I believe we are still a long way from fully incorporating all genomic features into the definition of the word "gene," but we're on our way there.

You may find the article below both interesting and informative.

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

I believe we are still a long way from fully incorporating all genomic features into the definition of the word "gene," but we're on our way there.

You may find the article below both interesting and informative.

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

How about: Gene is coding region for protein or functional RNA (ribosomal, tRNA etc.)  not regulatory RNA such as MicroRNA. Rest is regulatory region of a gene.

I direct you to interesting sites which can bring you without doubts of the answers to your question

http://www.liberation.fr/sciences/2012/0...-adn-seul-n-est-rien_84614

The expression of the new gene or genes can then alter the DNA or RNA transcript used to synthesis proteins and therefore correct the disease.

http://www.news-medical.net/health/What-is-Gene-Therapy.aspx

... and a few years down the road we might *discover* that the either the definition of the concept *DNA* is in need to be revised and changed - or the definition of the concept *Gene*....  How good are we at incorporating our "knowledge" on sub-atomic relationships and aspects within the current  definitions of "Gene-related" concepts? How about *life* - as in the second law of thermodynamics and maxwells demon?

just like a single word (science), containing a huge details. similarly In a simple word "the gene" we can define it as a region on chromosome specified for a function. but it needs classifications, explanations and sub definitions for complete understanding 

@Fadel: THe link does not work anymore, could you provide an updated link or upload the article?

I attach a link to a book addressing this issue with a historical perspective.

http://www.abebooks.it/servlet/BookDetailsPL?bi=15220711422&searchurl=an%3Dhans+jorg+rheinberger

Also you could read this paper, it might help you.

I consider safe to state that the cells do it in the reverse of what we are attempting to. When a product is present, the process of its production is repressed. When it is absent, the process is derepressed and all DNA segments and other components get into work to produce it. So, the gene is a construction at each right time and context. The process of construction also defines which of the alternative transcription and processing routes will be launched, and also the post-translational modifications, and so forth. This is the core of our 1992 MIMC Pardini and RC Guimaraes ´Systemic definiton of the gene´, available from this site. The natural definition is ´bottom up´, from product to producer, not ´top down´ as our theories are attempting to write. Thanks.

@Ulrich

Indeed the link does not work any more and thank you for link sharing

Regards

Thanks, Ricardo. One can not fail to notice reading the abstract of the paper, you have posted, that at the end of the day:"the gene is discrete genomic region ... portion of genetic information at the level of ultimate product (protein or RNAs)". i.e. Gene is a coding region for protein or functional RNA (ribosomal, tRNA etc.). rest is regulatory regions, elements etc. I think "ultimate product" is not quite correct, as Micro-RNA is a product but it is not involved in actual  chemistry/structure of a cell, just involved in change of concentration of FUNCTIONAL product ( be it a protein or rRNA etc.). So, I think brief definition above is up to the point. One might want to explain what functional RNA means by excluring non-functional (regulatory RNAs) as RNA not involved in chemical and  stractural elements of the cell.

Historically the problem was the relation between trait and gene. This remains problematic since there are the so called monogenic disease traits that are caused by mutation in a single gene although other genes may modify the phenotype to a Greater or lesser extent.

But even the operative definition that puts into relation genes, proteins and ncRNAs is problematic since there is certainly a physical equivalent, a genomic region, but it is hard to define this region since regulatory elements obviously are part of the "gene" yet it is hard to define what actually is a regulatory region. What contributes to gene regulation is highly context dependent and for a good part unknown.  

Definition of gene has been evolving since the introduction of this term by Bateson in 1905. It has been been changing with the understanding of new features of the gene. The definition of the term gene will keep on changing as we continue to know more and more about it. It is rather difficult to give a precise definition of gene; it can be best described. Definition of gene will vary depending on criteria we use - structural, functional, etc. 

