Landscape of transcription in human cells

By S. Djebali, Carrie A. Davis, A. Merkel, Alexander Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, F. Schlesinger and 75 more. Nature, 2012

4,961 citations recorded by the source corpus.

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/76185686d188fe7b8cd36f916d4fd5e4634165a3

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Citations in the corpus

Modeling gene expression using chromatin features in various cellular contexts (2012, positive): “Moreover, gene expression levels were quantified in two forms: RNA-Seq [15] was used to quantify transcript (Tx)-based expression levels; and CAGE [16,17] and 5 ’ tags of RNA-PET [18] were used to capture transcription start site (TSS)-based expression levels [19].”
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. (2014, background): “Recent study showed that with an average of 10 to 12 isoforms per gene, most genes tend to express multiple isoforms simultaneously [21].”
Transcriptional Regulation and its Misregulation in Disease (2013, neutral): “Nonetheless, recent studies have identified a vast number and variety of ncRNAs in human cells, so there is promise that improved human genome annotation is at hand (Djebali et al., 2012).”
Gene regulation by the act of long non-coding RNA transcription (2013, background): “LncRNAs - a new layer of genome regulatory information It is now well appreciated that less than two percent of the human genome codes for proteins and the majority of the genome gives rise to non-protein-coding RNAs (ncRNAs) [1], which are predicted to play essential roles in a variety of biologica”
Single-cell RNA-seq: advances and future challenges (2014, neutral): “Genome-wide RNA-seq analyses have recently uncovered an unexpected complexity in the transcriptomes of organisms from all domains of life with respect to gene structure and output from non-coding regions (12–27).”
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors (2012, methodology): “In this study, we integrated the following additional ENCODE data sets: the nucleosome occupancy profiles in GM12878 and K562 (Kundaje et al. 2012), RNA-seq data (Djebali et al. 2012), and DNase-seq data (Neph et al. 2012).”
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse (2016, background): “The Encyclopedia of DNA Elements (ENCODE) Consortium has provided high quality processed genome-wide histone modification, chromatin regulator and transcription factor binding data in a selected set of human cell lines (3,11) and the NIH Roadmap Epigenomics Project has built a similar resource for h”
Integrative annotation of chromatin elements from ENCODE data (2012, neutral): “Also as expected, the DNA segments in states associated with repression are depleted for transcripts (Figure 4), only a minority of the protein-coding genes overlapping these states are transcribed (Supplementary Figure S20), and the expression levels (29) for these genes are low (Figure 4).”
Non-coding RNA: what is functional and what is junk? (2015, neutral): “…to ENCODE’s own estimates, fewer than 1,000 lncRNAs are present at greater than one copy per cell in the typical human tissue culture cell line (Djebali et al., 2012; Palazzo and Gregory, 2014), although some other estimates have determined that the levels may be substantially higher…”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “One likely reason for the disparity between the validation of the two ends of the gene is the limited tissue coverage of the TSS set, which is derived from 24 whole-cell line polyA+ CAGE experiments (Djebali et al. 2012).”