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1. Full Text Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
by Dowen, Jill M and Fan, Zi Peng and Hnisz, Denes and Ren, Gang and Abraham, Brian J and Zhang, Lyndon N and Weintraub, Abraham S and Schuijers, Jurian and Lee, Tong Ihn and Zhao, Keji and Young, Richard A
Cell, ISSN 0092-8674, 10/2014, Volume 159, Issue 2, pp. 374 - 387
The pluripotent state of embryonic stem cells (ESCs) is produced by active transcription of genes that control cell identity and repression of genes encoding... 
PLURIPOTENCY FACTORS | DEVELOPMENTAL REGULATORS | SUPER-ENHANCERS | DROSOPHILA-MELANOGASTER | BIOCHEMISTRY & MOLECULAR BIOLOGY | EMBRYONIC STEM-CELLS | BINDING SITES | CHROMATIN INTERACTIONS | TOPOLOGICAL DOMAINS | TRANSCRIPTIONAL REGULATION | GENOME ORGANIZATION | CELL BIOLOGY | Embryonic Stem Cells - metabolism | Embryonic Stem Cells - cytology | Chromosomal Proteins, Non-Histone - metabolism | Cell Cycle Proteins - metabolism | Organ Specificity | Sequence Analysis, DNA | Pluripotent Stem Cells - metabolism | Animals | Chromatin Immunoprecipitation | CCCTC-Binding Factor | High-Throughput Nucleotide Sequencing | Mice | Chromosomes, Mammalian - metabolism | Genome | Repressor Proteins - metabolism | Genetic research | Embryonic stem cells | Genes | Genomics | Index Medicus
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2. Full Text Wnt-induced transcriptional activation is exclusively mediated by TCF/LEF
by Schuijers, Jurian and Mokry, Michal and Hatzis, Pantelis and Cuppen, Edwin and Clevers, Hans
EMBO Journal, ISSN 0261-4189, 01/2014, Volume 33, Issue 2, pp. 146 - 56
Active canonical Wnt signaling results in recruitment of β-catenin to DNA by TCF/LEF family members, leading to transcriptional activation of TCF target genes.... 
β‐catenin | Wnt pathway | TCF | transcriptional regulation | Seq | β-catenin | ChIP-Seq | Transcriptional regulation | beta-catenin | FUNCTIONAL INTERACTION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SELF-RENEWAL | CHROMATIN OCCUPANCY | CELL BIOLOGY | COLON-CANCER | INTESTINAL EPITHELIUM | WNT/BETA-CATENIN | TARGET GENE-TRANSCRIPTION | COLORECTAL-CANCER CELLS | CATENIN-TCF COMPLEX | Chromatin - metabolism | TCF Transcription Factors - physiology | Transcriptional Activation - genetics | Humans | Cells, Cultured | Gene Expression Profiling | beta Catenin - metabolism | Animals | Microarray Analysis | HEK293 Cells | Mice | Wnt Proteins - physiology | Binding Sites | Transcription factors | Genomes | Genes | Binding sites | Deoxyribonucleic acid--DNA | Index Medicus
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3. Full Text Erratum: Adult mammalian stem cells: The role of Wnt, Lgr5 and R-spondins (The EMBO Journal (2012) 31, (2685-2696) DOI:10.1038/emboj.2012.149)
by Schuijers, Jurian and Clevers, Hans
EMBO Journal, ISSN 0261-4189, 07/2012, Volume 31, Issue 13, pp. 3031 - 3032
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4. Full Text Coactivator condensation at super-enhancers links phase separation and gene control
by Sabari, BR and Dall'Agnese, A and Boija, A and Klein, IA and Coffey, EL and Shrinivas, K and Abraham, BJ and Hannett, NM and Zamudio, AV and Manteiga, JC and Li, CH and Guo, YE and Day, DS and Schuijers, J and Vasile, E and Malik, S and Hnisz, D and Lee, TI and Cisse, II and Roeder, RG and Sharp, PA and Chakraborty, AK and Young, RA
SCIENCE, ISSN 0036-8075, 07/2018, Volume 361, Issue 6400, p. 379
Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes... 
