A gene is an inherited functional unit of genetic material. In cellular organisms, a gene is a region of DNA whose information produces a functional RNA or contributes to a protein. This connects inheritance to cellular chemistry: a change in a gene can alter the amount or activity of a protein, and thereby a phenotype. See NHGRI: gene.
Alternative inherited versions at a genetic locus are alleles. The distinction matters: two parents can carry the same gene but different alleles, and a genetic locus can have variation outside a gene. Neither the word gene nor a change in DNA alone specifies the resulting phenotype.
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The human gene encoding a transcription factor implicated in speech and language development through rare pathogenic variants. Related genes in other vertebrates provide mechanistic models, but the human phenotype is not equivalent to any single animal motor task. A gene-to-phenotype relationship does not by itself isolate one affected brain structure.[ref]
A forkhead-domain gene is mutated in a severe speech and language disorder by Cecilia S. L. Lai and others. Nature 413, 519–523; KE-family cosegregation and independent chromosome-translocation case
The Drosophila gene encoding Hunchback. Maternal transcript regulation and Bicoid-dependent zygotic transcription are distinct developmental inputs.
A gene whose perturbation changes the timing of developmental programmes, for example reiterating an earlier cell-fate pattern at a later stage.
A Caenorhabditis elegans heterochronic regulator whose post-transcriptional control by lin-4 contributes to developmental timing.
A conserved DNA sequence encoding a homeodomain, shared by many transcription factor families. Not every homeobox-containing gene is a Hox gene.
A fly transcriptional-regulatory gene family involved in developmental and pigmentation patterns. Its interaction with developmental and chromatin regulators can affect temperature-dependent pigmentation.
A homeotic transcription-factor gene involved in posterior developmental identity in flies, with context-dependent effects on pigmentation regulation.
A gene whose regulatory variation contributes to wing-pattern differences in Heliconius; association with nearby preference loci does not prove that the same causal change controls both traits.
The intestinal alkaline-phosphatase gene used to mark enterocyte-lineage progenitors in experimental fate-mapping systems. A driver's initially labelled population must be verified before interpreting long-lived descendants.
In the Pseudomonas aeruginosa pathway, glcB encodes malate synthase. Its expression contributes to glyoxylate-shunt capacity.
In the Pseudomonas aeruginosa pathway, aceA encodes isocitrate lyase. Its transcriptional regulation changes potential enzyme capacity, not uniquely the instantaneous metabolic flux.
The MYC proto-oncogene regulates growth-associated gene-expression programmes. Retroviral promoter insertion near it provided an experimental example of transformation through deregulated expression of a cellular gene rather than carriage of a viral oncogene.
A proto-oncogene is a normal cellular gene that can contribute to oncogenic transformation when its expression or activity is altered. Its normal presence is not evidence that a cell is malignant.
c-src is the normal cellular counterpart of viral src, encoding a regulated protein tyrosine kinase. Conservation in normal cells distinguishes a proto-oncogene from an exclusively virus-specific genetic invention.
v-src is the transforming src determinant carried by Rous sarcoma virus. Its product is a deregulated protein tyrosine kinase related to the normal cellular c-src product.
A coding sequence is the part of a nucleotide sequence that specifies a polypeptide through the genetic code. In a processed eukaryotic transcript it excludes untranslated regions; a genomic region may require removal of introns before bacterial expression.
A receptor tyrosine kinase gene also called HER2, expressed at different levels in some tumours and normal tissues. Target abundance alone does not establish a safe therapeutic window.
A gene whose normal activity restrains tumour development. Loss-of-function alterations can be diverse, and allelic requirements vary among genes and contexts.
A microRNA whose endogenous activity restrains tumour development or progression in a specified context. Specific loss, controlled restoration and target tests provide stronger evidence than an expression correlation.
A gene whose altered activity can promote tumour development, commonly through activating or expression-increasing changes that retain a useful protein function.
The gene encoding the p53 regulatory protein, frequently altered in tumours. Different alleles can cause loss of function, dominant-negative effects or additional context-dependent effects.
The gene encoding the p110-alpha catalytic subunit of PI3K, with recurrent activating variants in cancers.
A RAF-family kinase gene with activating oncogenic variants such as V600E; the consequences of inhibition depend on the surrounding signalling circuitry.
A RAS-family gene whose activating mutations can promote constitutive growth signalling in multiple tumour lineages.
A conserved component implicated in the catalytic formation of programmed meiotic DNA double-strand breaks.[ref]
Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family by Scott Keeney and others. Cell 88, pp. 375–384; biochemical identification
A developmental transcription factor whose pelvic regulatory region provides an experimental example of localized cis-regulatory evolution in sticklebacks.[ref]
Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer by Yingguang Frank Chan and others. Pelvic enhancer deletion and restoration experiments
A fruit-fly developmental regulator whose targeted gene expression can induce eye structures in competent tissues at abnormal locations.[ref]
A regulator of the positions of meiotic recombination hotspots in relevant mammals. An engineered DNA-binding region rescued fertility in a particular mouse hybrid cross.[ref]
Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice by Benjamin Davies and others. Figure 1 and hybrid-fertility rescue
A developmental regulator associated with variation in beak shape in Darwin's finches.[ref]
Evolution of Darwin's finches and their beaks revealed by genome sequencing by Sangeet Lamichhaney and others. ALX1-region association with beak morphology
A regulator involved in establishing and maintaining local identities within repeated insect segments, downstream of earlier segmentation patterns.
A segmentation regulator associated with an initial double-segment periodicity in the early Drosophila melanogaster trunk.
A segmentation regulator whose altered activity can affect a broad contiguous region of the insect embryonic body pattern.
A member of the vertebrate HoxB cluster; sequential activation in progenitors can be coupled to their timing of entry into axial tissues.
A member of the developmental gene family assigning regional identities along the body axis. Temporal and spatial expression order can be related, but need not follow one universal rule in all animals.
A context-dependent tendency for posterior Hox functions to dominate more anterior Hox functions where their domains overlap. It is not a universal rule for all tissues.
A grouping of related Hox genes corresponding to an ancestral member retained in duplicated clusters. Sequence relationships, synteny and gene history jointly support the assignment.
A genomic grouping of related Hox genes whose organization can support shared and sequential developmental regulation. Clustering is widespread but is not a universal requirement for positional Hox expression.
The cis-regulatory domains flanking the mouse HoxD cluster. Developmental changes in enhancer contacts support distinct proximal and distal limb expression programmes.
An association between genomic position and expression level or prevalence in a developmental domain. It is a separate property from spatial and temporal order.
Sequential onset of Hox expression following genomic order in relevant developmental contexts. Rearrangements can alter onset timing without equivalently changing every later spatial boundary.
Correspondence between gene order and the anterior boundaries of Hox expression domains along a body axis. It must be distinguished from temporal collinearity.
An insect developmental regulatory gene; an avian hairy-related gene supplied early molecular evidence for a vertebrate segmentation clock.
Articles by others on the same topic
A gene is a fundamental unit of heredity in living organisms. It is a segment of DNA (deoxyribonucleic acid) that contains the instructions necessary for the synthesis of proteins, which perform a wide range of functions in the body, including structural, regulatory, and enzymatic roles. Genes are organized along chromosomes, which are structures found in the nucleus of cells. Each gene has a specific location, known as a locus, on a chromosome and can vary in size.
