The lncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression.

Long non-coding RNAs (lncRNAs) regulate diverse biological processes, including cell lineage specification. Here, we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allows us to identify hundreds of lncRNAs that exhibit differentiation-stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA, definitive endoderm-associated lncRNA1 (DEANR1), and demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating expression of the endoderm factor FOXA2. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1 facilitates FOXA2 activation by facilitating SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation-stage-specific lncRNAs but also characterizes a functional lncRNA that is important for endoderm differentiation.

[1]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[2]  E. Kroon,et al.  Production of pancreatic hormone–expressing endocrine cells from human embryonic stem cells , 2006, Nature Biotechnology.

[3]  Howard Y. Chang,et al.  Control of somatic tissue differentiation by the long non-coding RNA TINCR , 2012, Nature.

[4]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[5]  J. Flanagan,et al.  APC Is an RNA-Binding Protein, and Its Interactome Provides a Link to Neural Development and Microtubule Assembly , 2014, Cell.

[6]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[7]  Albert E. Almada,et al.  Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells , 2013, Proceedings of the National Academy of Sciences.

[8]  T. Derrien,et al.  Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.

[9]  Sean Thomas,et al.  A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development , 2012, Cell.

[10]  R. Derynck,et al.  SPECIFICITY AND VERSATILITY IN TGF-β SIGNALING THROUGH SMADS , 2005 .

[11]  Wei Jiang,et al.  Highly efficient differentiation of human ES cells and iPS cells into mature pancreatic insulin-producing cells , 2009, Cell Research.

[12]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[13]  J. Massagué,et al.  Smad transcription factors. , 2005, Genes & development.

[14]  Boris Lenhard,et al.  Antisense Transcription in the Mammalian Transcriptome RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium , 2005 .

[15]  G. Daley,et al.  Stage-specific signaling through TGF b family members and WNT regulates patterning and pancreatic specification of human pluripotent stem cells , 2022 .

[16]  M. Grompe,et al.  Isolation of major pancreatic cell types and long-term culture-initiating cells using novel human surface markers. , 2008, Stem cell research.

[17]  Hao Zhang,et al.  Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS , 2006, Nucleic acids research.

[18]  Michael Q. Zhang,et al.  Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells , 2013, Cell.

[19]  H. Deng,et al.  In vitro derivation of functional insulin-producing cells from human embryonic stem cells , 2007, Cell Research.

[20]  Michael Morse,et al.  Multiple knockout mouse models reveal lincRNAs are required for life and brain development , 2013, eLife.

[21]  Prabhakar R. Gudla,et al.  Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. , 2008, Genes & development.

[22]  J. Schug,et al.  Epigenomic plasticity enables human pancreatic α to β cell reprogramming. , 2013, The Journal of clinical investigation.

[23]  M. Weiss,et al.  Self-renewing endodermal progenitor lines generated from human pluripotent stem cells. , 2012, Cell stem cell.

[24]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[25]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[26]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[27]  Edward Chuong,et al.  Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs. , 2011, Developmental biology.

[28]  J. Schug,et al.  Transcriptomes of the major human pancreatic cell types , 2011, Diabetologia.

[29]  James D. Johnson,et al.  Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells , 2014, Nature Biotechnology.

[30]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[31]  Manolis Kellis,et al.  The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. , 2013, Developmental cell.

[32]  M. Trotter,et al.  Pluripotency factors regulate definitive endoderm specification through eomesodermin. , 2011, Genes & development.

[33]  Vincent L. Butty,et al.  Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment , 2013, Cell.

[34]  Xuetao Cao,et al.  The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation , 2014, Science.

[35]  Jeannie T. Lee,et al.  Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embryos , 2011, Nature Protocols.

[36]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[37]  A. Zorn,et al.  Sox17 and beta-catenin cooperate to regulate the transcription of endodermal genes. , 2004, Development.

[38]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[39]  Howard Y. Chang,et al.  Genome regulation by long noncoding RNAs. , 2012, Annual review of biochemistry.

[40]  D. Melton,et al.  Generation of Functional Human Pancreatic β Cells In Vitro , 2014, Cell.

[41]  E. Kroon,et al.  Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo , 2008, Nature Biotechnology.

[42]  Pei-Rong Wang,et al.  Deconstructing pancreas development to reconstruct human islets from pluripotent stem cells. , 2010, Cell stem cell.

[43]  Guoping Fan,et al.  Pancreatic β cell identity is maintained by DNA methylation-mediated repression of Arx. , 2011, Developmental cell.

[44]  D. Bartel,et al.  lincRNAs: Genomics, Evolution, and Mechanisms , 2013, Cell.

[45]  Jonathan Schug,et al.  Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. , 2013, Cell stem cell.

[46]  M. McCarthy,et al.  Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. , 2012, Cell metabolism.

[47]  H. Lodish,et al.  Regulation of mammalian cell differentiation by long non‐coding RNAs , 2012, EMBO reports.

[48]  N. Bursac,et al.  WNT3 Is a Biomarker Capable of Predicting the Definitive Endoderm Differentiation Potential of hESCs , 2013, Stem cell reports.

[49]  A. Zorn,et al.  Sox17 and β-catenin cooperate to regulate the transcription of endodermal genes , 2004 .

[50]  R. Derynck,et al.  Specificity and versatility in tgf-beta signaling through Smads. , 2005, Annual review of cell and developmental biology.

[51]  M. Gerstein,et al.  Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing , 2010, Proceedings of the National Academy of Sciences.

[52]  Wei Jiang,et al.  Histone H3K27me3 demethylases KDM6A and KDM6B modulate definitive endoderm differentiation from human ESCs by regulating WNT signaling pathway , 2012, Cell Research.

[53]  H. Deng,et al.  CD24: A Novel Surface Marker for PDX1‐Positive Pancreatic Progenitors Derived from Human Embryonic Stem Cells , 2011, Stem cells.

[54]  Rui Liu,et al.  Tet1 controls meiosis by regulating meiotic gene expression , 2012, Nature.

[55]  Aaron M Zorn,et al.  Vertebrate endoderm development and organ formation. , 2009, Annual review of cell and developmental biology.