RNA-POLYMERASE-II | INTRINSIC DISORDER | PROTEIN | MULTIDISCIPLINARY SCIENCES | CELL IDENTITY | LIQUID DROPLETS | PLURIPOTENCY | TRANSITIONS | BINDING | TRANSCRIPTIONAL ELONGATION | P-TEFB | Embryonic Stem Cells - metabolism | NIH 3T3 Cells | Immunoprecipitation | Transcription Factors - chemistry | Fluorescence Recovery After Photobleaching | Humans | Molecular Imaging | Trans-Activators - chemistry | Cell Nucleus - metabolism | HEK293 Cells | Trans-Activators - genetics | Conserved Sequence | Nuclear Proteins - genetics | Mediator Complex Subunit 1 - chemistry | Mediator Complex Subunit 1 - metabolism | Serine - genetics | Nuclear Proteins - metabolism | Transcription Factors - genetics | Nuclear Proteins - chemistry | Serine - chemistry | Intrinsically Disordered Proteins - genetics | Enhancer Elements, Genetic - drug effects | Glycols - pharmacology | Gene Expression Regulation - drug effects | Transcription Factors - metabolism | Animals | Intrinsically Disordered Proteins - chemistry | Trans-Activators - metabolism | Mice | Cell Nucleus - drug effects | Mediator Complex Subunit 1 - genetics | Intrinsically Disordered Proteins - metabolism | Genetic research | Transcription factors | Genetic aspects | Research | Mammals | Chromatin | Nucleation | Transcription elongation | Genes | Gene regulation | Embryo cells | Fluorescence | Stem cell transplantation | Density | DNA-directed RNA polymerase | Cofactors | Complexity | Proteins | Nucleoli | Condensates | Clusters | Droplets | Hubs | Elongation | Deoxyribonucleic acid--DNA | Photobleaching | Collapsing | Pol II | Amino acid sequence | Gene expression | Molecular chains | Polymerase | Organic chemistry | Enhancers | Properties (attributes) | Sensitivity | Inhibitors | Ribonucleic acids | Phase separation | Stem cells | Nuclei (cytology) | Protein interaction | Transcription initiation | Nuclear reactions | Cancer | Index Medicus
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5. Full Text Adult mammalian stem cells: the role of Wnt, Lgr5 and R-spondins
: Corrigendum
by Schuijers, Jurian and Clevers, Hans
The EMBO Journal, ISSN 0261-4189, 06/2012, Volume 31, Issue 13, pp. 3031 - 3032
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6. Full Text Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis
by Huch, M and Bonfanti, P and Boj, S.F and Sato, T and Loomans, C.J and van de Wetering, M and Sojoodi, M and Li, V.S and Schuijers, J and Gracanin, A and Ringnalda, F and Begthel, H and Hamer, K and Mulder, J and van Es, J.H and de Koning, E and Vries, R.G.J and Heimberg, H and Clevers, H
EMBO Journal, ISSN 0261-4189, 2013, Volume 32, Issue 20, pp. 2708 - 2721
Lgr5 marks adult stem cells in multiple adult organs and is a receptor for the Wnt-agonistic R-spondins (RSPOs). Intestinal, stomach and liver Lgr5(+) stem... 
beta cell | duct cell | stem cell | Wnt | pancreas | MOUSE PANCREAS | REGENERATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | EMBRYONIC STEM-CELLS | BETA-CELLS | SMALL-INTESTINE | SELF-RENEWAL | ACINAR-CELLS | DIFFERENTIATION | LGR5 | ENDOCRINE-CELLS | CELL BIOLOGY | Adult Stem Cells - physiology | Cell Proliferation | Receptors, G-Protein-Coupled - metabolism | Thrombospondins - genetics | Embryo, Mammalian | Multipotent Stem Cells - metabolism | Pancreas - cytology | Cell Culture Techniques | Multipotent Stem Cells - physiology | Receptors, G-Protein-Coupled - physiology | Adult Stem Cells - cytology | Mice, Inbred C57BL | Cells, Cultured | Rats | Mice, Transgenic | Signal Transduction - genetics | Pancreas - metabolism | Mice, SCID | Rats, Sprague-Dawley | Adult Stem Cells - metabolism | Animals | Thrombospondins - physiology | Mice, Nude | Models, Biological | Multipotent Stem Cells - cytology | Mice | Receptors, G-Protein-Coupled - genetics | Thrombospondins - metabolism | Pancreas | Cell culture | Signal transduction | Index Medicus
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7. Full Text Adult mammalian stem cells: the role of Wnt, Lgr5 and R‐spondins
by Schuijers, Jurian and Clevers, Hans
The EMBO Journal, ISSN 0261-4189, 06/2012, Volume 31, Issue 13, pp. 3031 - 3032
BIOCHEMISTRY & MOLECULAR BIOLOGY | CELL BIOLOGY
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8. Full Text Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism
by Schuijers, Jurian and Manteiga, John Colonnese and Weintraub, Abraham Selby and Day, Daniel Sindt and Zamudio, Alicia Viridiana and Hnisz, Denes and Lee, Tong Ihn and Young, Richard Allen
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 2, pp. 349 - 360
Transcriptional dysregulation of the oncogene is among the most frequent events in aggressive tumor cells, and this is generally accomplished by acquisition of... 
