메뉴 건너뛰기




Volumn 2016, Issue 112, 2016, Pages

Prediction and validation of gene regulatory elements activated during retinoic acid induced embryonic stem cell differentiation

Author keywords

ChIP seq; Developmental biology; Embryonic stem cell; Enhancer; ERNA; Gene expression; Issue 112; Luciferase assay; Retinoic acid; Retinoic acid receptor; Transcription

Indexed keywords

RETINOIC ACID;

EID: 84977470988     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/53978     Document Type: Article
Times cited : (5)

References (28)
  • 1
    • 84899494117 scopus 로고    scopus 로고
    • Distal enhancers: New insights into heart development and disease
    • Wamstad, J. A., Wang, X., Demuren, O. O., & Boyer, L. A. Distal enhancers: new insights into heart development and disease. Trends in cell biology. 24, 294-302 (2014).
    • (2014) Trends in Cell Biology , vol.24 , pp. 294-302
    • Wamstad, J.A.1    Wang, X.2    Demuren, O.O.3    Boyer, L.A.4
  • 3
    • 34547630151 scopus 로고    scopus 로고
    • ChIP-seq: Welcome to the new frontier
    • Mardis, E. R. ChIP-seq: welcome to the new frontier. Nature methods. 4, 613-614 (2007).
    • (2007) Nature Methods , vol.4 , pp. 613-614
    • Mardis, E.R.1
  • 4
    • 84896703296 scopus 로고    scopus 로고
    • Chromatin and DNA sequences in defining promoters for transcription initiation
    • Muller, F., & Tora, L. Chromatin and DNA sequences in defining promoters for transcription initiation. Biochim Biophys Acta. 1839, 118-128 (2013).
    • (2013) Biochim Biophys Acta , vol.1839 , pp. 118-128
    • Muller, F.1    Tora, L.2
  • 5
    • 84941996167 scopus 로고    scopus 로고
    • The promise of enhancer-associated long noncoding RNAs in cardiac regeneration
    • Ounzain, S., & Pedrazzini, T. The promise of enhancer-associated long noncoding RNAs in cardiac regeneration. Trends Cardiovasc Med. (2015).
    • (2015) Trends Cardiovasc Med
    • Ounzain, S.1    Pedrazzini, T.2
  • 6
    • 84897446230 scopus 로고    scopus 로고
    • Enhancer RNAs and regulated transcriptional programs
    • Lam, M. T., Li, W., Rosenfeld, M. G., & Glass, C. K. Enhancer RNAs and regulated transcriptional programs. Trends Biochem Sci. 39, 170-182 (2014).
    • (2014) Trends Biochem Sci , vol.39 , pp. 170-182
    • Lam, M.T.1    Li, W.2    Rosenfeld, M.G.3    Glass, C.K.4
  • 7
    • 84899692444 scopus 로고    scopus 로고
    • Function-based identification of mammalian enhancers using site-specific integration
    • Dickel, D. E. et al. Function-based identification of mammalian enhancers using site-specific integration. Nature methods 11, 566-571 (2014).
    • (2014) Nature Methods , vol.11 , pp. 566-571
    • Dickel, D.E.1
  • 8
    • 84871603480 scopus 로고    scopus 로고
    • Genome-wide identification of enhancers in skeletal muscle: The role of MyoD1
    • Blum, R., Vethantham, V., Bowman, C., Rudnicki, M., & Dynlacht, B. D. Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. Genes Dev. 26, 2763-2779 (2012).
    • (2012) Genes Dev , vol.26 , pp. 2763-2779
    • Blum, R.1    Vethantham, V.2    Bowman, C.3    Rudnicki, M.4    Dynlacht, B.D.5
  • 9
    • 84919655613 scopus 로고    scopus 로고
    • Large-scale identification of coregulated enhancer networks in the adult human brain
    • Vermunt, M. W. et al. Large-scale identification of coregulated enhancer networks in the adult human brain. Cell reports 9, 767-779 (2014).
    • (2014) Cell Reports , vol.9 , pp. 767-779
    • Vermunt, M.W.1
  • 10
    • 0028907753 scopus 로고
    • Embryonic stem cells express neuronal properties in vitro
    • Bain, G., Kitchens, D., Yao, M., Huettner, J. E., & Gottlieb, D. I. Embryonic stem cells express neuronal properties in vitro. Dev Biol. 168, 342-357 (1995).
    • (1995) Dev Biol , vol.168 , pp. 342-357
    • Bain, G.1    Kitchens, D.2    Yao, M.3    Huettner, J.E.4    Gottlieb, D.I.5
  • 11
    • 78651309953 scopus 로고    scopus 로고
    • Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
    • Mahony, S. et al. Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 12, R2 (2011).
    • (2011) Genome Biol , vol.12
    • Mahony, S.1
  • 12
    • 77954174222 scopus 로고    scopus 로고
    • Activation of retinoic acid receptor signaling coordinates lineage commitment of spontaneously differentiating mouse embryonic stem cells in embryoid bodies
    • Simandi, Z., Balint, B. L., Poliska, S., Ruhl, R., & Nagy, L. Activation of retinoic acid receptor signaling coordinates lineage commitment of spontaneously differentiating mouse embryonic stem cells in embryoid bodies. FEBS Lett. 584, 3123-3130 (2010).
