RNA exosome depletion reveals transcription upstream of active human promoters. Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin. It also maps enhancers across the human genome using their characteristic pattern of unstable, divergent transcription. This study identifies the unified architecture of regulatory elements at genes and enhancers, comprising two core initiation regions to coordinate divergent transcription. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Regulatory enhancer-core-promoter communication via transcription factors and cofactors. Ever-changing landscapes: transcriptional enhancers in development and evolution. On the dependency of cellular protein levels on mRNA abundance. HTSeq-a Python framework to work with high-throughput sequencing data. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. BEDTools: a flexible suite of utilities for comparing genomic features. clusterProfiler: an R package for comparing biological themes among gene clusters. LBNL-7065E (Lawrence Berkeley National Laboratory, 2014). BBMap: A Fast, Accurate, Splice-aware Aligner Report No. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. STAR: ultrafast universal RNA-seq aligner. Cutadapt removes adapter sequences from high-throughput sequencing reads. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Modulation of RNA polymerase II phosphorylation downstream of pathogen perception orchestrates plant immunity. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. C-terminal domain (CTD) phosphatase links Rho GTPase signaling to Pol II CTD phosphorylation in Arabidopsis and yeast. Emerging roles for RNA polymerase II CTD in Arabidopsis. Distinctive patterns of transcription and RNA processing for human lincRNAs. Defining the status of RNA polymerase at promoters. Isolation of Arabidopsis nuclei and measurement of gene transcription rates using nuclear run-on assays. melanogaster is transcriptionally engaged. ![]() The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. Separation and partial characterization of three functional steps in transcription initiation by human RNA polymerase II. Arabidopsis ARGONAUTE 1 binds chromatin to promote gene transcription in response to hormones and stresses. RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nascent RNA sequencing reveals distinct features in plant transcription. Nascent transcription affected by RNA polymerase IV in Zea mays. Transcription factors in plant defense and stress responses. Abiotic stress signaling and responses in plants. ![]() Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. TT-seq maps the human transient transcriptome. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
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