enhancer docking | gene regulation | super-enhancers | chromosome structure | 3D GENOME | SUPER-ENHANCERS | DNA METHYLATION | INSULATED NEIGHBORHOODS | CELL IDENTITY GENES | C-MYC | CTCF | CHROMATIN INTERACTIONS | REGULATORY LANDSCAPE | PLURIPOTENT CELLS | CELL BIOLOGY
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9. Full Text Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
by Hnisz, Denes and Schuijers, Jurian and Lin, Charles Y and Weintraub, Abraham S and Abraham, Brian J and Lee, Tong Ihn and Bradner, James E and Young, Richard A
Molecular Cell, ISSN 1097-2765, 04/2015, Volume 58, Issue 2, pp. 362 - 370
Super-enhancers and stretch enhancers (SEs) drive expression of genes that play prominent roles in normal and disease cells, but the functional importance of... 
TARGET | STEM-CELLS | INFLAMMATION | MYC | BIOCHEMISTRY & MOLECULAR BIOLOGY | CELL IDENTITY | GENE-EXPRESSION | CELL BIOLOGY | Cell Line | Embryonic Stem Cells - metabolism | Signal Transduction | HCT116 Cells | Humans | Gene Expression Regulation, Neoplastic | Transcription Factors - metabolism | Animals | Enhancer Elements, Genetic | Neoplasms - genetics | Gene Expression Regulation, Developmental | HEK293 Cells | Mice | Genetic aspects | Genetic transcription | Embryonic stem cells | Analysis | Index Medicus
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10. Full Text Coactivator condensation at super-enhancers links phase separation and gene control
by Sabari, Benjamin R and Dall'Agnese, Alessandra and Boija, Ann and Klein, Isaac A and Coffey, Eliot L and Shrinivas, Krishna and Abraham, Brian J and Hannett, Nancy M and Zamudio, Alicia V and Manteiga, John C and Li, Charles H and Guo, Yang E and Day, Daniel S and Schuijers, Jurian and Vasile, Eliza and Malik, Sohail and Hnisz, Denes and Lee, Tong Ihn and Cisse, Ibrahim I and Roeder, Robert G and Sharp, Phillip A and Chakraborty, Arup K and Young, Richard A
Science, ISSN 0036-8075, 07/2018, Volume 361, Issue 6400
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11. Full Text Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts
by Schuijers, Jurian and Junker, Jan Philipp and Mokry, Michal and Hatzis, Pantelis and Koo, Bon-Kyoung and Sasselli, Valentina and van der Flier, Laurens G and Cuppen, Edwin and van Oudenaarden, Alexander and Clevers, Hans
Cell Stem Cell, ISSN 1934-5909, 02/2015, Volume 16, Issue 2, pp. 158 - 170
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and in many other adult organs. The transcription factor Ascl2 (a Wnt target... 
MOUSE INTESTINE | IN-VITRO | WNT/BETA-CATENIN | GENE-EXPRESSION | TRANSCRIPTIONAL REGULATORY CIRCUITRY | PANETH CELLS | EXPRESSION PATTERN | BETA-CATENIN | LGR5 | WNT RECEPTORS | CELL & TISSUE ENGINEERING | CELL BIOLOGY | Intestinal Mucosa - cytology | Intestinal Mucosa - metabolism | Animals | Basic Helix-Loop-Helix Transcription Factors - metabolism | Thrombospondins - genetics | Mice | Stem Cells - cytology | Stem Cells - metabolism | Thrombospondins - metabolism | Wnt Signaling Pathway | Index Medicus
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12. Full Text Robust Cre-Mediated Recombination in Small Intestinal Stem Cells Utilizing the Olfm4 Locus
by Schuijers, Jurian and van der Flier, Laurens G and van Es, Johan and Clevers, Hans
Stem Cell Reports, ISSN 2213-6711, 08/2014, Volume 3, Issue 2, pp. 234 - 241
The epithelium of the small intestine is the most rapidly self-renewing tissue in mammals. We previously demonstrated the existence of a long-lived pool of... 
