# How CRISPR edits a gene

> A process map exported from forks.world (https://forks.world). Author: Brian. Source: https://forks.world/p/cmv0kpv650052jn06381mybcn
> It describes who does what, in what order, and with which technology. Read the plain-language sections first; the JSON at the end is the exact, complete data.

## Summary

- 19 steps across 2 layers
- Persona: Scientists, Guide RNA, The cell
- Technology / systems: The Cas9 protein

## Pain points

Where this process hurts, worst first:

- **Heritable edits are banned or restricted in most countries** (How CRISPR edits a gene; critical): Debated: the 2018 birth of gene-edited babies in China drew global condemnation
- **It may cut the wrong place (off-target)** (How CRISPR edits a gene; painful): Off-target cuts are a key safety risk

## How to read this file

- A process is made of **layers**. The main layer is the top level; any step of kind `subprocess` opens a detail layer with its own lanes and steps.
- **Lanes** are either persona (people/roles) or technology (systems). Each step belongs to one lane; `using` lists tools a person uses for that step.
- Step kinds: `start`, `task`, `decision` (its arrows carry the answer as a label), `subprocess`, `end`.

## How CRISPR edits a gene

Lanes:
- Scientists: person / role (id `sci`)
- Guide RNA: person / role (id `guide`)
- The Cas9 protein: technology / system (id `cas`)
- The cell: person / role (id `cell`)

Steps, in the order they run:

1. **Choose the gene to change** [start; Scientists; id `c1`]
   - then Design a guide RNA that matches it
2. **Design a guide RNA that matches it** [task; Scientists; id `c2`]
   - then Deliver the guide and Cas9 into cells
3. **Deliver the guide and Cas9 into cells** [task; Scientists; id `c3`]
   - then The guide leads Cas9 to the matching spot
4. **The guide leads Cas9 to the matching spot** [task; Guide RNA; id `c4`]
   - then Does the guide match exactly?
5. **Does the guide match exactly?** [decision; The Cas9 protein; id `c5`]
   - if "Yes" go to Cut both strands of the DNA; if "No — a near match" go to It may cut the wrong place (off-target)
6. **Cut both strands of the DNA** [task; The Cas9 protein; id `c6`]
   - then The cell repairs the break
7. **The cell repairs the break** [subprocess; The cell; id `c7`], opens the detail layer "How the cell repairs the cut"
   - then Check the result: did the edit work?
8. **Check the result: did the edit work?** [decision; Scientists; id `c8`]
   - if "Yes" go to Study it, or treat patients with the edited cells; if "No" go to Redesign and retry
9. **Study it, or treat patients with the edited cells** [task; Scientists; id `c9`]
   - then Edit body cells only, or embryos too?
10. **Edit body cells only, or embryos too?** [decision; Scientists; id `c11`]
   - if "Body cells only" go to Treatments, like the first approved therapy for sickle cell disease; if "Embryos (heritable)" go to Heritable edits are banned or restricted in most countries
11. **Treatments, like the first approved therapy for sickle cell disease** [end; Scientists; id `c12`]
12. **Heritable edits are banned or restricted in most countries** [task; Scientists; id `c13`] ⚠ PAIN POINT (critical): Debated: the 2018 birth of gene-edited babies in China drew global condemnation
   - then The debate over the limits continues
13. **The debate over the limits continues** [end; Scientists; id `c14`]
14. **Redesign and retry** [task; Scientists; id `c10`]
   - then Design a guide RNA that matches it
15. **It may cut the wrong place (off-target)** [task; The Cas9 protein; id `c5a`] ⚠ PAIN POINT (painful): Off-target cuts are a key safety risk
   - then Cut both strands of the DNA

```mermaid
flowchart LR
  subgraph l_sci["Scientists"]
    n_c1(["Choose the gene to change"])
    n_c2["Design a guide RNA that matches it"]
    n_c3["Deliver the guide and Cas9 into cells"]
    n_c8{"Check the result: did the edit work?"}
    n_c10["Redesign and retry"]
    n_c9["Study it, or treat patients with the edited cells"]
    n_c11{"Edit body cells only, or embryos too?"}
    n_c12(["Treatments, like the first approved therapy for sickle cell disease"])
    n_c13["Heritable edits are banned or restricted in most countries"]
    n_c14(["The debate over the limits continues"])
  end
  subgraph l_guide["Guide RNA"]
    n_c4["The guide leads Cas9 to the matching spot"]
  end
  subgraph l_cas["The Cas9 protein"]
    n_c5{"Does the guide match exactly?"}
    n_c5a["It may cut the wrong place (off-target)"]
    n_c6["Cut both strands of the DNA"]
  end
  subgraph l_cell["The cell"]
    n_c7[["The cell repairs the break"]]
  end
  n_c1 --> n_c2
  n_c2 --> n_c3
  n_c3 --> n_c4
  n_c4 --> n_c5
  n_c5 -->|"Yes"| n_c6
  n_c5 -->|"No — a near match"| n_c5a
  n_c5a --> n_c6
  n_c6 --> n_c7
  n_c7 --> n_c8
  n_c8 -->|"Yes"| n_c9
  n_c8 -->|"No"| n_c10
  n_c10 --> n_c2
  n_c9 --> n_c11
  n_c11 -->|"Body cells only"| n_c12
  n_c11 -->|"Embryos (heritable)"| n_c13
  n_c13 --> n_c14
```

