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What is a GENE?
GENOMICS
MIRIAM SÁEZ
HISTORY AND CURRENT DEFINITION
INDEX
1. HISTORY OF THE CONCEPT
2. CONCEPT AND CONTEXT
3. CAUSES OF RENEWING THE CONCEPT
4. CRITERIA TO FOLLOW
5. NEW DEFINITION
6. REFERENCES
1. HISTORY OF THE CONCEPT
DEFINITION 1860s-1900s
Particular characteristic
+
Heritability
Gene as a discret unit of
heredity
1. HISTORY OF THE CONCEPT
DEFINITION 1910s
Gene as a distinct locus
Mutations Recombining
Regions
1. HISTORY OF THE CONCEPT
DEFINITION 1940s-1950s
Gene as a blueprint for a protein
or as a physical molecule
One gene One polypeptide
1. HISTORY OF THE CONCEPT
DEFINITION 1960s
Gene as transcribed code
Central Dogma of Molecular
Biology
FUNCTIONAL PRODUCT
1. HISTORY OF THE CONCEPT
DEFINITION 1970s-1980s
Gene as open reading frame (ORF)
Cloning
+
Sequencing
+
Genetic Code
+
Computational tools
1. HISTORY OF THE CONCEPT
DEFINITION 1990s-2000s
Annotated genomic
entity, enumerated
in the databanks…
“DNA segment that contributes to
phenotype/function. In the absence of
demonstrated function a gene may be
characterized by sequence, transcription or
homology”
2. CONCEPT AND CONTEXT
INSTRUMENTAL GENE
Genotype
+
Phenotype
Nucleotide sequence
Structure
+
Function
NOMINAL GENE
POST GENOMIC GENE
3. CAUSES OF RENEWING THE CONCEPT
B. GENE FUSIONS
• NO clear structural boundaries
• TRANSCRIPTS
• Derived from both DNA strands
• Overlap
• Use the same coding sequences
• EXONS
A. COMPLEX TRANSCRIPTOME
3. CAUSES OF RENEWING THE CONCEPT
D. INHERITABLE FUNCTIONAL STATUS
C. ENCRYPTED GENES
E. GENETIC RESTORATION
Genes separated around the genome
Epigenetic Non-Mendelian inheritance of extra-genomic information
Are not heritable acquired characters?
4. CRITERIA TO FOLLOW
Backward compatible
Organism-independent
Simple idea
Practical
Compatible with digital gene
5. NEW DEFINITION PROPOSED
1 Genomic Sequence Protein
RNA
UNION of all
overlapping
genomic
sequences
COHERENT
done separately
for final protein
and RNA
products
2
3
5. NEW DEFINITION PROPOSED
“A gene is a union of genomic sequences encoding a
coherent set of potentially overlapping functional
products"
6. REFERENCES
• Akiva, P., Toporik, A., Edelheit, S. et al. 2006. Transcription- mediated gene fusion in the
human genome. – Genome Res. 16: 30–36.
• Gerstein, M., Bruce, C., Rozowsky, J., Zheng, D., Du, J., Korbel, J., Emanuelsson, O.,
Zhang, Z., Weissman, S. and Snyder, M. (2007). What is a gene, post-ENCODE? History
and updated definition. Genome Research, 17(6), pp.669-681.
• Lolle, S. J., Victor, J. L., Young, J. M. et al. 2005. Genome-wide non-mendelian
inheritance of extra-genomic information in Arabidopsis . – nature 434: 505–509.
• Portin, P. (2009). The elusive concept of the gene. Hereditas, 146(3), pp.112-117.
Thanks!
GENOMICS
HISTORY AND CURRENT DEFINITION

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Genomics PPT2018_1_19P18_25_55.pdf

  • 1. What is a GENE? GENOMICS MIRIAM SÁEZ HISTORY AND CURRENT DEFINITION
  • 2. INDEX 1. HISTORY OF THE CONCEPT 2. CONCEPT AND CONTEXT 3. CAUSES OF RENEWING THE CONCEPT 4. CRITERIA TO FOLLOW 5. NEW DEFINITION 6. REFERENCES
  • 3.
  • 4. 1. HISTORY OF THE CONCEPT DEFINITION 1860s-1900s Particular characteristic + Heritability Gene as a discret unit of heredity
  • 5. 1. HISTORY OF THE CONCEPT DEFINITION 1910s Gene as a distinct locus Mutations Recombining Regions
  • 6. 1. HISTORY OF THE CONCEPT DEFINITION 1940s-1950s Gene as a blueprint for a protein or as a physical molecule One gene One polypeptide
  • 7. 1. HISTORY OF THE CONCEPT DEFINITION 1960s Gene as transcribed code Central Dogma of Molecular Biology FUNCTIONAL PRODUCT
  • 8. 1. HISTORY OF THE CONCEPT DEFINITION 1970s-1980s Gene as open reading frame (ORF) Cloning + Sequencing + Genetic Code + Computational tools
  • 9. 1. HISTORY OF THE CONCEPT DEFINITION 1990s-2000s Annotated genomic entity, enumerated in the databanks… “DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology”
  • 10. 2. CONCEPT AND CONTEXT INSTRUMENTAL GENE Genotype + Phenotype Nucleotide sequence Structure + Function NOMINAL GENE POST GENOMIC GENE
  • 11. 3. CAUSES OF RENEWING THE CONCEPT B. GENE FUSIONS • NO clear structural boundaries • TRANSCRIPTS • Derived from both DNA strands • Overlap • Use the same coding sequences • EXONS A. COMPLEX TRANSCRIPTOME
  • 12. 3. CAUSES OF RENEWING THE CONCEPT D. INHERITABLE FUNCTIONAL STATUS C. ENCRYPTED GENES E. GENETIC RESTORATION Genes separated around the genome Epigenetic Non-Mendelian inheritance of extra-genomic information Are not heritable acquired characters?
  • 13. 4. CRITERIA TO FOLLOW Backward compatible Organism-independent Simple idea Practical Compatible with digital gene
  • 14. 5. NEW DEFINITION PROPOSED 1 Genomic Sequence Protein RNA UNION of all overlapping genomic sequences COHERENT done separately for final protein and RNA products 2 3
  • 15. 5. NEW DEFINITION PROPOSED “A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products"
  • 16. 6. REFERENCES • Akiva, P., Toporik, A., Edelheit, S. et al. 2006. Transcription- mediated gene fusion in the human genome. – Genome Res. 16: 30–36. • Gerstein, M., Bruce, C., Rozowsky, J., Zheng, D., Du, J., Korbel, J., Emanuelsson, O., Zhang, Z., Weissman, S. and Snyder, M. (2007). What is a gene, post-ENCODE? History and updated definition. Genome Research, 17(6), pp.669-681. • Lolle, S. J., Victor, J. L., Young, J. M. et al. 2005. Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis . – nature 434: 505–509. • Portin, P. (2009). The elusive concept of the gene. Hereditas, 146(3), pp.112-117.