    • (2010) FEBS Lett , vol.584 , pp. 3123-3130
    • Simandi, Z.1    Balint, B.L.2    Poliska, S.3    Ruhl, R.4    Nagy, L.5
  • 13
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 14
    • 77952567987 scopus 로고    scopus 로고
    • Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
    • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38, 576-589 (2010).
    • (2010) Mol Cell , vol.38 , pp. 576-589
    • Heinz, S.1
  • 15
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson, J. T. et al. Integrative genomics viewer. Nat Biotechnol 29, 24-26 (2011).
    • (2011) Nat Biotechnol , vol.29 , pp. 24-26
    • Robinson, J.T.1
  • 16
    • 85047689062 scopus 로고    scopus 로고
    • The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages
    • Daniel, B. et al. The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages. Genes Dev 28, 1562-1577 (2013).
    • (2013) Genes Dev , vol.28 , pp. 1562-1577
    • Daniel, B.1
  • 17
    • 84890397089 scopus 로고    scopus 로고
    • Predicting enhancer transcription and activity from chromatin modifications
    • Zhu, Y. et al. Predicting enhancer transcription and activity from chromatin modifications. Nucleic Acids Res 41, 10032-10043 (2013).
    • (2013) Nucleic Acids Res , vol.41 , pp. 10032-10043
    • Zhu, Y.1
  • 18
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel, A. et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854-858 (2009).
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1
  • 19
    • 33847334699 scopus 로고    scopus 로고
    • Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
    • Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39, 311-318 (2007).
    • (2007) Nat Genet , vol.39 , pp. 311-318
    • Heintzman, N.D.1
  • 20
    • 79951516056 scopus 로고    scopus 로고
    • A unique chromatin signature uncovers early developmental enhancers in humans
    • Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2010).
    • (2010) Nature , vol.470 , pp. 279-283
    • Rada-Iglesias, A.1
  • 21
    • 84856239091 scopus 로고    scopus 로고
    • Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    • Bonn, S. et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44, 148-156 (2012).
    • (2012) Nat Genet , vol.44 , pp. 148-156
    • Bonn, S.1
  • 22
    • 0023649571 scopus 로고
    • Colocalization of DNA-binding and transcriptional activation functions in the human glucocorticoid receptor
    • Hollenberg, S. M., Giguere, V., Segui, P., & Evans, R. M. Colocalization of DNA-binding and transcriptional activation functions in the human glucocorticoid receptor. Cell. 49, 39-46 (1987).
    • (1987) Cell , vol.49 , pp. 39-46
    • Hollenberg, S.M.1    Giguere, V.2    Segui, P.3    Evans, R.M.4
  • 23
    • 84865022311 scopus 로고    scopus 로고
    • Primer3--new capabilities and interfaces
    • Untergasser, A. et al. Primer3--new capabilities and interfaces. Nucleic Acids Res 40, e115 (2012).
    • (2012) Nucleic Acids Res , vol.40
    • Untergasser, A.1
  • 24
    • 75549089967 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: Update 2010
    • Rhead, B. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38, D613-619 (2010).
    • (2010) Nucleic Acids Res , vol.38 , pp. D613-D619
    • Rhead, B.1
  • 25
    • 77952367798 scopus 로고    scopus 로고
    • Widespread transcription at neuronal activity-regulated enhancers
    • Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
    • (2010) Nature , vol.465 , pp. 182-187
    • Kim, T.K.1
  • 26
    • 79959198166 scopus 로고    scopus 로고
    • Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
    • Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-394 (2011).
    • (2011) Nature , vol.474 , pp. 390-394
    • Wang, D.1
  • 27
    • 84923228096 scopus 로고    scopus 로고
    • PRMT1 and PRMT8 regulate retinoic acid-dependent neuronal differentiation with implications to neuropathology
    • Simandi, Z. et al. PRMT1 and PRMT8 regulate retinoic acid-dependent neuronal differentiation with implications to neuropathology. Stem Cells 33, 726-741 (2014).
    • (2014) Stem Cells , vol.33 , pp. 726-741
    • Simandi, Z.1
  • 28
    • 84918551761 scopus 로고    scopus 로고
    • A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential
    • Zhou, H. Y. et al. A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential. Genes Dev 28, 2699-2711 (2014).
    • (2014) Genes Dev , vol.28 , pp. 2699-2711
    • Zhou, H.Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.