What is a gene, post-ENCODE? History and updated definition.
By Mark Gerstein, Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, S. Weissman, Michael Snyder. Genome Research, 2007
715 citations recorded by the source corpus.
While sequencing of the human genome surprised us with how many protein-coding genes there are, it did not fundamentally change our perspective on what a gene is. In contrast, the complex patterns of dispersed regulation and pervasive transcription uncovered by the ENCODE project, together with non-genic conservation and the abundance of noncoding RNA genes, have challenged the notion of the gene. To illustrate this, we review the evolution of operational definitions of a gene over the past century--from the abstract elements of heredity of Mendel and Morgan to the present-day ORFs enumerated in the sequence databanks. We then summarize the current ENCODE findings and provide a computational metaphor for the complexity. Finally, we propose a tentative update to the definition of a gene: A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Our definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene. It also manifests how integral the concept of biological function is in defining genes.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/5200459c620ce4f0077487e4b7433bf429480819
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
Citations in the corpus
- Genomic Similarity and Kernel Methods II: Methods for Genomic Information (2010, background): “For example, in light of the complexity of the genetic architecture revealed by the ENCODE project, Gerstein et al. [33] state: ‘In the context of interpreting high-throughput experiments such as tiling arrays, the concept of a gene has an added practical importance – as a statistical model to help…”
- Evolution and functions of long noncoding RNAs. (2009, background): “What, then, is a gene (Gerstein et al., 2007; Gingeras, 2007)? One previous definition is that it is a genomic region that, when transcribed, produces a polyadenylated mRNA that encodes a protein.”
- NONCODEv4: exploring the world of long non-coding RNA genes (2013, background): “Following the classical definition of ‘gene’ for protein-coding RNAs (13), NONCODE version 4.”
- The Landscape of long non-coding RNA classification (2015, neutral): “The second aspect moves from phenomenological description of lncRNAs to their genomic coordinates, which parallels the evolution of the concept of the gene [129].”