Fig. 1 Design for toggle switch[48]Repressors 1 and 2 inhibit transcription driven by Promoters 1 and 2, respectively, which is induced by Inducers 1 and 2 correspondingly

Fig. 2 Summary for three-input and 16-state RSM[55](a) RSM mechanism. A chemical input induces the expression of a recombinase encoded by a gene on the input plasmid, which modifies a DNA register with overlapping and orthogonal recombinase recognition sites. Specific recombinases can be controlled by corresponding inputs. Each of these recombinases can target multiple orthogonal pairs of their cognate recognition sites (shown as triangles and half-ovals) to catalyze inversion (when the sites are anti-aligned) or excision (when the sites are aligned). (b) The register is designed to adopt a specific DNA state for every identity and order of inputs. Three different inputs are represented by colored arrows (orange, blue, and purple), each of which expresses a specific recombinase. Unrecombined recognition sites are shown by solid symbols, and symbols without filling highlight recombined recognition sites

Fig. 3 SCRIBE-based distributed encoded memory at genome levels [25]In the presence of an input, ssDNAs (orange curved lines) are produced from a plasmid-borne cassette (gray circles) and recombined into specific genomic loci (orange circles) that are targeted on the basis of sequence homology. This results in the accumulation of precise mutations (stars in green cells) as a function of the magnitude and duration of exposure to the input

Fig. 4 Transcriptional record of RNA extracted from CRISPR spacer acquisition[59](a) Record-seq uses the RNA-acquiring RT-Cas1-Cas2 complex from Fusicatenibacter saccharivorans to encode transcriptional information into plasmid-borne CRISPR arrays. The transcriptional record is generated by CRISPR spacer acquisition directly from intracellular RNAs followed by reverse transcription of RNA protospacers through the RT domain of FsRT-Cas1-Cas2. (b) Extraction of plasmid DNA followed by the selective amplification of expanded CRISPR arrays (SENECA) and deep sequencing enable the reconstruction of transcriptional histories

Fig. 5 Multiple analog of cellular recording by CAMERA systems in bacteria and mammalian cells[39]CAMERA 1 records stimuli as changes in the ratio of mutually exclusive DNA sequences. CAMERA 2 uses base editors to record the duration or amplitude of signals as single-nucleotide changes. Both systems can be repeatedly used to independently record multiple events, including exposure to antibiotics, nutrients, viruses, and light, as well as Wnt signaling

Fig. 6 Sequential genome editing with DNA typewriter[40](a) Schematic of two successive editing events at the type guide, which shifts in position with each editing event. The DNA tape consists of a tandem array of CRISPR–Cas9 target sites (grey boxes), all but the first of which are truncated at their 5′ ends and therefore inactive. The 5-bp insertion includes a 2-bp pegRNA-specific barcode as well as a 3-bp key that activates the next monomer. Because genome editing is sequential in this scheme, the temporal order of recorded events can simply be read out by their physical order along the array. (b) Schematic of prime editing with DNA typewriter. Prime editing recognizes a CRISPR–Cas9 target and modifies it with the edit specified by the pegRNA. With DNA typewriter, an insertional editing event generates a new prime editing target at the subsequent monomer. (c) Schematic of ordered recording via DNA typewriter. Individual pegRNAs are potentially event-driven or constitutively expressed, together with the PE2 enzyme

Fig. 7 Design of the CRISPR-Cas9-based signal conductor to link one signal with another[70]General illustration of the strand-displacement mechanism by which the redesigned sgRNA acts to deactivate (a) or activate (b) gene expression. The antisense sequence of the sgRNA is shown in blue, and the aptamer stem is shown in yellow. In the absence of signal A/B, the guide region of sgRNA is paired within the antisense stem and the sgRNA is in the 'off' state. In the presence of signal A/B, the conformation of the redesigned sgRNA is switched to the 'on' state. In this state, the guide region of the sgRNA binds to its target DNA, and thus turns the production of signal B/A on and off through the dCas9-VP64 fusion protein and the dCas9 protein, respectively.