Genome-wide analysis of mammalian promoter architecture and evolution

By Piero Carninci, Albin Sandelin, Boris Lenhard, S. Katayama, Kazuro Shimokawa, J. Ponjavic, C. Semple, Martin S. Taylor, Pär G. Engström, Martin C. Frith and 31 more. Nature Genetics, 2006

1,400 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/747a4156f0533140515c5622089a93e16fd49b5b

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Citations in the corpus

Non‐coding RNAs: regulators of disease (2010, background): “An explanation for this apparent paradox comes from two unexpected findings: (a) that biological complexity generally correlates with the proportion of the genome that is non-protein-coding [1]; and (b) that, while only 2% of the mammalian genome encodes mRNAs, the vast majority is transcribed, larg”
The Genetic Signatures of Noncoding RNAs (2009, background): “Moreover, many 39 UTRs in mouse appear to be expressed separately from their mRNAs in a developmentally regulated manner [171].”
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, neutral): “Design of the Hidden Markov Model— Previous CAGE studies have shown that TSS regions can be both “sharp” (highly peaked) and “broad” 58–60 .”
Discovery and characterization of chromatin states for systematic annotation of the human genome (2010, methodology): “The ROC curve for the CAGE data was based on the number of CAGE tags mapping to a 200 bp interval retrieved from the Fantom database and converted from hg17 to hg18 using the UCSC genome browser liftover too”
RNA sequencing: advances, challenges and opportunities (2010, methodology): “One of the first high-throughput TSS mapping methods was the cap analysis of gene expression (CAGE) approach, which was initially developed for Sanger sequencin”
An expression atlas of human primary cells: inference of gene function from coexpression networks (2013, background): “MITF is expressed in both humans and mice from multiple promoters [60,61].”
A promoter-level mammalian expression atlas (2014, background): “CAGE has advantages over RNA-seq or microarrays for this purpose, because it permits separate analysis of multiple promoters linked to the same gene 13 .”
DNA Methylation and Its Basic Function (2013, background): “Although B50% of CpG islands contain known transcription start sites, CpG islands are often devoid of common promoter elements such as TATA boxes (Carninci et al, 2006).”
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles (2009, background): “The increasing amount of assembled genome sequences, transcriptome data (1), as well as high-throughput studies revealing genome-wide locations of core promoters (2) and enhancer elements (3,4) have resulted in the greatest demand for TF binding site content analyses.”
A mitochondrial protein compendium elucidates complex I disease biology (2008, neutral): “Their promoters tend to have CpG islands and lack TATA boxes, a feature shared with other ‘‘housekeeping’’ genes that may account for their higher expression (Carninci et al., 2006).”
CpG islands and the regulation of transcription. (2011, neutral): “Transcription factor binding at CGIs CGIs share little long-range sequence conservation, apart from an elevated CpG density and G+C content, and often lack core promoter elements such as the TATA box (Carninci et al. 2006; Juven-Gershon et al. 2008).”
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. (2007, background): “Definition of macroRNA core promoters and further classification We defined the core promoter region for macroRNAs as the region extending from 400 bp upstream up until an associated transcription start site (Carninci et al. 2006; Cooper et al. 2006).”