Genome-wide transcription and the implications for genomic organization

@article{Kapranov2007GenomewideTA,
  title={Genome-wide transcription and the implications for genomic organization},
  author={Philipp Kapranov and Aarron T. Willingham and Thomas R. Gingeras},
  journal={Nature Reviews Genetics},
  year={2007},
  volume={8},
  pages={413-423}
}
Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations suggest that genomic architecture is not colinear, but is instead interleaved and modular, and that the same genomic… 

Figures, Tables, and Topics from this paper

Pervasive transcription constitutes a new level of eukaryotic genome regulation
TLDR
Recent findings that point to cryptic transcription as a fundamental component of the regulation of eukaryotic genomes are reviewed.
Chromatin-based mechanisms to coordinate convergent overlapping transcription.
In eukaryotic genomes, the transcription units of genes often overlap with other protein-coding and/or noncoding transcription units1,2. In such intertwined genomes, the coordinated transcription of
Studying chromosome-wide transcriptional networks: new insights into disease?
TLDR
Exons of annotated and unannotated transcripts separated by large genomic distances can be joined together in chimeric transcripts, and the implications for the understanding of disease are discussed.
Antisense transcription: A critical look in both directions
TLDR
Facing the large-scale antisense transcription observed in eukaryotic genomes, it still remains an open challenge to distinguish transcriptional noise from biological function of gene overlapping patterns.
The central role of RNA in the genetic programming of complex organisms.
  • J. Mattick
  • Biology, Medicine
    Anais da Academia Brasileira de Ciencias
  • 2010
Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the
Chromatin-based mechanisms to coordinate convergent overlapping transcription
TLDR
It is shown in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of overlapping bidirectional transcripts and that these bidirectionally transcribed genes are regulated by a putative LSD1 family histone demethylase, FLD.
A global view of genomic information--moving beyond the gene and the master regulator.
TLDR
The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action and the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities.
Landscape of transcription in human cells
TLDR
Evidence that three-quarters of the human genome is capable of being transcribed is reported, 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 that prompt a redefinition of the concept of a gene.
Understanding the regulatory and transcriptional complexity of the genome through structure.
TLDR
It is proposed that the local and global three-dimensional structure of the genome provides a consistent, integrated, and intuitive framework for interpreting and understanding the regulatory and transcriptional complexity of the human genome.
Ubiquitous antisense transcription in eukaryotes: novel regulatory mechanism or byproduct of opportunistic RNA polymerase?
TLDR
Four recent reports have addressed the strandedness of pervasive transcripts in eukaryotic genomes and made the startling discovery that many loci of mRNA sense gene transcription are associated with very active antisense or divergent transcription that begins at mapped transcription start sites and proceeds in an upstream direction.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 139 REFERENCES
Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
TLDR
Different explanations for the large amounts of transcription observed in polyadenylated RNA samples appear to be derived from intergenic regions, from introns of known genes and from sequences antisense to known transcripts.
The Transcriptional Landscape of the Mammalian Genome
TLDR
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
A high-resolution map of transcription in the yeast genome.
  • L. David, W. Huber, +6 authors L. Steinmetz
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2006
TLDR
By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts.
Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum.
TLDR
An overview of recent advances in the identification and function of eukaryotic ncRNAs and the roles played by these RNAs in chromatin organization, gene expression, and disease etiology is provided.
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
TLDR
Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
Global Identification of Human Transcribed Sequences with Genome Tiling Arrays
TLDR
This work constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome and found 10,595 transcribed sequences not detected by other methods.
Large-Scale Transcriptional Activity in Chromosomes 21 and 22
TLDR
Empirically derived maps identifying active areas of RNA transcription on these chromosomes have been constructed with the use of cytosolic polyadenylated RNA obtained from 11 human cell lines with results that indicate there are approximately 770 well-characterized and predicted genes.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome
Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence
Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts.
TLDR
It is demonstrated that human SA pairs tend to be co-expressed and/or inversely expressed more frequently than expected by chance and exhibit a striking pattern of evolutionary conservation, suggesting that antisense regulation is a common and important mechanism of gene regulation in the human genome.
...
1
2
3
4
5
...