Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types

[1]  D. Fargo,et al.  Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks. , 2015, Molecular cell.

[2]  John T. Lis,et al.  Getting up to speed with transcription elongation by RNA polymerase II , 2015, Nature Reviews Molecular Cell Biology.

[3]  Christopher M. Weber,et al.  Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. , 2014, Molecular cell.

[4]  B. Williams,et al.  From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing , 2014, Genome research.

[5]  J. Lis,et al.  Control of transcriptional elongation. , 2013, Annual review of genetics.

[6]  Yan Li,et al.  A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.

[7]  Ruiqiang Li,et al.  Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells , 2013, Nature Structural &Molecular Biology.

[8]  D. Gilmour,et al.  Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor , 2013, The EMBO journal.

[9]  Julia Zeitlinger,et al.  Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo , 2013, Cell.

[10]  André L. Martins,et al.  Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. , 2013, Molecular cell.

[11]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[12]  Rona S. Gertner,et al.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.

[13]  Peter J Park,et al.  A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity , 2013, Genome research.

[14]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[15]  Leighton J. Core,et al.  Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing , 2013, Science.

[16]  Kairong Cui,et al.  H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. , 2013, Cell stem cell.

[17]  Alexander S. Garruss,et al.  The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation , 2013, Cell.

[18]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[19]  Leighton J. Core,et al.  Defining the status of RNA polymerase at promoters. , 2012, Cell reports.

[20]  Charles Y. Lin,et al.  Transcriptional Amplification in Tumor Cells with Elevated c-Myc , 2012, Cell.

[21]  John T. Lis,et al.  Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans , 2012, Nature Reviews Genetics.

[22]  D. Fargo,et al.  Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. , 2012, Genes & development.

[23]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[24]  M. Levine.  Paused RNA Polymerase II as a Developmental Checkpoint , 2011, Cell.

[25]  H. Aburatani,et al.  Genome-Wide Approaches Reveal Functional Interleukin-4-Inducible STAT6 Binding to the Vascular Cell Adhesion Molecule 1 Promoter , 2011, Molecular and Cellular Biology.

[26]  Leighton J. Core,et al.  Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. , 2011, Genes & development.

[27]  Uwe Ohler,et al.  Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level , 2011, PLoS genetics.

[28]  Bin Xie,et al.  Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation , 2010, Cell.

[29]  Jorja G. Henikoff,et al.  H2A.Z nucleosomes enriched over active genes are homotypic , 2010, Nature Structural &Molecular Biology.

[30]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[31]  D. Fargo,et al.  Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila , 2010, Science.

[32]  Kairong Cui,et al.  H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions in the human genome , 2009, Nature Genetics.

[33]  Alistair N Boettiger,et al.  Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo , 2009, Science.

[34]  Michael Y Tolstorukov,et al.  Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. , 2009, Genome research.

[35]  P. Park,et al.  Design and analysis of ChIP-seq experiments for DNA-binding proteins , 2008, Nature Biotechnology.

[36]  Leping Li,et al.  NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. , 2008, Genes & development.

[37]  David A. Hendrix,et al.  Promoter elements associated with RNA Pol II stalling in the Drosophila embryo , 2008, Proceedings of the National Academy of Sciences.

[38]  Manolis Kellis,et al.  RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo , 2007, Nature Genetics.

[39]  A. Rougvie,et al.  The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged , 1988, Cell.

[40]  J. Lis,et al.  In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster , 1985, Molecular and cellular biology.