If one try to include regulatory elements into gene definition, knowing complexity of gene regulation, both, expression and splicing, - one will ends up with physically very amorphous body (or practically without a body) And prevailing line of thought about what gene is that it is above all - physical element. To avoid this complication, one can define a gene as a continues region of DNA encoding functional RNA or protein. Remaining physical elements associated with a gene (all those promoters, enhancers, regulatory RNA etc.) are regulatory elements - not genes!. Same way as in a file there is a body of  text and plenty of labels: where are start of the text, where are new paragraphs start, notes to the text ets. This are not the text itself - just a notes helping to read the text correctly, some times reading different variants etc. 

I am less optimistic than Ricardo that we will have a clear and simple definition. One of the "worst" examples is splicing together RNAs transcribed from two different chromosomes. Or almost as "bad": splicing transcripts together from the opposite strands of a chromosome. This is no longer "one" region!

There is additional confusion with genes inside genes.

The term "functional RNA" was a bad idea! Are miRNAs not functional? Is Xist a "non-functional" RNA? What about protein coding genes that contain miRNAs (mirtrons)?

I am afraid we have to go for "functional terms" of a gene, well knowing that all definitions are imperfect

In my teaching I use the following definition:

a gene contains all DNA or RNA sequences required for the correct spatio-temporal expression of an RNA or a set of related RNAs

In reply to Wolfgang. miRNA is  "a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression". So, yes, it is non-coding and as such not a gene. Xist is functional RNA it is involved in Chromosomal structure forming a large (by nuclear size) physical complex. Yes it is involved in gene regulation, but on rather different scale than miRNA, - on a mass scale. Gene within gene is not a problem - it two genes shearing some sequence. I don't see any complications here. Mitrons are not genes just miRNA within genes. Trans-splicing is a bit of a problem but could be included in description as a rare exception of a split regions forming one gene variant. To go for "functional terms" is precisely to go for protein (has a function) and functional RNA ( involved in enzymatic, structural futures of chromosome/macro-molecules etc.), and exclude regulatory RNA - not involved in latter, just regulating levels of functional RNA and proteins and variants of functional RNA/proteins to be expressed.

The discussion of miRNAs, lncRNAs, mitrons ecc (one might add Others like piRNAs etc) is in my eyes not a real problme. If it were to find a name for these objects there could be simply many different names that have in common to be encoded by DNA. We need, if we need it, the term "gene" in relation to "traits". Since this relation is complex and involves many different molecules (such like mRNAs, miRNAs, lnsRNAs, proteins etc) the definition of the coding power behind a phenotypical trait is very complex.

I might be wrong, but it's impossible to built gene definition using trait as a base. Precisely due to the fact that trait very often is multi-gene phenomenon. One might have consider a trait as a possible deciphering "code" behind a gene, but only in the case of one to one relationship. In fact, one gene sometimes plays role in multiple traits, so there is no way to use trait as bases in gene definition. And in simple logic, genes are behind traits, not the other way around.

@Dmitry: That's why I'm not sure that we need a definition of the term "gene". Everybody understands when I refer to the "gene" PTGS2 or the "gene" mir281b or the "gene" H19. I refer to regions of the genome able to encode RNA products that can or cannot be translated into protein, that have regualtory regions etc.

When I say the "gene" for phenylketonuria the problems begin, since there is one "gene" linked to this condition, but the phenotype depends on other "genes" and the environment (in an environment devoid of phenylalanine there is no specific phenotype).

@Ulrich: agreed. I guess, I misunderstood your point. I agree that biologist, probably, don't need rigid  formal "gene" definition. Discussion here is, may be, related to for-student definition, and as we see, everybody has it's favorite one. Thank god, I am not teaching. :)  

But teachers like me do need a definition of gene at least for students' curiosity. As a  precise definition of gene is really not possible, it will be better to describe term gene with ifs and buts depending upon level of the students attending a course.

