Genome-wide transcription and the implications for genomic organization

By Philipp Kapranov, A. Willingham, Thomas R. Gingeras. Nature reviews genetics, 2007

731 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b26e8abe3dc64b0c6428530034d27e88566171a8

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Citations in the corpus

Epigenetics and gene expression (2010, background): “More recent studies indicate that the majority of the genome is transcribed into RNA transcripts, most of which do not code for protein (Kapranov et al., 2007; Amaral and Mattick, 2008 and references therein).”
Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription (2008, background): “S5b), while the N-terminus (1-211) interacted with CBP (Fig.”
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, background): “These data imply that the amount of information contained in the complex genomes of eukaryotes, and higher eukaryotes in particular, is much higher than the classical linear models of genomic organization can accommodate [6].”
Single-cell RNA-seq: advances and future challenges (2014, positive): “While the focus of single-cell RNA-seq has thus far been on polyadenylated mRNAs of eukaryotes, many other transcript classes remain to be fully explored.”
Evolution and functions of long noncoding RNAs. (2009, background): “A similar clustering of shorter noncoding RNAs is also observed (Kapranov et al., 2007a).”
LncRNA-mediated regulation of cell signaling in cancer (2017, background): “Introduction It is well known that although a large number of RNA species are transcribed from the human genome, protein-coding sequences account for a very small fraction of total transcripts (Birney et al 2007, Kapranov et al 2007).”
Non-coding RNAs in disease: from mechanisms to therapeutics (2023, neutral): “%) encodes for RNAs that are not translated into proteins, termed non-coding RNAs (ncRNAs) 1–3 .”
Noncoding transcription by RNA Polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes (2008, positive): “In humans, such conventional genes account for less than 2% of the genome, yet 90% of the genome is transcribed (Kapranov et al., 2007; Prasanth and Spector, 2007; Willingham et al., 2006).”
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. (2011, background): “More recent studies have reported new classes of RNA species, such as ‘‘promoter associated RNAs’’ (Kapranov et al. 2007b; Tsuritani et al. 2007; Preker et al. 2008; Seila et al. 2008; Affymetrix/ Cold Spring Harbor Laboratory ENCODE Transcriptome Project 2009; Neil et al. 2009; Taft et al. 2009)…”
The Landscape of long non-coding RNA classification (2015, positive): “The transcriptional forest concept implies that multiple RNA species share the same genomic space, either transcribed independently or derived by processing of longer precursors [38, 43, 120].”