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I know that gene is a segment of DNA that codes for a specific protein. But is it a segment of a single DNA molecule or a DNA duplex?

The given image shows a section of a dsDNA.

enter image description here

Source of image: https://en.wikipedia.org/wiki/Intron#/media/File:Gene.png

Suppose its the blue portion that codes for a particular protein. However, the figure tells that the blue portion + its complementary red portion make a gene. Shouldn't the blue portion alone be considered the gene for that particular protein ?

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  • $\begingroup$ As you have recently edited this old question, I assume you are keen to have it discussed. Although I have already answered, I intend to revise my answer extensively Could you therefore clarify two points. 1. Are you asking (a) Whether the term gene, as it is generally used in science (and defined in textbooks, for example), is restricted to one strand, OR (b) Should the term gene which does not normally have this stipulation, be changed or clarified to restrict it to one strand. 2. Are you sure which strand? The strand actually copied into mRNA is the red anti-sense strand. $\endgroup$
    – David
    Sep 11 at 11:54
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None of the highlighted regions in your figure, is a gene. A gene is a section of DNA which gives rise to a product. Basically, a gene has an orientation (5'→ 3') i.e. it is essentially a single stranded region. However, the strand that mechanistically contributes to RNA synthesis (template) has the reverse-complementary sequence of the gene (in other words, anti-sense). Therefore, a gene, as it is annotated is not a functional entity but a genomic representation of a product. Some viruses (such as M13 phage) have a single stranded genome; for them the transcript is always antisense to the genomic DNA region.

Same section of dsDNA can harbour multiple genes in both orientations and this is clearly seen in viruses which have an highly compact genomes. Other prokaryotic and eukaryotic genomes also have overlapping genes.

Some related posts:


Does that mean only the indicated region of molecule A is a gene? Or, does the Indicated portion of molecule A + Complementary portion present in molecule B comprise a single gene, such that A is sense and B is non-sense strand of the same gene?

If the molecules A and B are expressed from opposite strands, then they are considered products of different genes, even if the gene region overlaps.

The situation is more unclear if both the molecules are expressed from the same strand and the transcribed region overlaps. Sometimes they are classified under the same gene (splice variants) and sometimes they are not.

These are some lines from the human genome annotation file which tells the location of genes in the genome (+ and - denote opposite strands):

chr1    HAVANA  gene    1567474 1570639 .   +   .   gene_id "ENSG00000189409.8"; transcript_id "ENSG00000189409.8"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "MMP23B"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "MMP23B"; level 2; havana_gene "OTTHUMG00000074713.4";
chr1    HAVANA  gene    1590786 1594063 .   +   .   gene_id "ENSG00000272004.1"; transcript_id "ENSG00000272004.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "RP11-345P4.10"; transcript_type "antisense"; transcript_status "NOVEL"; transcript_name "RP11-345P4.10"; level 2; havana_gene "OTTHUMG00000185638.1";
chr1    HAVANA  gene    1603429 1604850 .   +   .   gene_id "ENSG00000269737.1"; transcript_id "ENSG00000269737.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "RP11-345P4.7"; transcript_type "antisense"; transcript_status "NOVEL"; transcript_name "RP11-345P4.7"; level 2; havana_gene "OTTHUMG00000182604.1";
chr1    HAVANA  gene    1604714 1605836 .   +   .   gene_id "ENSG00000269227.1"; transcript_id "ENSG00000269227.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "RP11-345P4.6"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "RP11-345P4.6"; level 1; tag "pseudo_consens"; havana_gene "OTTHUMG00000182605.1";
chr1    HAVANA  gene    1570603 1590473 .   -   .   gene_id "ENSG00000248333.3"; transcript_id "ENSG00000248333.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CDK11B"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CDK11B"; level 2; havana_gene "OTTHUMG00000078638.4";
chr1    HAVANA  gene    1592939 1624167 .   -   .   gene_id "ENSG00000189339.7"; transcript_id "ENSG00000189339.7"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "SLC35E2B"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "SLC35E2B"; level 2; havana_gene "OTTHUMG00000078639.1";
chr1    HAVANA  gene    1634169 1655766 .   -   .   gene_id "ENSG00000008128.18"; transcript_id "ENSG00000008128.18"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "CDK11A"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "CDK11A"; level 2; havana_gene "OTTHUMG00000000703.14";
chr1    HAVANA  gene    1634175 1669127 .   -   .   gene_id "ENSG00000268575.1"; transcript_id "ENSG00000268575.1"; gene_type "processed_transcript"; gene_status "NOVEL"; gene_name "RP1-283E3.8"; transcript_type "processed_transcript"; transcript_status "NOVEL"; transcript_name "RP1-283E3.8"; level 2; havana_gene "OTTHUMG00000183552.1";