I ponder that at every instance of discussion, it is wise to try to distinguish clearly, especially for the students, the two points of view: (1) of the cells, that are the real users of the material and functional genes; (2) of us, describers, humans, attempting to use some kind of rationality or logic, which we don´t know if coincids or not with the cell´s. Difficult task: attempting to understand nature, from it´s point of view or through our point of view? Thanks again, colleagues.

Yes, you are right, Dr. Romeu Guimaraes. There is a problem.

Collection of Gene definitions (few)

As per Pearson Campbell Biology "A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule."

Or

"A discrete unit of hereditary information Consisting of a specific nucleotide sequence in DNA (or RNA in some viruses). "

Evolution Douglas J. Futuyma (Third Edition) "The functional unit of heredity."

NIH (National Human Genome Research Institute) "The gene is the basic physical unit of inheritance. Genes are passed from parents to offspring and contain the information needed to specify traits. Genes are Arranged, one after another, on structures called chromosomes. A chromosome contains a single, long DNA molecule, only a portion of Which corresponds to a single gene. Humans have 20,000 genes Approximately Arranged On Their chromosomes. "

University of Utah, Health Sciences "Genes are instruction manuals for our bodies. They are the directions for building all the proteins did make our bodies function."

UMLS (Unified Medical Language System) US National Library of Medicine "The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein." 

University of Washington & NCBI (National Center for Biotechnology Information) "The basic unit of heredity, Consisting of a segment of DNA Arranged in a linear manner along a chromosome, Which codes for a specific protein or segment of protein leading to a Particular characteristic or function. "

National Human Genome Research Institute  "The gene is the basic physical unit of inheritance. Genes are passed from parents to offspring and contain the information needed to specify traits. Genes are Arranged, one after another, on structures called chromosomes. A chromosome contains a single , long DNA molecule, only a portion of Which corresponds to a single gene. Humans have 23,000 genes Approximately Arranged On Their chromosomes. "

Human Genome Project Information US Department of Energy "The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a position on a Particular chromosome That Encodes a specific functional product (ie a protein or RNA molecule)."

Elmar Schmid, San Diego Mesa College "Each existing and individual organism Consists a hidden plan, or blueprint, for the development, synthesis invisible information Containing elements, called genes, are made of a distinct matter or molecule; today we know dass die Heredity-carrying molecule is a nucleic acids called the DNA. "

UIC (University of Illinois) "Gene - basic unit of heredity; codes for a specific trait."

Scitable by Nature Education "A region of DNA (deoxyribonucleic acid) coding Either Hanes messenger RNA encoding the amino acid sequence in a polypeptide chain or a functional RNA molecule for."

Understanding Evolution. Your one-stop source for information on evolution "The unit of heredity. Generally, It Means a region of DNA with a Particular phenotypic effect. Technically, it may mean a stretch of DNA did includes a transcribed and regulatory region."

Evolution - Mark Ridley (Third Edition) "Specifically, a gene is a sequence of nucleotides coding for a protein (or, in some cases, part of a protein) A gene may exist in alternative forms, called alleles Most genes have Existed .. unaltered for millions of years; Genes do not change except in the rare event of mutation ".

More Generally, a gene is the unit of heredity. Williams defined the gene as "That Which segregates and recombines with appreciable frequency."

On this definition, the gene can be any length of chromosome That has Sufficient permanence for natural selection to adjust its frequency; It is what Dawkins calls the replicator. This is important: because it tells us what it is, indeed adaptations benefit.

Biologists disagree about what Exactly a gene is. The geneticist Linda Partridge gives her own definition. "The definition of a gene has itself evolved over the years. Now we would recognize it as a sequence of nucleotides coding for a product, Either a protein product or a RNA product plus all the other sequences round about that control the way That gene is turned on and off in different sexes, in different parts of the body and at different times during Their life history. " 

many investigators have focused on epigenetic inheritance, in which information is passed from parent to offspring independent of the DNA sequence.

