I. Characterizing the Concept of ‘Genetic M aterial’

1. I. Characterizing the Concept of ‘Genetic Material’

2. ‘Genetic Material’ • Acomplex and nuanced concept with varied interpretations, and about which there is a long history of discussion and debate. • see https://groups.google.com/d/msg/obi-developer/EdqD5EZ8rFg/NpcIqeRp_QwJ • Need for a shared, clearly defined class for this concept that is precise enough to allow us to determine what things do and do not qualify in the domain of experimental biology.   • External requirements and use cases coming from Asiayah, and other ontologies such as GENO and SO which use this term.Internal use cases for this class stems mainly from use of the term 'genetic material' in definitions of many key OBI classes (next slide)

3. OBI Definitions Referencing ‘genetic material’ genetic transformation - the introduction, alteration, or integration of genetic material into a cell or organismgenetic modification design - a study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. genetic characteristics information - a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.genotype information - a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.

4. Key Criteria For Defining this Concept • 1. ‘Organismal’ Nucleic Acid: part of a host cell or virion or viroid • any cell, not just gametes (e.g. terminally differentiated neurons) • DNA of a dead/fixed cell does not qualify, nor does a genomic DNA extract (these would be 'genetic material specimens'?). • 2. ‘Heritability’: • a) Any nucleic acid in a cell does not qualify (e.g. an injected oligo or • plasmid) - must be heritable by progeny or inherited from an ancestor • in dividing cells, it must be capable of replication & inheritance by progeny • in non-dividing cells, this disposition for inheritance is not relevant, but nucleic acids inherited from its immediate ancestor cell would qualify* • b) Nucleic acids gained through a horizontal gene transfer, such as conjugation or experimental incorporation, can still qualify if they are incorporated in such a way that they are capable of inheritance by progeny • experimentally delivered plasmids or transposons or extra-chromosomal arrays that are replicative, and therefore able to be passed to successive generations of progeny (may or may not be integrated into the chromosomal genome)

5. Proposed Definitions • Proposal from 2011 following  listserv and call discussions: • Concern:Defined at level of organism instead of cell/virion • 1. Not all genetic material is 'part of an organism' (e.g. can be part of a cell culture). • 2. Cells (and virions) are the more fundamental level at which ‘genetic material’ is inherited • The phrase 'derived from immediate ancestor' in the definition above seems to imply that all my genetic material must be physically derived from my parents • This is not the case for most of what we would consider my genetic material content (e.g. the nuclear DNA of my somatic stem cells or neurons is not physically derived from my ancestors) • Rather, such physical continuity holds at the cell/virion level of replication - where genetic material is physically duplicated and passed as nucleic acid molecules to progeny. This is the fundamental level at which ‘genetic material’ applies. “a nucleic acid macromolecule that is part of an organism and is either derived from an immediate ancestor or incorporated in a manner that it has the disposition to be replicated in its descendants”

6. Revised Definitions 2011 Proposal: “a nucleic acid macromolecule that is part of an organism and is either derived from an immediate ancestor or incorporated in a manner that it has the disposition to be replicated in its descendants” Revised Definitions: 1. Proposed: “a nucleic acid macromolecule that is part of a cell or virionand is inheritedfrom an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants.” 2. Simpler: “a nucleic acid macromolecule that is part of a cell or virion and has the disposition to be replicated and inherited by descendants.”* 3. More Explicit: “a nucleic acid macromolecule that is part of a organism and is inherited from an immediate ancestor cell or virion, or incorporated in a manner that it has the disposition to be replicated and inherited by descendant cells or virions.”

7. II. A Further Refinement?

8. ‘Genomic’ vs ‘Genetic’ Material • An alternative proposal for defining ‘genetic material’ was for it to cover “any nucleic acid part of a cell/virionthat is manifest in gene expression of its host” • a more inclusive concept with no ‘heritability’ criteria, so things like and transiently transfected expression constructs would qualify • Value to defining an additional class to represent this broader group of entities as well? • is this concept referenced in OBI definitions (genetic transformation*, genetic modification design)? • Labels? • Our first set of criteria which focus on ‘heritability’ seem to describe what is in a genome**. “the entirety of an organism's hereditary information (macromolecules)” • consider distinguishing ‘genomic material’ from ‘genetic material’?

9. ‘Genetic’ vs ‘Genomic’ Material • These labels may not be ideal and will likely be changed – the key point here is that there is a need to define classes for these two concepts in OBI, as they are referenced in defining several related terms (see slide 3) • ‘genetic material’ • SubClassOf:nucleic acid • Definition: a nucleic acid macromolecule that is part of a cell or virionand has the disposition to affect gene expression in its host • Comment: This class includes any nucleic acid that participates in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA). It is not necessarily heritable by progeny or inherited from ancestors, so things like transiently transfected plasmids and siRNAs would qualify. • ‘genomic material’ • SubClassOf: genetic material • Definition: genetic material that is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants

10. Test Examples: • Classify the following: (as ‘genomic material’, ‘genetic material’, neither, or both) • chromosomal* DNA in germ cells, stem cells, fully differentiated cells • chromosomal DNA in cell line cells • DNA/RNA content of a virion • a gene targeting DNA construct transfected into a cell • prior to chromosomal integration • following chromosomal integration • a stable extra-chromosomal replicon delivered into dividing cells (e.g. a plasmid in bacterial host with ori allowing indefinite propagation) • a stable extra-chromosomal replicon delivered into a culture of fully differentiated cells (e.g. neurons) • DNA or siRNA expression constructs transiently transfected (not disposed for chromosomal integration or extra-chromosomal replication) • a microinjected siRNA oligo in a cell • DNA in fixed cells? nuclear DNA extracts? • a cloning vector propagated in bacteria that is not expressed**