Not evident in these examples but there are many overlapping genes in opposite strands. Anti-sense lncRNAs would be an example to have a quick look at.


Bottomline: The definition of gene is constantly changing but usually a gene has an strand orientation. The opposite strand can also sometimes synthesize a product but it is considered a different gene in that case.

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What is a gene?

The term gene was coined in 1909 “to describe the Mendelian unit of heredity”, long before it was suggested and established that these units resided in the chromosomal DNA of organisms.

I would suggest that this definition is as good as any that followed the latter discovery. Thus, modern general dictionary definitions such as the one below from Mirriam–Webster are an explanation to the layman of the chemical nature of genes, and the example given of lay usage bears no relation to this.

Definition of gene
a specific sequence of nucleotides in DNA or RNA that is located usually on a chromosome and that is the functional unit of inheritance controlling the transmission and expression of one or more traits by specifying the structure of a particular polypeptide and especially a protein or controlling the function of other genetic material

Examples of gene in a Sentence
She inherited a good set of genes from her parents.

I am most surprised that @WYSYWYG wrote:

A single gene is on one of the DNA strands, not both.

In my whole career as a molecular biologist I have never read this in any textbook or research paper, and challenge him or anyone else to produce one. So despite the votes for his accepted answer, I would maintain that it is incorrect and that in general scientific usage

In referring to genes encompassing regions of a double-stranded DNA chromosome, the term includes both strands.

When it was found by sequencing that certain bacterial genes overlap (I remember it well) there was no redefinition of the word gene.

Supporting argument

It is difficult to support my point of view just by saying “I have never heard anyone use the term that way”, so let us consider the implications of the ‘one-stranded gene’ thesis.

The concern would appear to be that only one strand of the DNA is transcribed into the precursor of the mRNA that is expressed as protein. On the ‘one-stranded gene’ thesis the gene would only be on the anti-sense strand — the strand complementary to the mRNA.

Let us now consider the genes of viruses — nobody would deny viruses have genes. However some viruses, both DNA and RNA viruses are single stranded. Single-stranded DNA viruses come in both ‘flavours’ — what are called ‘positive sense’ and ‘negative sense‘ genomes. And paroviruses package single-stranded DNA of both types. So clearly among these genomes are heredity units in the DNA that are not ‘anti-sense’ as well as some that are ‘anti-sense’. On the ‘one-stranded gene’ thesis these would not be genes, but would only become so when the double-stranded replicative form of the DNA was formed! This is patently absurd!

Likewise there are positive and negatively stranded RNA viruses. In the positive-stranded ones the genomic RNA is also the mRNA, but in the negative-stranded ones it is not. Presumably this latter genome has no genes at all, perhaps it is even wrong to say it has a genome.

Conclusion

Scientific terminology can be important for clarity of communication. However gene terminology is not of that type. Our knowledge of the structure of genes has developed, but rather than argue about what precisely is a gene (do we include introns?) we describe its different structural features and try to understand their function.

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  • $\begingroup$ May be my poor wording but there can be two different genes oriented in opposite direction but at the same dsDNA locus. Sometimes mRNA isoforms are considered to be the products of the same gene but antisense transcripts are considered products of a different gene. That's what I meant. However, the definition of gene is still being constantly updated. The last comprehensive article I read, that called for redefining a gene, was in 2007. $\endgroup$
    – WYSIWYG
    Sep 8 at 13:08
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    $\begingroup$ On units of inheritance. Traits can be inherited via cis regulatory elements that are not considered a part of a gene. So that definition is also not perfect. $\endgroup$
    – WYSIWYG
    Sep 8 at 13:09

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