Pp 469 - Minoo Rassoulzadegan’s team at the French National Institute for Health and Medical Research (INSERM) in Nice, France, reports that RNA may sometimes be complicating traditional models of inheritance

http://paul.representinggenes.org/Stotz/OtherPapers/Pearson.Gene%2006.pdf

Krishnan you have raised important point. Genomic Imprinting/Epigenetics hot topic of science. Mono alleleic expression/Parent of origin dependent contradict classical Mendelian Genetics. Interestingly this phenomena (genomic imprinting) is specific to mammals.

Bartolomei MS & Tilghman SM. Genomic imprinting in mammals. Annual Reviews of Genetics. 1997;31:493-525.

http://learn.genetics.utah.edu/content/epigenetics/imprinting/

Thanks, Jetty! Very nice eclectic collection. Personally, I like US Department of Energy definition:

 "The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a position on a particular chromosome that encodes a specific functional product (i.e. a protein or RNA molecule).",

which, BTW, does not bother to include regulatory elements directly into defenition.

If one tries to include regulatory elements, in my opinion, Linda Partridge's definition works great, with possible highlighted changes:

"Gene is a sequence of nucleotides coding for a product, either a protein or a RNA, plus all the other sequences round about that control that gene temporal and spatial expression on cellular and organism level, and has sufficient permanence for natural selection to adjust its frequency."

The last, italic  one, comes from Dawkins, and just substitutes well for "The fundamental physical and functional unit of heredity" BUT! explaining what is "unit of heredity".

@Dmitry: but thisa definition is problematic in the case of multigenic inheritance where "the functional unit" would be many "genes".

Giving a precise definition of gene is the biggest challenge of biology as no one definition would be able to include all the features known about gene. Certainly the present discussion is a very good exercise in this direction.

All products coming out of these nucleotides are inheritable?

@Ulrich: I think there is a difference. Inheritable trait is one thing. Inheritable sequence of a gene (be it one in a set of determining that trait) is another. Functional unit here is about a gene. It does determine a composite nature of a trait in a way that it sequence conserved and some mutation is beneficial, other - harmful. So as such it is "functional unit" on a gene level, not on a trait level. 

I like the discussion on traits ;-)

what is a trait? yellow peas? a short tail of a cat? multi-factorial phenotypes like open-field activity in mice (you have to do an experiment to find out)? lactose intolerance (you have to drink milk first to find out!)? a predisposition to get a certain type of cancer (you may find out by PCR)? a difference in microsatellite repeats (you have to do a PCR)? a difference in one nucleotide in the rRNA spacer sequence (you have to do sequencing to find out)?

In my opinion a trait (in the sense of genetics) is whatever you look for and that comes in different flavors due to genetic differences.

My point was that historically the problem was the relation between traits (phenotype) and genes (genotype). The problem in this relation is that what we intuitively call "gene" is not the functional unit encoding a "trait" since even the trait phenylketonuria comes in different manifestations that most likely depend on modifier genes.

We have been grown with the concept of "the gene for this or that" which created the idea that there is a univocal relation between genes and traits. Today we know that traits encoded in the genome with one or several elements ("genes") having a highly penetrating effect and many others having a tiny effect (if we could measure it, most likely any gene has some effect on any trait though most of the times a very small one).

If it is not for the trait-gene relation, so what do we need the definition of gene for? Or in other words, we could keep completely out any reference to inheritance and accept a pragmatical definition like "a stretch of DNA or RNA (in some virus) that contains sequences that are transcribed to form functional RNA molecules and the related regulatory sequence elements whereby different genes may refer to overlapping DNA sequences or sequences on opposite strands of the same stretch".