PATTERN | GENE | MARKER | PROSTATE-CANCER | CRYPT | DIFFERENTIATION | IDENTIFICATION | LGR5 | EXPRESSION | CELL & TISSUE ENGINEERING | CELL BIOLOGY | Glycoproteins - genetics | Receptors, G-Protein-Coupled - metabolism | Mice, Inbred C57BL | Cells, Cultured | Stem Cells - cytology | Genetic Loci | Stem Cells - metabolism | Gene Knockdown Techniques | Cell Lineage | Phenotype | Animals | Intestine, Small - cytology | Recombination, Genetic | Alleles | Mice | Integrases - genetics | Index Medicus
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13. Full Text TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions
by Michael P. Verzi and Pantelis Hatzis and Rita Sulahian and Juliet Philips and Jurian Schuijers and Hyunjin Shin and Ellen Freed and John P. Lynch and Duyen T. Dang and Myles Brown and Hans Clevers and X. Shirley Liu and Ramesh A. Shivdasan and Eric N. Olson
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 8/2010, Volume 107, Issue 34, pp. 15157 - 15162
Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many... 
Transcription factors | Epithelial cells | Genes | DNA | Cell lines | Colorectal cancer | Genomes | Gene expression | Caco 2 cells | Binding sites | Genome-wide chromatin immunoprecipitation | Signaling | Tissue-specific gene regulation | Context specificity of signaling | Wnt signaling in intestine | signaling | MULTIDISCIPLINARY SCIENCES | MOUSE | HOMEOBOX | MODEL-BASED ANALYSIS | context specificity of signaling | EPITHELIUM | GENE-EXPRESSION | METAPLASIA | tissue-specific gene regulation | genome-wide chromatin immunoprecipitation | COLORECTAL-CANCER CELLS | DIFFERENTIATION | PROMOTER | TRANSGENIC MICE | Caco-2 Cells | Colonic Neoplasms - genetics | Intestinal Mucosa - metabolism | Transcription Factor 4 | Signal Transduction | Homeodomain Proteins - metabolism | Humans | RNA, Messenger - genetics | Regulatory Sequences, Nucleic Acid | Molecular Sequence Data | Binding Sites - genetics | RNA, Messenger - metabolism | Wnt Proteins - metabolism | Genetic Complementation Test | RNA, Neoplasm - metabolism | Colonic Neoplasms - metabolism | Homeodomain Proteins - genetics | Transcription Factors - metabolism | Base Sequence | RNA, Neoplasm - genetics | Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - metabolism | CDX2 Transcription Factor | Intestines | Genetic aspects | Research | Health aspects | Tissue | Mammals | Genomics | Cells | Deoxyribonucleic acid--DNA | Index Medicus | Chromatin | Immunoprecipitation | Nucleotide sequence | Wnt protein | CDX2 protein | Regulatory sequences | Single-nucleotide polymorphism | Myc protein | Epithelium | Signal transduction | Enhancers | Intestine | Biological Sciences
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14. Full Text Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles
by Mokry, Michal and Hatzis, Pantelis and de Bruijn, Ewart and Koster, Jan and Versteeg, Rogier and Schuijers, Jurian and van de Wetering, Marc and Guryev, Victor and Clevers, Hans and Cuppen, Edwin
PLoS ONE, ISSN 1932-6203, 2010, Volume 5, Issue 11, pp. e15092 - e15092
Immunoprecipitated crosslinked protein-DNA fragments typically range in size from several hundred to several thousand base pairs, with a significant part of... 
GENOME-WIDE ANALYSIS | SITES | COLORECTAL-CANCER CELLS | BETA-CATENIN | BIOLOGY | Chromatin - metabolism | Transcription Factor 4 | Humans | Nucleotides - genetics | Binding Sites - genetics | DNA - metabolism | Transcription Factors - genetics | DNA-Binding Proteins - genetics | Nucleotides - metabolism | DNA - genetics | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Base Sequence | Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - genetics | Cell Line, Tumor | Protein Binding | Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - metabolism | Chromatin Immunoprecipitation - methods | Crosslinked polymers | Chromatin | Genomes | Genomics | DNA | Protein binding | Binding | Integrated software | Immunoprecipitation | Base pairs | Colorectal cancer | Fragments | Crosslinking | Gene expression | Fragmentation | Proteins | Binding sites | Deoxyribonucleic acid--DNA | Index Medicus | Deoxyribonucleic acid
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