### How the cell repairs the cut (detail of step "The cell repairs the break")

Lanes:
- The cell: person / role (id `cell`)

Steps, in the order they run:

1. **Which repair path?** [start; The cell; id `r1`]
   - if "Fast and sloppy (NHEJ)" go to Small random changes often switch the gene off; if "Precise with a template (HDR)" go to It copies a supplied DNA template to rewrite the gene
2. **Small random changes often switch the gene off** [task; The cell; id `r2`]
   - then The edit is done
3. **The edit is done** [end; The cell; id `r4`]
4. **It copies a supplied DNA template to rewrite the gene** [task; The cell; id `r3`]
   - then The edit is done

```mermaid
flowchart LR
  subgraph l_cell["The cell"]
    n_r1(["Which repair path?"])
    n_r2["Small random changes often switch the gene off"]
    n_r3["It copies a supplied DNA template to rewrite the gene"]
    n_r4(["The edit is done"])
  end
  n_r1 -->|"Fast and sloppy (NHEJ)"| n_r2
  n_r1 -->|"Precise with a template (HDR)"| n_r3
  n_r2 --> n_r4
  n_r3 --> n_r4
```

## Full data (JSON)

```json
{
  "title": "How CRISPR edits a gene",
  "maps": {
    "m_root": {
      "id": "m_root",
      "lanes": [
        {
          "id": "sci",
          "name": "Scientists",
          "type": "person"
        },
        {
          "id": "guide",
          "name": "Guide RNA",
          "type": "person"
        },
        {
          "id": "cas",
          "name": "The Cas9 protein",
          "type": "system"
        },
        {
          "id": "cell",
          "name": "The cell",
          "type": "person"
        }
      ],
      "steps": [
        {
          "id": "c1",
          "kind": "start",
          "lane": "sci",
          "next": [
            {
              "to": "c2"
            }
          ],
          "uses": [],
          "label": "Choose the gene to change"
        },
        {
          "id": "c2",
          "kind": "task",
          "lane": "sci",
          "next": [
            {
              "to": "c3"
            }
          ],
          "uses": [],
          "label": "Design a guide RNA that matches it"
        },
        {
          "id": "c3",
          "kind": "task",
          "lane": "sci",
          "next": [
            {
              "to": "c4"
            }
          ],
          "uses": [],
          "label": "Deliver the guide and Cas9 into cells"
        },
        {
          "id": "c4",
          "kind": "task",
          "lane": "guide",
          "next": [
            {
              "to": "c5"
            }
          ],
          "uses": [],
          "label": "The guide leads Cas9 to the matching spot"
        },
        {
          "id": "c5",
          "kind": "decision",
          "lane": "cas",
          "next": [
            {
              "to": "c6",
              "label": "Yes"
            },
            {
              "to": "c5a",
              "label": "No — a near match"
            }
          ],
          "uses": [],
          "label": "Does the guide match exactly?"
        },
        {
          "id": "c5a",
          "kind": "task",
          "lane": "cas",
          "next": [
            {
              "to": "c6"
            }
          ],
          "pain": {
            "note": "Off-target cuts are a key safety risk",
            "level": 2
          },
          "uses": [],
          "label": "It may cut the wrong place (off-target)"
        },
        {
          "id": "c6",
          "kind": "task",
          "lane": "cas",
          "next": [
            {
              "to": "c7"
            }
          ],
          "uses": [],
          "label": "Cut both strands of the DNA"
        },
        {
          "id": "c7",
          "kind": "subprocess",
          "lane": "cell",
          "next": [
            {
              "to": "c8"
            }
