not only highlight genes that may be involved in lens aging but also indicate a lack of H3K4me3/H3K27me3 bivalency on hematopoietic genes in HSCs.
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
authors.forename: Xiaobin
authors.initials: X
authors.lastname: Zheng
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
authors.forename: Sibiao
authors.initials: S
authors.lastname: Yue
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
authors.forename: Blake
authors.initials: B
authors.lastname: Weber
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang 310058, PRC. Electronic address: junlingjia@zju.edu.cn.
authors.forename: Junling
authors.initials: J
authors.lastname: Jia
authors.affiliation: Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA. Electronic address: zheng@ciwemb.edu.
authors.forename: Yixian
authors.initials: Y
authors.lastname: Zheng
mesh_terms: D000375:Aging; D000818:Animals; D002454:Cell Differentiation; D002478:Cells, Cultured; D002874:Chromosome Mapping; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D006410:Hematopoiesis; D006412:Hematopoietic Stem Cells / Q000502:physiology; D006657:Histones / Q000378:metabolism; D007908:Lens, Crystalline / Q000473:pathology; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000502:physiology; D011401:Promoter Regions, Genetic
chemical_list: D006657:Histones