TY - JOUR
T1 - Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis
AU - Huang, Xiao
AU - Ferris, Stephen T.
AU - Kim, Sunkyung
AU - Choudhary, Mayank N.K.
AU - Belk, Julia A.
AU - Fan, Changxu
AU - Qi, Yanyan
AU - Sudan, Raki
AU - Xia, Yu
AU - Desai, Pritesh
AU - Chen, Jing
AU - Ly, Nghi
AU - Shi, Quanming
AU - Bagadia, Prachi
AU - Liu, Tiantian
AU - Guilliams, Martin
AU - Egawa, Takeshi
AU - Colonna, Marco
AU - Diamond, Michael S.
AU - Murphy, Theresa L.
AU - Satpathy, Ansuman T.
AU - Wang, Ting
AU - Murphy, Kenneth M.
N1 - Funding Information:
WT C57BL6/J mice and R26 Cas9/+ mice (B6N.129(Cg)-Gt(ROSA)26Sor tm1.1(CAG-cas9∗,-EGFP)Fezh /J) were obtained from the Jackson Laboratory. ZEB2-EGFP fusion protein reporter (STOCK Zfhxlb tm2.1Yhi ) mice were derived from biological material provided by the RIKEN BioResource Center through the National BioResource Project of the Ministry of Education, Culture, Sports, Science and Technology, Japan. Id2–IRES–GFP mice ( Jackson et al., 2011 ) were generously donated by G. Belz.
Funding Information:
We thank the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis, which is supported by the National Cancer Institute’s Cancer Center support grant ( P30 CA91842 ) to the Siteman Cancer Center and by the Institute of Clinical and Translational Sciences/Clinical and Translational Science Award grant ( UL1TR000448 ) from the National Center for Research Resources s (NCRR) and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of the NCRR or NIH. This work benefitted from data assembled by the ImmGen Consortium ( Heng et al., 2008 ). This work was supported by NIH ( R01AI150297 to K.M.M.) A.T.S. was supported by a Bridge Scholar Award from the Parker Institute for Cancer Immunotherapy , a Technology Impact Award from the Cancer Research Institute , a Career Award for Medical Scientists from the Burroughs Wellcome Fund , and NIH ( K08CA230188 ). T.E. was supported by a Scholar Award from the Leukemia and Lymphoma Society and NIH ( R01AI130152 ).
Funding Information:
We thank the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis, which is supported by the National Cancer Institute's Cancer Center support grant (P30 CA91842) to the Siteman Cancer Center and by the Institute of Clinical and Translational Sciences/Clinical and Translational Science Award grant (UL1TR000448) from the National Center for Research Resourcess (NCRR) and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of the NCRR or NIH. This work benefitted from data assembled by the ImmGen Consortium (Heng et al. 2008). This work was supported by NIH (R01AI150297 to K.M.M.) A.T.S. was supported by a Bridge Scholar Award from the Parker Institute for Cancer Immunotherapy, a Technology Impact Award from the Cancer Research Institute, a Career Award for Medical Scientists from the Burroughs Wellcome Fund, and NIH (K08CA230188). T.E. was supported by a Scholar Award from the Leukemia and Lymphoma Society and NIH (R01AI130152). X.H. T.L.M. and K.M.M. designed the study, X.H. and S.F. performed experiments related to analysis of immune populations, cell sorting, and culture with assistance from S.K. J.C. P.B. and T.L. and advice from M.G. X.H. performed all experiments related to gene microarray and generation of mice. X.H. and R.S. performed analysis related to ILCs with advice from M.C. X.H. and S.K. performed analysis on ChIP-seq and ATAC-seq data. X.H. Y.Q. J.A.B. N.L. Q.S. and A.T.S. performed and analyzed single-cell ATAC-sequencing. X.H. Y.X. and P.D. performed all infections with advice from T.E. and M.S.D. X.H. performed T cell Hi-C. M.N.K.C. performed hybrid-capture Hi-C (Hi-C2) experiments. M.N.K.C. C.F. and T.W. analyzed Hi-C and Hi-C2 data. S.K. drew the graphical abstract with advice from X.H. X.H. and K.M.M. wrote the manuscript with advice from all authors. A.T.S. is a scientific founder of Immunai and receives research funding from Arsenal Biosciences.
Funding Information:
A.T.S. is a scientific founder of Immunai and receives research funding from Arsenal Biosciences.
Publisher Copyright:
© 2021 Elsevier Inc.
PY - 2021/7/13
Y1 - 2021/7/13
N2 - The transcriptional repressor ZEB2 regulates development of many cell fates among somatic, neural, and hematopoietic lineages, but the basis for its requirement in these diverse lineages is unclear. Here, we identified a 400-basepair (bp) region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins at several E-box motifs and was active in hematopoietic lineages. Germline deletion of this 400-bp region (Zeb2Δ−165mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC)-derived lineages. Zeb2Δ−165 mice lacked development of plasmacytoid dendritic cells (pDCs), monocytes, and B cells. All macrophages in Zeb2Δ−165 mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164-kb that was selectively active in embryonically derived lineages, but not HSC-derived ones. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the –165-kb Zeb2 enhancer.
AB - The transcriptional repressor ZEB2 regulates development of many cell fates among somatic, neural, and hematopoietic lineages, but the basis for its requirement in these diverse lineages is unclear. Here, we identified a 400-basepair (bp) region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins at several E-box motifs and was active in hematopoietic lineages. Germline deletion of this 400-bp region (Zeb2Δ−165mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC)-derived lineages. Zeb2Δ−165 mice lacked development of plasmacytoid dendritic cells (pDCs), monocytes, and B cells. All macrophages in Zeb2Δ−165 mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164-kb that was selectively active in embryonically derived lineages, but not HSC-derived ones. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the –165-kb Zeb2 enhancer.
KW - Zeb2
KW - chromatin structure
KW - enhancer
KW - hematopoiesis
KW - transcriptional regulation
KW - zinc finger E-box binding homeobox 2
UR - http://www.scopus.com/inward/record.url?scp=85107277206&partnerID=8YFLogxK
U2 - 10.1016/j.immuni.2021.04.015
DO - 10.1016/j.immuni.2021.04.015
M3 - Article
C2 - 34004142
AN - SCOPUS:85107277206
SN - 1074-7613
VL - 54
SP - 1417-1432.e7
JO - Immunity
JF - Immunity
IS - 7
ER -