Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

Te Ling; Yehudit Birger; Monika J. Stankiewicz; Nissim Ben-Haim; Tomer Kalisky; Avigail Rein; Eitan Kugler; Wei Chen; Chunling Fu; Kevin Zhang; Hiral Patel; Jacek W. Sikora; Young Ah Goo; Neil Kelleher; Lihua Zou; Shai Izraeli; John D. Crispino

doi:10.1182/blood.2019001234

Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

Te Ling, Yehudit Birger, Monika J. Stankiewicz, Nissim Ben-Haim, Tomer Kalisky, Avigail Rein, Eitan Kugler, Wei Chen, Chunling Fu, Kevin Zhang, Hiral Patel, Jacek W. Sikora, Young Ah Goo, Neil Kelleher, Lihua Zou, Shai Izraeli^*, John D. Crispino

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

34 Scopus citations

Abstract

Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N terminus, are seen in patients with Diamond-Blackfan anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic gene expression patterns were altered by the loss of the N terminus, including aberrant upregulation of Gata2 and Runx1. Dysregulation of global H3K27 methylation was found in the erythroid progenitors upon loss of N terminus of GATA1. Chromatin-binding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 and Runx1 genes. Consistent with the observation that overexpression of GATA2 has been reported to impair erythropoiesis, we found that haploinsufficiency of Gata2 rescued the erythroid defects of Gata1s fetuses. Together, our integrated genomic analysis of transcriptomic and epigenetic signatures reveals that, Gata1 mice provide novel insights into the role of the N terminus of GATA1 in transcriptional regulation and red blood cell maturation which may potentially be useful for DBA patients.

Original language	English (US)
Pages (from-to)	1619-1631
Number of pages	13
Journal	Blood
Volume	134
Issue number	19
DOIs	https://doi.org/10.1182/blood.2019001234
State	Published - 2019

Funding

The next-generation sequencing reactions were performed by the Northwestern University NGS Core Facility. The authors also thank Steven Henikoff (Fred Hutchinson Cancer Research Center, Seattle, WA) for providing CUT&RUN protocol and related reagents and Itamar Kanter for contributing to RNA-seq data analysis. This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). Conflict-of-interest disclosure: J.D.C. receives research funding from Scholar Rock and Forma Therapeutics and is a consultant for Sierra Oncology. S.I. is a consultant of SIGHTDX. The remaining authors declare no competing financial interests. This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). 1Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL; 2The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; 3Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Tel Aviv University, Tel Aviv, Israel; 4Division of Pediatric Hematology and Oncology, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel; 5Faculty of Engineering and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel; 6Blood Disease Institute, Xuzhou Medical University, Xuzhou, China; 7Proteomics Center of Excellence, Northwestern University, Chicago, IL; 8Department of Chemistry and Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL; and 9Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL

ASJC Scopus subject areas

Hematology
Biochemistry
Cell Biology
Immunology

Access to Document

10.1182/blood.2019001234

Cite this

Ling, T., Birger, Y., Stankiewicz, M. J., Ben-Haim, N., Kalisky, T., Rein, A., Kugler, E., Chen, W., Fu, C., Zhang, K., Patel, H., Sikora, J. W., Goo, Y. A., Kelleher, N., Zou, L., Izraeli, S., & Crispino, J. D. (2019). Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis. Blood, 134(19), 1619-1631. https://doi.org/10.1182/blood.2019001234

@article{e2be3b69af914637b57a8f2d0ef4b8db,

title = "Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis",

abstract = "Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N terminus, are seen in patients with Diamond-Blackfan anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic gene expression patterns were altered by the loss of the N terminus, including aberrant upregulation of Gata2 and Runx1. Dysregulation of global H3K27 methylation was found in the erythroid progenitors upon loss of N terminus of GATA1. Chromatin-binding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 and Runx1 genes. Consistent with the observation that overexpression of GATA2 has been reported to impair erythropoiesis, we found that haploinsufficiency of Gata2 rescued the erythroid defects of Gata1s fetuses. Together, our integrated genomic analysis of transcriptomic and epigenetic signatures reveals that, Gata1 mice provide novel insights into the role of the N terminus of GATA1 in transcriptional regulation and red blood cell maturation which may potentially be useful for DBA patients.",

author = "Te Ling and Yehudit Birger and Stankiewicz, {Monika J.} and Nissim Ben-Haim and Tomer Kalisky and Avigail Rein and Eitan Kugler and Wei Chen and Chunling Fu and Kevin Zhang and Hiral Patel and Sikora, {Jacek W.} and Goo, {Young Ah} and Neil Kelleher and Lihua Zou and Shai Izraeli and Crispino, {John D.}",

note = "Funding Information: The next-generation sequencing reactions were performed by the Northwestern University NGS Core Facility. The authors also thank Steven Henikoff (Fred Hutchinson Cancer Research Center, Seattle, WA) for providing CUT&RUN protocol and related reagents and Itamar Kanter for contributing to RNA-seq data analysis. This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). Funding Information: Conflict-of-interest disclosure: J.D.C. receives research funding from Scholar Rock and Forma Therapeutics and is a consultant for Sierra Oncology. S.I. is a consultant of SIGHTDX. The remaining authors declare no competing financial interests. Funding Information: This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). Funding Information: 1Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL; 2The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children{\textquoteright}s Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; 3Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Tel Aviv University, Tel Aviv, Israel; 4Division of Pediatric Hematology and Oncology, Schneider Children{\textquoteright}s Medical Center of Israel, Petach Tikva, Israel; 5Faculty of Engineering and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel; 6Blood Disease Institute, Xuzhou Medical University, Xuzhou, China; 7Proteomics Center of Excellence, Northwestern University, Chicago, IL; 8Department of Chemistry and Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL; and 9Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL Publisher Copyright: {\textcopyright} 2019 by The American Society of Hematology.",

