Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones

Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap...

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Published inNature genetics Vol. 52; no. 4; pp. 418 - 427
Main Authors Iwafuchi, Makiko, Cuesta, Isabel, Donahue, Greg, Takenaka, Naomi, Osipovich, Anna B., Magnuson, Mark A., Roder, Heinrich, Seeholzer, Steven H., Santisteban, Pilar, Zaret, Kenneth S.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.04.2020
Nature Publishing Group
Subjects
38
38/35
38/39
38/91
45
631/136
631/208
631/337
631/532
64
64/60
82
82/80
Agriculture
Amino Acid Sequence
Amino acids
Animal Genetics and Genomics
Animals
Arrays
Binding sites
Biomedical and Life Sciences
Biomedicine
Cancer Research
Cell Line
Chromatin
Chromatin - genetics
Deoxyribonucleic acid
DNA
DNA - genetics
Embryonic development
Embryos
Female
Gene Expression Regulation, Developmental - genetics
Gene Function
Gene Regulatory Networks - genetics
Genetic algorithms
Genetic aspects
Histones
Histones - genetics
Human Genetics
Humans
Mice
Mice, Inbred C57BL
Molecular interactions
Mutation
Nucleosomes - genetics
Peptides
Physiological aspects
Proteins
Transcription factors
Transcription Factors - genetics
Transcription, Genetic - genetics
United States
Online AccessGet full text
ISSN1061-4036
1546-1718
1546-1718
DOI10.1038/s41588-020-0591-8

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Abstract Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming. An α-helical region conserved among FOXA pioneer factors interacts with core histones and promotes chromatin opening in vitro. This region also promotes chromatin opening in early mouse embryos and is required for normal development.
AbstractList Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short alpha-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short [alpha]-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short [alpha]-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming. An [alpha]-helical region conserved among FOXA pioneer factors interacts with core histones and promotes chromatin opening in vitro. This region also promotes chromatin opening in early mouse embryos and is required for normal development.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short a-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.
Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming. An α-helical region conserved among FOXA pioneer factors interacts with core histones and promotes chromatin opening in vitro. This region also promotes chromatin opening in early mouse embryos and is required for normal development.
Audience Academic
Author Roder, Heinrich
Santisteban, Pilar
Zaret, Kenneth S.
Cuesta, Isabel
Donahue, Greg
Takenaka, Naomi
Osipovich, Anna B.
Magnuson, Mark A.
Seeholzer, Steven H.
Iwafuchi, Makiko
AuthorAffiliation 2 Instituto de Investigaciones Biomédicas ‘Alberto Sols’, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
1 Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
7 Present address: Division of Developmental Biology, Center for Stem Cell & Organoid Medicine, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
5 Children’s Hospital of Philadelphia, Philadelphia, PA, USA
3 Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
6 Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
4 Department of Molecular Physiology and Biophysics and Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
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– fundername: Astellas Foundation for Research on Metabolic Disorders
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– fundername: Naito Foundation
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– fundername: NIGMS NIH HHS
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content type line 14
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Conceptualization: K.S.Z., M.I., I.C. Experiments: M.I, I.C., N.T., G.D., A.O., H.R., S.S., and P.S. Bioinformatic analysis: M.I and G.D. Writing: M.I., I.C., and K.S.Z. Supervision: K.S.Z and M.A.M. Funding acquisition: K.S.Z.
Author contributions
ORCID 0000-0003-1291-6246
0000-0001-8932-3145
0000-0003-1860-2491
OpenAccessLink https://proxy.k.utb.cz/login?url=https://www.ncbi.nlm.nih.gov/pmc/articles/7901023
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Agriculture
Amino Acid Sequence
Amino acids
Animal Genetics and Genomics
Animals
Arrays
Binding sites
Biomedical and Life Sciences
Biomedicine
Cancer Research
Cell Line
Chromatin
Chromatin - genetics
Deoxyribonucleic acid
DNA
DNA - genetics
Embryonic development
Embryos
Female
Gene Expression Regulation, Developmental - genetics
Gene Function
Gene Regulatory Networks - genetics
Genetic algorithms
Genetic aspects
Histones
Histones - genetics
Human Genetics
Humans
Mice
Mice, Inbred C57BL
Molecular interactions
Mutation
Nucleosomes - genetics
Peptides
Physiological aspects
Proteins
Transcription factors
Transcription Factors - genetics
Transcription, Genetic - genetics
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Title Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones
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