Integrating epigenetic marks for identification of transcriptionally active miRNAs.

[1]  Yun Xiao,et al.  Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. , 2013, Neuro-oncology.

[2]  Qin Xu,et al.  Downregulation of miR-153 contributes to epithelial-mesenchymal transition and tumor metastasis in human epithelial cancer. , 2013, Carcinogenesis.

[3]  S. Robson,et al.  Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing , 2012, Cell.

[4]  R. Gregory,et al.  How does Lin28 let-7 control development and disease? , 2012, Trends in cell biology.

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

[6]  Xia Li,et al.  Prioritizing cancer-related key miRNA–target interactions by integrative genomics , 2012, Nucleic acids research.

[7]  A. Pasquinelli.  MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship , 2012, Nature Reviews Genetics.

[8]  Si-yong Huang,et al.  miR-153 sensitized the K562 cells to As2O3-induced apoptosis , 2012, Medical Oncology.

[9]  Monika S. Kowalczyk,et al.  Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.

[10]  R. Gregory,et al.  Molecular Basis for Interaction of let-7 MicroRNAs with Lin28 , 2011, Cell.

[11]  Sebastian D. Mackowiak,et al.  miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.

[12]  M. Stampfer,et al.  Epigenetic regulation of normal human mammary cell type-specific miRNAs. , 2011, Genome research.

[13]  Tzong-Yi Lee,et al.  Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data , 2011, Nucleic acids research.

[14]  Kenta Nakai,et al.  Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. , 2011, Genome research.

[15]  E. Olson,et al.  Pervasive roles of microRNAs in cardiovascular biology , 2011, Nature.

[16]  Kenneth P. Nephew,et al.  RNA Polymerase II Binding Patterns Reveal Genomic Regions Involved in MicroRNA Gene Regulation , 2010, PloS one.

[17]  T. Mikkelsen,et al.  Comparative Epigenomic Analysis of Murine and Human Adipogenesis , 2010, Cell.

[18]  W. Filipowicz,et al.  The widespread regulation of microRNA biogenesis, function and decay , 2010, Nature Reviews Genetics.

[19]  Manolis Kellis,et al.  Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.

[20]  Peter C. Hollenhorst,et al.  Human RNA Polymerase III transcriptomes and relationships to Pol II promoters, enhancer-binding factors and chromatin domains , 2010, Nature Structural &Molecular Biology.

[21]  B. Ren,et al.  Genome-wide prediction of transcription factor binding sites using an integrated model , 2010, Genome Biology.

[22]  Ting Wang,et al.  ENCODE whole-genome data in the UCSC Genome Browser , 2009, Nucleic Acids Res..

[23]  Leighton J. Core,et al.  Divergent transcription: A new feature of active promoters , 2009, Cell cycle.

[24]  D. Corcoran,et al.  Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data , 2009, PloS one.

[25]  P. Menéndez,et al.  The miR-302-367 cluster as a potential stemness regulator in ESCs , 2009, Cell cycle.

[26]  V. Ambros,et al.  Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. , 2008, Genome research.

[27]  G. Melen,et al.  Embryonic Stem Cell-Specific miR302-367 Cluster: Human Gene Structure and Functional Characterization of Its Core Promoter , 2008, Molecular and Cellular Biology.

[28]  Srinivas R. Viswanathan,et al.  Selective Blockade of MicroRNA Processing by Lin28 , 2008, Science.

[29]  Michael Q. Zhang,et al.  Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. , 2007, Genome research.

[30]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[31]  T. Swigut,et al.  H3K27 Demethylases, at Long Last , 2007, Cell.

[32]  R. Jaenisch,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[33]  S. Berger.  The complex language of chromatin regulation during transcription , 2007, Nature.

[34]  Weixiong Zhang,et al.  Characterization and Identification of MicroRNA Core Promoters in Four Model Species , 2007, PLoS Comput. Biol..

[35]  B. Davidson,et al.  RNA polymerase III transcribes human microRNAs , 2006, Nature Structural &Molecular Biology.

[36]  Peter A. Jones,et al.  Epigenetic Activation of Tumor Suppressor MicroRNAs in Human Cancer Cells , 2006, Cell cycle.

[37]  A. Malhotra,et al.  Muscle-specific microRNA miR-206 promotes muscle differentiation , 2006, The Journal of cell biology.

[38]  Yuriy Gusev,et al.  Real-time expression profiling of microRNA precursors in human cancer cell lines , 2005, Nucleic acids research.

[39]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[40]  Jun S. Song,et al.  Chromatin structure analyses identify miRNA promoters , 2008 .

[41]  B. Thiers.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2008 .

[42]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[43]  Supplemental Materials and Methods: Linker Ligation , 2022 .