Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate

Pioneer transcription factors establish new cell-fate competence by triggering chromatin remodeling. However, many features of pioneer action, such as their kinetics and stability, remain poorly defined. Here, we show that Pax7, by opening a unique repertoire of enhancers, is necessary and sufficient for specification of one pituitary lineage. Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. Enhancers opened by Pax7 show a loss of DNA methylation and acquire stable epigenetic memory, as evidenced by binding of nonpioneer factors after Pax7 withdrawal. This work shows that transient Pax7 expression is sufficient for stable specification of cell identity.Analysis of Pax7 dynamics during pituitary lineage specification shows that Pax7 binds rapidly at uniquely marked heterochromatin pioneer sites and initiates chromatin opening that remains stable after Pax7 withdrawal, with loss of DNA hypermethylation at pioneered enhancers.

[1]  W. Herr,et al.  Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. , 2003, Genes & development.

[2]  Greg Donahue,et al.  Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome , 2012, Cell.

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

[4]  Tatsunori B. Hashimoto,et al.  Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape , 2014, Nature Biotechnology.

[5]  J. Wysocka,et al.  Modification of enhancer chromatin: what, how, and why? , 2013, Molecular cell.

[6]  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.

[7]  P. Smialowski,et al.  NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program , 2016, The EMBO journal.

[8]  B. Pugh,et al.  Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution , 2011, Cell.

[9]  Yu Xin Wang,et al.  Carm1 regulates Pax7 transcriptional activity through MLL1/2 recruitment during asymmetric satellite stem cell divisions. , 2012, Cell stem cell.

[10]  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.

[11]  J. Drouin,et al.  PITX genes are required for cell survival and Lhx3 activation. , 2005, Molecular endocrinology.

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

[13]  Clifford A. Meyer,et al.  Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1 , 2005, Cell.

[14]  Frank R. Lin,et al.  Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. , 2002, Molecular cell.

[15]  D. Figarella-Branger,et al.  The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling. , 2012, Genes & development.

[16]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[17]  K. Rizzoti.  Genetic regulation of murine pituitary development , 2015, Journal of molecular endocrinology.

[18]  H. Cedar,et al.  Maintenance of Epigenetic Information. , 2016, Cold Spring Harbor perspectives in biology.

[19]  Ty C. Voss,et al.  Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism , 2011, Cell.

[20]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[21]  J. Drouin,et al.  Tpit determines alternate fates during pituitary cell differentiation. , 2003, Genes & development.

[22]  Klaus Hansen,et al.  An interactive environment for agile analysis and visualization of ChIP-sequencing data , 2016, Nature Structural &Molecular Biology.

[23]  Céline Lefebvre,et al.  From the Cover: Location analysis of estrogen receptor alpha target promoters reveals that FOXA1 defines a domain of the estrogen response. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Drouin.  Chapter 1 – Pituitary Development , 2017 .

[25]  J. Drouin,et al.  A Pituitary Cell-Restricted T Box Factor, Tpit, Activates POMC Transcription in Cooperation with Pitx Homeoproteins , 2001, Cell.

[26]  Denis Thieffry,et al.  C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis , 2015, Stem cell reports.

[27]  J. Drouin,et al.  The Stat3/GR interaction code: predictive value of direct/indirect DNA recruitment for transcription outcome. , 2012, Molecular cell.

[28]  I. Goldstein,et al.  Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions , 2016, Cell.

[29]  Céline Lefebvre,et al.  Location analysis of estrogen receptor target promoters reveals that FOXA 1 defines a domain of the estrogen response , 2005 .

[30]  Fan Liu,et al.  Beyond transcription factors: how oncogenic signalling reshapes the epigenetic landscape , 2016, Nature Reviews Cancer.

[31]  K. Pienta,et al.  A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. , 2007, Molecular cell.

[32]  J. Drouin,et al.  Adult pituitary cell maintenance: lineage-specific contribution of self-duplication. , 2013, Molecular endocrinology.

[33]  Rodolfo Ghirlando,et al.  CTCF: making the right connections , 2016, Genes & development.

[34]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[35]  H. Westphal,et al.  Early steps in pituitary organogenesis. , 1999, Trends in genetics : TIG.

[36]  Howard Y. Chang,et al.  Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons , 2013, Cell.

[37]  H. Bourbon,et al.  Genome Regulation by Polycomb and Trithorax: 70 Years and Counting , 2017, Cell.

[38]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[39]  J. Drouin,et al.  Developmental dependence on NurRE and EboxNeuro for expression of pituitary proopiomelanocortin. , 2008, Molecular endocrinology.

[40]  M. Pellegrini,et al.  Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming , 2015, Cell.

[41]  J. Lerner,et al.  Chromatin Scanning by Dynamic Binding of Pioneer Factors. , 2016, Molecular cell.

[42]  Lukas Burger,et al.  Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming. , 2016, Immunity.