          ],
          "uses": [],
          "child": "m_repair",
          "label": "The cell repairs the break"
        },
        {
          "id": "c8",
          "kind": "decision",
          "lane": "sci",
          "next": [
            {
              "to": "c9",
              "label": "Yes"
            },
            {
              "to": "c10",
              "label": "No"
            }
          ],
          "uses": [],
          "label": "Check the result: did the edit work?"
        },
        {
          "id": "c10",
          "kind": "task",
          "lane": "sci",
          "next": [
            {
              "to": "c2"
            }
          ],
          "uses": [],
          "label": "Redesign and retry"
        },
        {
          "id": "c9",
          "kind": "task",
          "lane": "sci",
          "next": [
            {
              "to": "c11"
            }
          ],
          "uses": [],
          "label": "Study it, or treat patients with the edited cells"
        },
        {
          "id": "c11",
          "kind": "decision",
          "lane": "sci",
          "next": [
            {
              "to": "c12",
              "label": "Body cells only"
            },
            {
              "to": "c13",
              "label": "Embryos (heritable)"
            }
          ],
          "uses": [],
          "label": "Edit body cells only, or embryos too?"
        },
        {
          "id": "c12",
          "kind": "end",
          "lane": "sci",
          "next": [],
          "uses": [],
          "label": "Treatments, like the first approved therapy for sickle cell disease"
        },
        {
          "id": "c13",
          "kind": "task",
          "lane": "sci",
          "next": [
            {
              "to": "c14"
            }
          ],
          "pain": {
            "note": "Debated: the 2018 birth of gene-edited babies in China drew global condemnation",
            "level": 3
          },
          "uses": [],
          "label": "Heritable edits are banned or restricted in most countries"
        },
        {
          "id": "c14",
          "kind": "end",
          "lane": "sci",
          "next": [],
          "uses": [],
          "label": "The debate over the limits continues"
        }
      ],
      "title": "How CRISPR edits a gene",
      "parent": null
    },
    "m_repair": {
      "id": "m_repair",
      "lanes": [
        {
          "id": "cell",
          "name": "The cell",
          "type": "person"
        }
      ],
      "steps": [
        {
          "id": "r1",
          "kind": "start",
          "lane": "cell",
          "next": [
            {
              "to": "r2",
              "label": "Fast and sloppy (NHEJ)"
            },
            {
              "to": "r3",
              "label": "Precise with a template (HDR)"
            }
          ],
          "uses": [],
          "label": "Which repair path?"
        },
        {
          "id": "r2",
          "kind": "task",
          "lane": "cell",
          "next": [
            {
              "to": "r4"
            }
          ],
          "uses": [],
          "label": "Small random changes often switch the gene off"
        },
        {
          "id": "r3",
          "kind": "task",
          "lane": "cell",
          "next": [
            {
              "to": "r4"
            }
          ],
          "uses": [],
          "label": "It copies a supplied DNA template to rewrite the gene"
        },
        {
          "id": "r4",
          "kind": "end",
          "lane": "cell",
          "next": [],
          "uses": [],
          "label": "The edit is done"
        }
      ],
      "title": "How the cell repairs the cut",
      "parent": {
        "map": "m_root",
        "step": "c7"
      }
    }
  }
}
```