Nascent transcript sequencing visualizes transcription at nucleotide resolution

[1]  A. Hinnebusch,et al.  Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. , 2010, Molecular cell.

[2]  G. Dougan,et al.  Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation , 2010, Science.

[3]  J. Svejstrup,et al.  Evidence that Transcript Cleavage Is Essential for RNA Polymerase II Transcription and Cell Viability , 2010, Molecular cell.

[4]  J. Pérez-Ortín,et al.  The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors , 2010, Nucleic acids research.

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

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

[7]  Carlos Bustamante,et al.  Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II , 2009, Science.

[8]  A. Morillon,et al.  H3 lysine 4 di‐ and tri‐methylation deposited by cryptic transcription attenuates promoter activation , 2009, The EMBO journal.

[9]  M. Kashlev,et al.  Mechanism of sequence-specific pausing of bacterial RNA polymerase , 2009, Proceedings of the National Academy of Sciences.

[10]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[11]  Bing Li,et al.  Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription* , 2009, Journal of Biological Chemistry.

[12]  Irene K. Moore,et al.  The DNA-encoded nucleosome organization of a eukaryotic genome , 2009, Nature.

[13]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[14]  Melissa J. Moore,et al.  Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation , 2009, Cell.

[15]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[16]  Christophe Malabat,et al.  Widespread bidirectional promoters are the major source of cryptic transcripts in yeast , 2009, Nature.

[17]  Raymond K. Auerbach,et al.  Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing , 2009 .

[18]  Mikkel H. Schierup,et al.  RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters , 2008, Science.

[19]  Gene W. Yeo,et al.  Divergent Transcription from Active Promoters , 2008, Science.

[20]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[21]  Michelle D. Wang,et al.  High resolution dynamic mapping of histone-DNA interactions in a nucleosome , 2008, Nature Structural &Molecular Biology.

[22]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[23]  S. Buratowski,et al.  The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain , 2008, Nature Structural &Molecular Biology.

[24]  J. Lis,et al.  Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci , 2008, Cell.

[25]  Bing Li,et al.  The Role of Chromatin during Transcription , 2007, Cell.

[26]  J. Corden,et al.  Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. , 2006, Molecular cell.

[27]  Steven M. Block,et al.  Sequence-Resolved Detection of Pausing by Single RNA Polymerase Molecules , 2006, Cell.

[28]  Bing Li,et al.  Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription , 2005, Cell.

[29]  Nevan J. Krogan,et al.  Cotranscriptional Set2 Methylation of Histone H3 Lysine 36 Recruits a Repressive Rpd3 Complex , 2005, Cell.

[30]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

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

[32]  Vasily M Studitsky,et al.  Nature of the nucleosomal barrier to RNA polymerase II. , 2005, Molecular cell.

[33]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[34]  Joshua W. Shaevitz,et al.  Backtracking by single RNA polymerase molecules observed at near-base-pair resolution , 2003, Nature.

[35]  G. Cagney,et al.  Methylation of Histone H3 by Set2 in Saccharomyces cerevisiae Is Linked to Transcriptional Elongation by RNA Polymerase II , 2003, Molecular and Cellular Biology.

[36]  K. Struhl,et al.  TFIIS Enhances Transcriptional Elongation through an Artificial Arrest Site In Vivo , 2001, Molecular and Cellular Biology.

[37]  R. Conaway,et al.  Mechanism and regulation of transcriptional elongation by RNA polymerase II. , 1999, Current opinion in cell biology.

[38]  D. Bartel,et al.  RNA-catalysed nucleotide synthesis , 1998, Nature.

[39]  E. Nudler,et al.  The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase , 1997, Cell.

[40]  D. Luse,et al.  Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. , 1992, The Journal of biological chemistry.

[41]  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.

[42]  H. Cai,et al.  Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. , 1987, The Journal of biological chemistry.

[43]  M. Chamberlin,et al.  Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro. , 1981, The Journal of biological chemistry.

[44]  J. Smith,et al.  The structure of ribonucleic acid. I. Cyclic nucleotides produced by ribonuclease and by alkaline hydrolysis. , 1952, The Biochemical journal.

[45]  Nir Friedman,et al.  High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. , 2010, Genome research.

[46]  W. Guschlbauer The Structure of Ribonucleic Acids , 1976 .