Genetics: What is a gene?

  title={Genetics: What is a gene?},
  author={Helen R. Pearson},
The idea of genes as beads on a DNA string is fast fading. Protein-coding sequences have no clear beginning or end and RNA is a key part of the information package, reports Helen Pearson.Genes wilderThe genetic code ‘cracked’,protein synthesis ‘solved’ and complete genomes sequenced: surely we now know what a gene is and what it does. That may be true for those safely outside the field. But for geneticists close to the action, the concept of a gene is getting very complicated indeed. 
What is a gene, post-ENCODE? History and updated definition.
This definition side-steps the complexities of regulation and transcription by removing the former altogether from the definition and arguing that final, functional gene products (rather than intermediate transcripts) should be used to group together entities associated with a single gene.
The "Mendelian Gene" and the "Molecular Gene": Two Relevant Concepts of Genetic Units.
Replacement of the “genetic program” program
In this work, genes turn out to be the producers and consumers of regulatory or developmental information, rather than entities encoding such information, and this finding has consequences that link up with a broader debate in the philosophy of biology concerning inheritance systems.
The gene and the genon concept: a functional and information-theoretic analysis
The original concept of the gene as a function encoded in the genome, basis of genetic analysis, that is a polypeptide or other functional product is returned, to set the stage for mathematical analysis of gene storage and expression.
Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology.
This work looks at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and defines a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.
Beyond the Gene
The proposal of a genetic functor, or genitor, is a sweeping extension of the classical genotype/phenotype paradigm, yet it appears to be faithful to the findings of contemporary biology, encompassing many of the recently emerging—and surprisingly complex—links between structure and functionality.
“Matreshka” genes with alternative reading frames
The properties of “matreshka” genes of the second type and methods for their detection and verification are focused on, with particular attention paid to the biological properties of the polypeptides encoded by these genes.


Tandem chimerism as a means to increase protein complexity in the human genome.
Strong evidence is provided that at least 4%-5% of the tandem gene pairs in the human genome can be eventually transcribed into a single RNA sequence encoding a putative chimeric protein, and that this phenomenon is a common mechanism with the potential of generating hundreds of additional proteins in thehuman genome.
Transcription-mediated gene fusion in the human genome.
It is demonstrated that at least half of these fusions exist in human tissues, and it is shown that unique splicing patterns dominate the functional and regulatory nature of the resulting transcripts, and found intergenic distance bias in fused compared with nonfused genes.
Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis
This work shows that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD can inherit allele-specific DNA sequence information that was not present in the chromosomal genome of their parents but was present in previous generations, and postulates that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.
The Transcriptional Landscape of the Mammalian Genome
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
The transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A– annotated transcripts and unannotated transcripts of unknown function, which has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.
Antisense Transcription in the Mammalian Transcriptome
Experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs is presented, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.
RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse
This work reports a similar modification of the mouse Kit gene in the progeny of heterozygotes with the null mutant Kittm1Alf (a lacZ insertion), identifying an unexpected mode of epigenetic inheritance associated with the zygotic transfer of RNA molecules.
A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT
An ncRNA repressor of the nuclear factor of activated T cells (NFAT), which interacts with multiple proteins including members of the importin-beta superfamily and likely functions as a specific regulator of NFAT nuclear trafficking is identified.
Interchromosomal associations between alternatively expressed loci
An example of eukaryotic genes located on separate chromosomes associating physically in the nucleus via interactions that may have a function in coordinating gene expression is provided and there seems to be a cell-type-specific dynamic interaction between interacting chromatin partners whereby interchromosomal interactions are apparently lost in favour of intrachromosomal ones upon gene activation.