Global Quantitative Mapping of Enhancers in Rice by STARR-seq
暂无分享,去创建一个
Wei Shen | Longjian Niu | Yingzhang Huang | Li Li | Jialei Sun | Na He | Yuedong Zhang | Chunhui Hou | Chunhui Hou | Longjian Niu | W. Shen | Na He | Jialei Sun | Yuedong Zhang | Yingzhang Huang | Li Li
[1] Nathaniel D. Heintzman,et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.
[2] Alexandre P. Marand,et al. Towards genome-wide prediction and characterization of enhancers in plants. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.
[3] M. Groudine,et al. Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.
[4] Roland Eils,et al. EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations , 2018, BMC Genomics.
[5] R. Young,et al. Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.
[6] J. Keith Joung,et al. Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation , 2013, Cell.
[7] P. Scacheri,et al. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.
[8] S. Rossmann,et al. Specific expression of LATERAL SUPPRESSOR is controlled by an evolutionarily conserved 3' enhancer. , 2011, The Plant journal : for cell and molecular biology.
[9] D. S. Gross,et al. Nuclease hypersensitive sites in chromatin. , 1988, Annual review of biochemistry.
[10] Fidel Ramírez,et al. deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..
[11] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[12] Yuge Li,et al. A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes , 2011, Plant Methods.
[13] Lan T M Dao,et al. Genome-wide characterization of mammalian promoters with distal enhancer functions , 2017, Nature Genetics.
[14] S Miyano,et al. Open source clustering software. , 2004, Bioinformatics.
[15] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[16] A. Visel,et al. ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.
[17] A. Visel,et al. Genomic Views of Distant-Acting Enhancers , 2009, Nature.
[18] Shuhui Song,et al. Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice. , 2016, The New phytologist.
[19] Hani Z. Girgis,et al. A High-Resolution Enhancer Atlas of the Developing Telencephalon , 2013, Cell.
[20] Łukasz M. Boryń,et al. Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.
[21] Sandy L. Klemm,et al. Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.
[22] U. Grossniklaus,et al. An Egg Apparatus-Specific Enhancer of Arabidopsis, Identified by Enhancer Detection1 , 2005, Plant Physiology.
[23] G. Kreiman,et al. Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.
[24] David A. Orlando,et al. Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.
[25] K. White,et al. Functional assessment of human enhancer activities using whole-genome STARR-sequencing , 2017, Genome Biology.
[26] R. Young,et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.
[27] E. Greer,et al. Histone methylation: a dynamic mark in health, disease and inheritance , 2012, Nature Reviews Genetics.
[28] Ann A. Ferguson,et al. What makes up plant genomes: The vanishing line between transposable elements and genes. , 2016, Biochimica et biophysica acta.
[29] B. Ayre,et al. A DNA element between At4g28630 and At4g28640 confers companion-cell specific expression following the sink-to-source transition in mature minor vein phloem , 2008, Planta.
[30] Bao Liu,et al. Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures[OPEN] , 2015, Plant Cell.
[31] P. Scacheri,et al. CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing , 2009, Development.
[32] Lan T M Dao,et al. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq , 2015, Nature Communications.
[33] Nathaniel D. Heintzman,et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.
[34] Yuwen Liu,et al. Systematic identification of regulatory variants associated with cancer risk , 2017, Genome Biology.
[35] Wenli Zhang,et al. Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice , 2017, BMC Genomics.
[36] Raymond K. Auerbach,et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.
[37] N. Ahituv,et al. Decoding enhancers using massively parallel reporter assays. , 2015, Genomics.
[38] Łukasz M. Boryń,et al. Resolving systematic errors in widely-used enhancer activity assays in human cells , 2017, Nature Methods.
[39] A. Schier,et al. Bivalent histone modifications in early embryogenesis. , 2012, Current opinion in cell biology.
[40] Morgan C. Giddings,et al. Defining functional DNA elements in the human genome , 2014, Proceedings of the National Academy of Sciences.
[41] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[42] Satoru Miyano,et al. Open source clustering software , 2004 .
[43] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[44] U. Grossniklaus,et al. Intronic regulatory elements determine the divergent expression patterns of AGAMOUS-LIKE6 subfamily members in Arabidopsis. , 2009, The Plant journal : for cell and molecular biology.
[45] Y. Qi,et al. Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids[W] , 2010, Plant Cell.
[46] Nathan M. Springer,et al. Transposable element influences on gene expression in plants. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.
[47] Richard M. Clark,et al. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture , 2006, Nature Genetics.
[48] Zhou Du,et al. agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update , 2017, Nucleic Acids Res..
[49] Dariusz M Plewczynski,et al. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription , 2015, Cell.
[50] James C. Schnable,et al. High-resolution mapping of open chromatin in the rice genome. , 2012, Genome research.
[51] Wenli Zhang,et al. Functional characterization of open chromatin in bidirectional promoters of rice , 2016, Scientific Reports.
[52] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.