@Ulrich: Agreed, that there might have been a problem in the past with misunderstanding gene-trait relationship, but, I think, it is long passed. These days and for some time already, the complexity of gene-trait association is known, if even not deciphered in many cases. And although " "gene" is not the functional unit encoding a "trait", ensemble of genes are, each one playing it's own role, and trait will be different without participation of each instrument in that orchestra!  To put it in Dawkins terms: We need understanding of what gene is, because it is a cogwheel in "Blind watchmaker" mechanism. And if you don't now it structure and properties, you can't understand how watch is build and how it is able to function the way it does. Don't you think? Traits is "essence" of organism but genes are "structure" of that essence. In other word, one can not talk seriously about "molecule" structure or properties without knowing what "atoms" are. I don't think I am overstretching my analogies here. :)

@Dmitry: it's not essence and structure. No doubt that it is importnat to study and to understand "genes". But the term "gene" as related inheritance is hard to define and as related to functional molecules it's relatively easy, important to know that there is no tight relation between these two aspects of "gene".

At the beginning of the 20th century Western biology favored the concept of "one gene - one trait" whereas Sovjet biology postulated inheritance as a transcendent activity of the genome in its whole. Than many genes causing so-called monogenetic diseases were found and the Western concept seemed "true". But now we know that its the whole genome to define traits with parts of the former making different contributions that in the extreme case appear as "monogenetic" though they are not. A kind of synthesis of the two concepts. Importantly, this new concept has not been received by laymen.

As mentioned by Dmitry "gene" is not the functional unit encoding a "trait".

Absolutely correct.

Wolfgang n Ulrich mentioned about this.

Shall we call the trait as Phenotype!!

Phenotype = Genotype (G) + Environment (E) + Interaction of both G and E.

Gene is DNA or RNA (in some viruses) piece which when expresses affects some biological property of an organism. Presence of a functional gene is felt from its expression.

Jetty is certainly right and also Ulrich's comparison between western and Soviet genetics is an interesting and important contribution.

But I am afraid that we have lost the original question what a gene is ;-)

Yes Wolfgang you are right when mention about Phenotype itself I thought of telling topic is getting diversion. Forgot to add.  

Anyway it is related to Gene(tics)

@Ulrich: I agree with your point. There is a difference between two major scientific approaches: from top to bottom (holistic) or from bottom to top. Each approach has it pluses and minuses and each has it admires. I understand, that there could be a difference for the same (identical) gene set manifestation in different genomic backgrounds, potentially producing qualitatively different trait. BUT as long as the same set of genes manifest itself the same way in the same genomic background, approach from gene to trait is valid one. Contribution of each gene in the set to some trait characteristic can be measured and explained. I personally, prefer that approach because it follows Nature logic: genes determine traits, very direct and understandable thing. There is feedback from traits to genes sequence on evolutionary scale much less direct and manifesting itself on the level of population (much more complex phenomena). So I prefer genes – traits approach be it with some complexity of what exactly gene is. I hope I understood your point correctly. :)

To discuss the definition of the gene, one needs to discuss the gene centric concept.

Since the gene only codes for the “part inheritance” rather than the “system inheritance” or blueprint, by and large, there is no precise correlation between “gene” and phenotype.  We have introduced the “genome theory” to address this issue.

Please read the article I published a few years back.  Our group is pushing this concept further and I appreciate your comments/advice.

Bioessays. 2009 May;31(5):512-25.

The genome-centric concept: resynthesis of evolutionary theory.

Abstract

Modern biology has been heavily influenced by the gene-centric concept. Paradoxically, this very concept--on which bioresearch is based--is challenged by the success of gene-based research. To overcome this major roadblock, it is essential to establish new theories, to not only solve the key puzzles presented by the gene-centric concept, but also to provide a conceptual framework that allows the field to grow. This paper discusses a number of paradoxes and illustrates how they can be addressed by the genome-centric concept in order to further resynthesize evolutionary theory. In particular, methodological breakthroughs that analyze genome evolution are discussed. The multiple interactions among different levels of a complex system provide the key to understanding the relationship between self-organization and natural selection. Darwinian natural selection applies to the biological level due to its unique genetic and heterogeneous features, but does not simply or directly apply to either the lower non-living level or higher intellectual society level. At the complex bio-system level, the genome context (the entire package of genes and their genomic physical relationship or genomic topology), not the individual genes, defines the system and serves as the principle selection platform for evolution.