year = "2019",

doi = "10.1182/blood.2019001234",

language = "English (US)",

volume = "134",

pages = "1619--1631",

journal = "Blood",

issn = "0006-4971",

publisher = "Elsevier B.V.",

number = "19",

}

Ling, T, Birger, Y, Stankiewicz, MJ, Ben-Haim, N, Kalisky, T, Rein, A, Kugler, E, Chen, W, Fu, C, Zhang, K, Patel, H, Sikora, JW, Goo, YA, Kelleher, N, Zou, L, Izraeli, S & Crispino, JD 2019, 'Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis', Blood, vol. 134, no. 19, pp. 1619-1631. https://doi.org/10.1182/blood.2019001234

TY - JOUR

T1 - Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

AU - Ling, Te

AU - Birger, Yehudit

AU - Stankiewicz, Monika J.

AU - Ben-Haim, Nissim

AU - Kalisky, Tomer

AU - Rein, Avigail

AU - Kugler, Eitan

AU - Chen, Wei

AU - Fu, Chunling

AU - Zhang, Kevin

AU - Patel, Hiral

AU - Sikora, Jacek W.

AU - Goo, Young Ah

AU - Kelleher, Neil

AU - Zou, Lihua

AU - Izraeli, Shai

AU - Crispino, John D.

N1 - Funding Information: The next-generation sequencing reactions were performed by the Northwestern University NGS Core Facility. The authors also thank Steven Henikoff (Fred Hutchinson Cancer Research Center, Seattle, WA) for providing CUT&RUN protocol and related reagents and Itamar Kanter for contributing to RNA-seq data analysis. This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). Funding Information: Conflict-of-interest disclosure: J.D.C. receives research funding from Scholar Rock and Forma Therapeutics and is a consultant for Sierra Oncology. S.I. is a consultant of SIGHTDX. The remaining authors declare no competing financial interests. Funding Information: This work was supported by the National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases (DK101329), the Samuel Waxman Cancer Research Foundation, the US Department of Defense (W81XWH-15-1-0227) (S.I.), the Israel US Binational Science Foundation, the DBA Foundation, the European Hematology Association, the Larger than Life Foundation, the Israel Science Foundation (ICORE 1902/12 and grants 1634/13 and 2017/13), the Israel Cancer Association (grant 20150911), the Israel Ministry of Health (grant 3-10146), an Israel Ministry of Science-DKFZ grant, and the EU-FP7 (Marie Curie International Reintegration Grant, 618592). Funding Information: 1Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL; 2The Gene Development and Environment Pediatric Research Institute, Pediatric Hemato-Oncology, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel; 3Department of Human Molecular Genetics and Biochemistry, Sackler Medical School, Tel Aviv University, Tel Aviv, Israel; 4Division of Pediatric Hematology and Oncology, Schneider Children’s Medical Center of Israel, Petach Tikva, Israel; 5Faculty of Engineering and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel; 6Blood Disease Institute, Xuzhou Medical University, Xuzhou, China; 7Proteomics Center of Excellence, Northwestern University, Chicago, IL; 8Department of Chemistry and Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL; and 9Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL Publisher Copyright: © 2019 by The American Society of Hematology.

PY - 2019

Y1 - 2019

N2 - Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N terminus, are seen in patients with Diamond-Blackfan anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic gene expression patterns were altered by the loss of the N terminus, including aberrant upregulation of Gata2 and Runx1. Dysregulation of global H3K27 methylation was found in the erythroid progenitors upon loss of N terminus of GATA1. Chromatin-binding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 and Runx1 genes. Consistent with the observation that overexpression of GATA2 has been reported to impair erythropoiesis, we found that haploinsufficiency of Gata2 rescued the erythroid defects of Gata1s fetuses. Together, our integrated genomic analysis of transcriptomic and epigenetic signatures reveals that, Gata1 mice provide novel insights into the role of the N terminus of GATA1 in transcriptional regulation and red blood cell maturation which may potentially be useful for DBA patients.

AB - Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N terminus, are seen in patients with Diamond-Blackfan anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic gene expression patterns were altered by the loss of the N terminus, including aberrant upregulation of Gata2 and Runx1. Dysregulation of global H3K27 methylation was found in the erythroid progenitors upon loss of N terminus of GATA1. Chromatin-binding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 and Runx1 genes. Consistent with the observation that overexpression of GATA2 has been reported to impair erythropoiesis, we found that haploinsufficiency of Gata2 rescued the erythroid defects of Gata1s fetuses. Together, our integrated genomic analysis of transcriptomic and epigenetic signatures reveals that, Gata1 mice provide novel insights into the role of the N terminus of GATA1 in transcriptional regulation and red blood cell maturation which may potentially be useful for DBA patients.

UR - http://www.scopus.com/inward/record.url?scp=85074610829&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85074610829&partnerID=8YFLogxK

U2 - 10.1182/blood.2019001234

DO - 10.1182/blood.2019001234

M3 - Article

C2 - 31409672

AN - SCOPUS:85074610829

SN - 0006-4971

VL - 134

SP - 1619

EP - 1631

JO - Blood

JF - Blood

IS - 19

ER -

Chromatin occupancy and epigenetic analysis reveal new insights into the function of the GATA1 N terminus in erythropoiesis

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this