Enhancer dependence of cell-type–specific gene expression increases with developmental age

Significance Gene regulatory logic reflects the occupancy of cis elements by transcription factors and the configuration of promoters and enhancers. As the majority of genome-wide analyses have focused on adult cells, scant attention has been paid to embryonic cells, other than embryonic stem cells. Focusing on genome-wide comparative analyses of two stages of erythroblasts, we discovered that regulation of embryonic-specific genes is promoter-centric through Gata1, whereas adult-specific control is combinatorial enhancer-driven and requires Myb, which is confirmed by increased enhancer–promoter interactions of adult specific genes. Extending genome-wide comparative analyses more broadly to available datasets of diverse mouse and human cells and tissues, we conclude that the progressively increased enhancer dependence of cell-type–specific genes with developmental age is conserved during development. How overall principles of cell-type–specific gene regulation (the “logic”) may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic, and three-dimensional (3D) genomic profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1, and Myb occupancy. EryP-/EryD-shared enhancers are highly correlated with red blood cell identity genes, whereas cell-type–specific regulation employs different cis elements in EryP and EryD cells. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes rely more on distal enhancers for regulation involving Myb-mediated enhancer activation. Gata1 HiChIP demonstrated an overall increased enhancer–promoter interactions at EryD-specific genes, whereas genome editing in selected loci confirmed distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer dependence of transcription, we observed a progressive reliance on cell-specific enhancers with increasing ontogenetic age among diverse tissues of mouse and human origin. Our findings highlight fundamental and conserved differences at distinct developmental stages, characterized by simpler promoter-centric regulation of cell-type–specific genes in embryonic cells and increased combinatorial enhancer-driven control in adult cells.

[1]  P. Fraser,et al.  Long-range enhancer–promoter contacts in gene expression control , 2019, Nature Reviews Genetics.

[2]  Elie N. Farah,et al.  Transcriptionally Active HERV-H Retrotransposons Demarcate Topologically Associating Domains in Human Pluripotent Stem Cells , 2019, Nature Genetics.

[3]  Guillaume J. Filion,et al.  Transcription factors and 3D genome conformation in cell-fate decisions , 2019, Nature.

[4]  S. Mundlos,et al.  H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome , 2019, Journal of Medical Genetics.

[5]  E. Furlong,et al.  Developmental enhancers and chromosome topology , 2018, Science.

[6]  A. Visel,et al.  Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis , 2018, Nature Genetics.

[7]  Daniel S. Day,et al.  Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism , 2018, Cell reports.

[8]  Howard Y. Chang,et al.  Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements , 2017, Nature Genetics.

[9]  C. Tickle,et al.  Sonic Hedgehog Signaling in Limb Development , 2017, Front. Cell Dev. Biol..

[10]  Aibin He,et al.  Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq , 2017, eLife.

[11]  J. Wysocka,et al.  Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution , 2016, Cell.

[12]  Howard Y. Chang,et al.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.

[13]  Michael Levine,et al.  Enhancer Control of Transcriptional Bursting , 2016, Cell.

[14]  James T. Robinson,et al.  Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. , 2016, Cell systems.

[15]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[16]  Peter H. L. Krijger,et al.  Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming , 2016, Cell stem cell.

[17]  L. Zon,et al.  Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. , 2016, Developmental cell.

[18]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[19]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[20]  Howard Y. Chang,et al.  Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.

[21]  Jing Liang,et al.  Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.

[22]  C. Glass,et al.  The selection and function of cell type-specific enhancers , 2015, Nature Reviews Molecular Cell Biology.

[23]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[24]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[25]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[26]  Matthew C. Canver,et al.  Generation of genomic deletions in mammalian cell lines via CRISPR/Cas9. , 2014, Journal of visualized experiments : JoVE.

[27]  J. Palis.  Primitive and definitive erythropoiesis in mammals , 2013, Front. Physiol..

[28]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[29]  David J. Arenillas,et al.  JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles , 2013, Nucleic Acids Res..

[30]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[31]  Gene W. Yeo,et al.  Coordinate Nodal and BMP inhibition directs Baf60c-dependent cardiomyocyte commitment , 2013, Genes & development.