Article link:

http://www.ncbi.nlm.nih.gov/pubmed/19334004

Heng Lab: http://genetics.wayne.edu/heng/lab/Home.html

In despite of recent findings, including alternative splicing and alternative promoters, the genes could still be defined as units of biological information and units of inheritance.

I am very happy to see that Henry Heng´s proposal converges and complements quite nicely MIMC Pardini and RC Guimaraes´s 1992 Systemic Concept of the Gene, that can be found in this ResearchGate depository. Thanks a lot.

With all proposed so far we can define what is a gene?

Dear Andrei

The fine and accuracy definition of a gene cannot be in a short statement but need many parts of a book , because definition must include structure ,functions and its relation with other genes , gene expression... etc .

Good Luck

It is not possible to give a one-line or two-line definition of a gene. Even a 10-line paragraph may not fully define a gene to include all different structural and functional aspects of gene.

Two important yet often ignored facts are:  1) gene codes “parts inheritance” while genome (karyotype) codes “system inheritance” or blueprint (by coding the genetic network structure). 2) the mechanism of genetic coding is rather “Fuzzy”.  That is the reason that we have pushed the concept of “Fuzzy inheritance”. 

Please check out one of our new papers: “Genotype, environment, and evolutionary mechanism of diseases”

Link: http://www.environmentmed.org/temp/EnvironDis1114-2218056_060940.pdf

If more info is needed, please see my recent book:  Debating Cancer: the paradox in cancer research

Link:

http://www.worldscientific.com/worldscibooks/10.1142/8879

I have glanced at Henry Heng's paper “Genotype, environment, and evolutionary mechanism of diseases” at http://www.environmentmed.org/temp/EnvironDis1114-2218056_060940.pdf. Find the paper very interesting. We know gene-environment is a very complex interaction. The more we are trying to unravel this secret relationship, more complex it is found to be. This relationship seems to be individual-specific rather than general.

Perhaps citing the characteristics of the gene we can begin to structure a new definition, I have these features:

1. ability to store information (proteins, DNA and regulation systems rep.).

2. stability in the system of information and fidelity in the transmission.

3. ability to express the information (code for the phenotype).

4. ability to accumulate changes over time (substrate for evolution).

5. ability to influence in regulation of chemical processes.

Thanks everyone for your contribution!!

The sequences that are involved in regulation of gene expression are also an important characteristic of gene.

The systemic concept of the gene, Pardini and Guimarães 1992, can be followed to say that there are the functional and the structural aspects. The functional may be easier, but both are complex. Functional: genes are memories that the system uses for the synthesis of proteins, which are the ultimate functional products. The memories include the protein sequences and all other components of the protein synthesis machinery and of gene regulation. Structural: I consider it is extremely difficult to try to define from the top down. It should be easier to do it from the bottom up, from the product to reconstruct the pathways that were taken to obtain it. Thanks to you all for the attention.

Depending species, one gene can have only one function or multiple functions(specially in higher organisms).

Things may become easier if we define a gene in relation to its product (transcript) in terms of a primary cellular function.

A gene is the part of a cell in a living thing which controls its physicalcharacteristics, growth, and development.

Yes, this is in the right direction. See the systemic (functional) concept of the gene, Pardini and Guimarães 1992. Happy New Year! Let it be better than 2018, which was not that much.

As we are knowing more and more about gene, the definition of gene is getting more and more complicated. A one-line definition of gene is no more possible. Rather we can describe a gene from various points of view, e.g., structure, function and regulation.

See Pardini and Guimarães 1992, available here in ResearchGate. A Systemic Concept of the Gene. The ´cell/organism system´ searches for what is necessary along the whole genome to conjoin a set of sequences - the gene at that time and context - that will correspond to the function it needs. The gene belongs to a system. It is the system that matters, with its metabolic dynamics. The gene(s) may vary across contexts and along times. Yours, Sincerely, Romeu.

I agree with you Dr. Romeu Guimaraes .