What is a gene, post-ENCODE?: History and updated definition

What is a gene, post-ENCODE? : History and updated definition

QC 20111206
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.

NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
HIDDEN MARKOV MODEL
CHIP-CHIP EXPERIMENTS
GENOME TILING ARRAYS
NONCODING RNAS
MESSENGER-RNA
TRANSCRIPTIONAL ACTIVITY
PROCESSED PSEUDOGENES
SYSTEMATIC DEFINITION
UNRELATED PROTEINS
PNEUMOCOCCAL TYPES

Bruce, Can (författare)
Rozowsky, Joel S (författare)
Zheng, Deyou (författare)
Du, Jiang (författare)
Korbel, Jan O (författare)
Emanuelsson, OlofStockholms universitet,Institutionen för biokemi och biofysik(Swepub:su)emanu (författare)
Zhang, Zhengdong D (författare)
Weissman, Sherman (författare)
Snyder, Michael (författare)
Stockholms universitetInstitutionen för biokemi och biofysik (creator_code:org_t)

Ingår i:Genome Research: Cold Spring Harbor Laboratory17:6, s. 669-6811088-90511549-5469

Av författaren/redakt...: Gerstein, Mark B; Bruce, Can; Rozowsky, Joel S; Zheng, Deyou; Du, Jiang; Korbel, Jan O; visa fler...; Emanuelsson, Olo ...; Zhang, Zhengdong ...; Weissman, Sherma ...; Snyder, Michael; visa färre...

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