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A neurogenic transcription factor whose role in direct neuronal conversion illustrates context-dependent chromatin engagement and hierarchical factor action.^[ref]

A mammalian stress-responsive transcription factor. Its synthesis can increase when ternary complex is limited because its leader contains regulatory upstream open reading frames.^[ref]

A T-box transcription factor important in posterior and mesodermal development, commonly used with Sox2 to identify neuromesodermal progenitors.

A homeobox transcription factor involved in posterior patterning and temporal regulation of insect segmentation.

A homeobox transcription factor used as a trophectoderm-associated regulator and marker, with species- and stage-dependent expression.

Cell differentiation is the acquisition of a specialized cell state, involving changes in structure, function and gene expression. A neuron and a red blood cell illustrate different outcomes: signaling and oxygen transport. Different functions usually do not require a different inherited DNA sequence for each function. The shared-genome principle concerns nucleated precursors and most nucleated descendants: a mature mammalian red blood cell has lost its cell nucleus and mitochondria, so it is not an example of two mature biological cells both retaining the same nuclear DNA. ^[ref]

The puzzle is how a shared set of genes supports different jobs. Gene expression changes which RNA and proteins a biological cell produces, and in what amounts. A transcription factor can regulate several genes; different combinations of regulators can interpret the same signal differently. Stable regulatory patterns can persist through the cell cycle, providing memory of developmental history. Specialization therefore usually changes use of inherited information, rather than replacing the genome wholesale. ^[ref]

A small counting example separates sequence from activity. Suppose the same three toy genes are present in every nucleated biological cell, and independently assign each gene an on/off state. There are $2^3=8$ possible expression profiles with no DNA replacement. The figure shows only two: H and A on versus H and B on. Real gene expression is graded and coordinated, so this count illustrates possible descriptions, not a prediction of eight actual cell types. The interesting consequence is that a stable cell state can depend on how a shared record is used.

Stem cells combine self-renewal with production of differentiated descendants; progenitor cells generally have more restricted developmental options and renewal capacity. Neither term means that a biological cell must give rise to every cell type. Terminal differentiation denotes advanced specialization within a lineage, often accompanied by exit from the cell cycle. Cell fate concerns the developmental outcome of a biological cell or its descendants, whereas cell state describes its current properties. A temporary change in gene expression after signal transduction is not, by itself, proof of a new cell fate. ^[ref]

A Sox-family transcription factor involved in developmental regulation, including insect segmentation timing.

An NF-kappaB-family maternal transcription factor whose ventral nuclear enrichment patterns the early Drosophila melanogaster embryo. Its name does not mean its nuclear activity is highest dorsally.

A forkhead-family transcription factor associated with axial mesendoderm and definitive endoderm specification.

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 GATA-family transcription factor used among markers of more mature hypoblast identity.

A GATA-family transcription factor associated with early hypoblast development; its initial coexpression with NANOG can precede lineage resolution.

A transcription factor family recognizing GATA-related DNA motifs. Successive GATA factors can implement specification, stabilization and differentiated gene expression in a developmental gene regulatory network.

A yeast transcription factor regulated through several upstream open reading frames during amino acid starvation.

A conserved DNA sequence encoding a homeodomain, shared by many transcription factor families. Not every homeobox-containing gene is a Hox gene.

A DNA sequence recognized by an activated hormone-regulated transcription factor. It connects ligand-dependent regulator activity to a particular target gene.

A Drosophila transcription factor supplied through maternal and zygotic expression. Posterior Nanos-dependent repression of the maternal messenger RNA and anterior Bicoid-dependent transcription make distinct contributions.

In an incoherent feed-forward loop, the direct path from an input to an output and the indirect path through a second transcription factor have opposite net signs. Their different response times can generate a pulse or adaptation. A nonzero basal production rate makes the final adapted output nonzero, so its logic and response time must be calculated from the actual gene regulation rule rather than assumed from a Boolean label.

A Krüppel-like transcription factor associated with the human early pluripotency programme and used in panels of epiblast markers.

A threshold approximation in which a regulatory input permits or blocks production according to whether a transcription factor exceeds a specified concentration. With first-order removal, $\dot{y}=\beta g-\alpha y$ and $g\in \{0,1\}$. A zero-initialized rising response reaches $K<\beta /\alpha$ at $-{\alpha }^{-1}\ln (1-\alpha K/\beta )$. Boolean rules must specify how several inputs combine; equal rate constants do not determine thresholds.