What is a GENE?

GENOMICSMIRIAM SÁEZ

HISTORY AND CURRENT DEFINITION

INDEX

1. HISTORY OF THE CONCEPT2. CONCEPT AND CONTEXT3. CAUSES OF RENEWING THE CONCEPT4. CRITERIA TO FOLLOW5. NEW DEFINITION6. REFERENCES

1. HISTORY OF THE CONCEPT

DEFINITION 1860s-1900s

Particular characteristic+

Heritability

Gene as a discret unit of heredity

1. HISTORY OF THE CONCEPTDEFINITION 1910s

Gene as a distinct locus

Mutations RecombiningRegions

1. HISTORY OF THE CONCEPT

DEFINITION 1940s-1950s

Gene as a blueprint for a proteinor 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 genomicentity, enumeratedin the databanks…

“DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be

characterized by sequence, transcription orhomology”

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

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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 thehuman 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? Historyand updated definition. Genome Research, 17(6), pp.669-681.

• Lolle, S. J., Victor, J. L., Young, J. M. et al. 2005. Genome-wide non-mendelianinheritance 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