[32]  D. Duboule,et al.  Topology of mammalian developmental enhancers and their regulatory landscapes , 2013, Nature.

[33]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[34]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[35]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[36]  Christian J Stoeckert,et al.  Ontogeny of erythroid gene expression. , 2013, Blood.

[37]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[38]  Shane J. Neph,et al.  Circuitry and Dynamics of Human Transcription Factor Regulatory Networks , 2012, Cell.

[39]  Wenqing Cai,et al.  A Nodal-to-TGF&bgr; Cascade Exerts Biphasic Control Over Cardiopoiesis , 2012, Circulation Research.

[40]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[41]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[42]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[43]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[44]  E. Furlong,et al.  Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development , 2012, Nature Genetics.

[45]  David Haussler,et al.  The Human Epigenome Browser at Washington University , 2011, Nature Methods.

[46]  Daniel Hidalgo,et al.  Identification and analysis of mouse erythroid progenitors using the CD71/TER119 flow-cytometric assay. , 2011, Journal of visualized experiments : JoVE.

[47]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[48]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[49]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[50]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[51]  G. Bejerano,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[52]  P. Scacheri,et al.  CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing , 2009, Development.

[53]  Stuart H. Orkin,et al.  Developmental and species-divergent globin switching are driven by BCL11A , 2009, Nature.

[54]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[55]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[56]  E. Davidson,et al.  Global regulatory logic for specification of an embryonic cell lineage , 2008, Proceedings of the National Academy of Sciences.

[57]  Jun S. Song,et al.  CEAS: cis-regulatory element annotation system. , 2006, Nucleic acids research.

[58]  M. Levine,et al.  Genomic regulatory networks and animal development. , 2005, Developmental cell.

[59]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[60]  S. Carotta,et al.  Directed differentiation and mass cultivation of pure erythroid progenitors from mouse embryonic stem cells. , 2004, Blood.

[61]  Harvey F Lodish,et al.  Role of Ras signaling in erythroid differentiation of mouse fetal liver cells: functional analysis by a flow cytometry-based novel culture system. , 2003, Blood.

[62]  S. Orkin,et al.  Distinct Domains of the GATA-1 Cofactor FOG-1 Differentially Influence Erythroid versus Megakaryocytic Maturation , 2002, Molecular and Cellular Biology.

[63]  S. Orkin,et al.  Transcriptional regulation of erythropoiesis: an affair involving multiple partners , 2002, Oncogene.

[64]  T. Ley,et al.  Independent formation of DnaseI hypersensitive sites in the murine beta-globin locus control region. , 2000, Blood.

[65]  M. Groudine,et al.  β-globin Gene Switching and DNase I Sensitivity of the Endogenous β-globin Locus in Mice Do Not Require the Locus Control Region , 2000 .

[66]  M. Kennedy,et al.  A common precursor for hematopoietic and endothelial cells. , 1998, Development.

[67]  Y Fujiwara,et al.  Arrested development of embryonic red cell precursors in mouse embryos lacking transcription factor GATA-1. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[68]  S. Ishii,et al.  CBP as a transcriptional coactivator of c-Myb. , 1996, Genes & Development.

[69]  S. Swerdlow,et al.  A functional c-myb gene is required for normal murine fetal hepatic hematopoiesis , 1991, Cell.

[70]  A. Skoultchi,et al.  Absolute rates of globin gene transcription and mRNA formation during differentiation of cultured mouse erythroleukemia cells. , 1985, The Journal of biological chemistry.

[71]  P. Marks,et al.  Gene expression in murine erythroleukemia cells. Transcriptional control and chromatin structure of the alpha 1-globin gene. , 1984, Journal of molecular biology.

[72]  Melissa C. Greven,et al.  An integrated encyclopedia of DNA elements in the human genome , 2014 .

[73]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[74]  S. Orkin,et al.  METHOD Open Access , 2014 .

[75]  M. Baron,et al.  Maturation and enucleation of primitive erythroblasts during mouse embryogenesis is accompanied by changes in cell-surface antigen expression. , 2007, Blood.

[76]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[77]  M. Groudine,et al.  Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. , 2000, Molecular cell.

[78]  S. Orkin,et al.  Development of hematopoietic cells lacking transcription factor GATA-1. , 1995, Development.