The Fragmented Gene

@article{Brosius2009TheFG,
  title={The Fragmented Gene},
  author={J{\"u}rgen Brosius},
  journal={Annals of the New York Academy of Sciences},
  year={2009},
  volume={1178}
}
  • J. Brosius
  • Published 1 October 2009
  • Biology
  • Annals of the New York Academy of Sciences
While once almost synonymous, there is an increasing gap between the expanding definition of what constitutes a gene and the conservative and narrowly defined terms code or coding, which for a long time, almost exclusively constituted the open reading frame. Much confusion results from this disparity, especially in light of the plethora of noncoding RNAs (more correctly termed “non‐protein‐coding RNAs”) that usually are encoded and transcribed by their own genes. A simple solution would be to… 
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33 Citations

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Does every transcript originate from a gene?
TLDR
It is suggested, in analogy to novel alternative splice variants that do not persist, that the vast majority of transcripts represent raw material for potential, albeit rare, exaptation events.
“Matreshka” genes with alternative reading frames
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The properties of “matreshka” genes of the second type and methods for their detection and verification are focused on, with particular attention paid to the biological properties of the polypeptides encoded by these genes.
The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function.
  • J. Brosius
  • Biology
    Cold Spring Harbor perspectives in biology
  • 2014
Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary…
Functional transcriptomics in the post-ENCODE era.
TLDR
The current state of human transcriptome annotation is discussed, drawing on the experience gained in generating the GENCODE gene annotation set, and it is proposed that an understanding of the true overlap between transcriptional complexity and functionality will not be gained in the short term.
Exonization of transposed elements: A challenge and opportunity for evolution.
GPAC-genome presence/absence compiler: a web application to comparatively visualize multiple genome-level changes.
TLDR
This paper presents the first tool to facilitate the parallel analysis of thousands of genomic loci for cross-species presence/absence patterns based on multiway genome alignments and provides examples of the versatile information content of such a screening system especially for 7SL-derived transposed elements, nuclear mitochondrial DNA, DNA transposons, and miRNAs in primates.
The struggle for life of the genome's selfish architects
TLDR
This review provides a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome, and explores the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution.
Exaptation at the molecular genetic level
TLDR
The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA—including transposed elements, formerly considered junk DNA—for the evolution of genes and genomes.
Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites
TLDR
These libraries were useful for assembling the internal structure of previously uncharacterized alternative promoter products, as well as intervening transcripts, and were also useful for identifying fusion gene transcripts in cancerous cells.
The agents of natural genome editing.
TLDR
As code editing agents, viral and subviral agents have been suggested because there are several indicators that demonstrate viruses competent in both RNA and DNA natural genome editing.
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