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Embryology of Somites
1. Overview
Somites (Greek: soma = body) are paired, segmented blocks of paraxial mesoderm that appear flanking the developing neural tube during the third and fourth weeks of embryonic development. They are among the most visually prominent features of the early embryo and are the precursors of the axial skeleton, skeletal musculature, and dermis of the back. Their orderly, craniocaudal formation is controlled by a molecular "segmentation clock" - one of the most precisely timed events in all of vertebrate development.
2. Timeline: From Gastrulation to Somite Formation
| Stage | Event |
|---|
| Week 2 | Bilaminar disc (epiblast + hypoblast) |
| Week 3 (Day 15-16) | Gastrulation: primitive streak appears; epiblast cells ingress to form intraembryonic mesoderm and endoderm |
| Week 3 (Day 17-19) | Paraxial mesoderm condenses as thick longitudinal columns flanking the notochord |
| Week 3 (end) | Paraxial mesoderm begins segmenting into somitomeres, then into distinct somites |
| Day 20 | First pair of somites appears (caudal to the future otic vesicle) |
| Day 26-32 | "Somite period": 38-39 pairs form |
| End of Week 5 | 42-44 pairs of somites present |
(The Developing Human, Moore)
3. Origin: Paraxial Mesoderm
During gastrulation, cells from the primitive node and primitive streak migrate cranially and laterally to form the intraembryonic mesoderm. The portion closest to the midline on either side of the notochord condenses into a thick longitudinal column called paraxial mesoderm (also called the presomitic mesoderm, PSM, before segmentation).
The mesoderm is organized in three lateral tiers:
Midline (notochord)
│
├── Paraxial mesoderm ← SOMITES form here
│ (thick, bilateral columns)
│
├── Intermediate mesoderm ← urogenital system
│ (thinner)
│
└── Lateral mesoderm ← body wall, gut wall, coelom
(thinnest; splits into somatic + splanchnic layers)
(The Developing Human; Fischer's Mastery of Surgery)
4. Somite Numbers by Region
| Region | Number of Somite Pairs |
|---|
| Occipital | 4-5 |
| Cervical | 8 |
| Thoracic | 12 |
| Lumbar | 5 |
| Sacral | 5 |
| Coccygeal | 8-12 |
The first occipital and the most caudal 5-7 coccygeal somites disappear. The remainder persist to form the axial skeleton, associated musculature, and dermis. (Fischer's Mastery of Surgery)
Figure: Right lateral view of a 5-week human embryo showing the regional distribution of somites (occipital, cervical, thoracic, lumbar, sacral, coccygeal) alongside the ear rudiment, optic rudiment, and limb buds. Preotic somites (blue/green, cranial to ear) give rise to extraocular and branchiogenic muscles innervated by cranial nerves. Postotic somites (red) give rise to somatic musculature. (Thieme Atlas of Anatomy)
5. The Molecular Segmentation Clock ("Clock and Wavefront" Model)
Figure: Somatogenesis and the molecular segmentation clock. From the tail bud (caudal) to formed somites (rostral), molecular control is organized in rostrocaudal zones: T-box/Fgf8 specify PSM identity; Lunatic fringe (Lnfg) is the oscillation/cycling gene; Notch-Delta and Mesp2 define somite boundary formation; HOX genes assign somite identity along the whole axis. (Emery's Elements of Medical Genetics and Genomics)
Somitogenesis is not random - it is controlled with extraordinary precision by a molecular clock:
The "Clock and Wavefront" Model (Cooke & Zeeman, 1970s)
- The clock is a wave of oscillating gene expression that sweeps from the caudal tail bud rostrally through the PSM. Each sweep "pinches off" one new pair of somites.
- The wavefront is a threshold of signaling activity (FGF8 and WNT gradients, high caudally) that determines where in the PSM the clock oscillation is interpreted as a boundary.
- As the embryo elongates caudally, the wavefront moves caudally too, allowing new somites to form progressively.
Key Molecular Players
| Gene/Pathway | Role |
|---|
| T-box genes (Tbx6) | Specification of PSM identity; Tbx6 mutations → failure to form somites |
| FGF8 (Fgf8) | High in caudal PSM; maintains PSM in undifferentiated state |
| WNT signaling | Interacts with FGF to maintain PSM and influence oscillation |
| Notch-Delta signaling (Notch receptor + Delta-like-1, Delta-like-3 ligands) | Core oscillation clock; establishes rostrocaudal polarity within each new somite; Mesoderm posterior-2 (Mesp2) defines somite boundaries |
| Lunatic fringe (Lnfg) | Modulates Notch signaling; key oscillation/cycling gene |
| Presenilin-1 | Component of Notch processing (γ-secretase complex) |
| HES genes (hes in mouse; c-hairy in chick) | Cycling genes downstream of Notch |
| FoxC1, FoxC2 | Forkhead transcription factors expressed in presomitic mesoderm before somite formation |
| HOX genes | Assign regional identity to each somite along the entire craniocaudal axis (which vertebral level it will form) |
(Emery's Elements of Medical Genetics and Genomics; The Developing Human)
6. Somite Structure: Epithelial-to-Mesenchymal Transitions
Newly formed somites are epithelial spheres - cuboidal cells arranged around a small lumen (somitocoele). They quickly undergo regionalization and differentiation:
SOMITE (epithelial sphere)
│
├─── SCLEROTOME (ventromedial) ──────► Vertebrae & ribs
│ (epithelial → mesenchymal)
│
└─── DERMOMYOTOME (dorsolateral) ────► remains epithelial
│
├── MYOTOME ─────────────────► Skeletal muscle
│
└── DERMATOME ───────────────► Dermis (back skin)
Signaling that Drives Differentiation
| Region | Signal | Source |
|---|
| Sclerotome induction | Sonic Hedgehog (SHH) | Notochord + floor plate of neural tube |
| Myotome induction | Wnt | Dorsal neural tube + surface ectoderm |
| Dermomyotome maintenance | Wnt + BMP | Surface ectoderm |
| Sclerotome also induced by | Noggin (BMP antagonist) | Notochord |
7. Somite Derivatives in Detail
A. Sclerotome → Axial Skeleton
The ventromedial cells of the somite undergo epithelial-to-mesenchymal transition (EMT) under SHH signaling and migrate medially to surround the notochord and neural tube. These sclerotomal cells form the vertebrae and ribs.
Resegmentation (von Ebner's concept):
Each sclerotome is divided into a cranial (rostral) and a caudal (dense) half. A vertebra forms from the caudal half of one sclerotome fusing with the cranial half of the next sclerotome below - not from a single somite. This means:
- Vertebral bodies are intersegmental - they bridge two adjacent somitic segments
- The spinal nerve (derived from the neural tube at the level of one somite) therefore exits between two vertebrae, running through the center of the original sclerotome
- The intervertebral disc forms at the junction between the cranial and caudal halves of a sclerotome
- The nucleus pulposus of the disc is a remnant of the notochord (which normally disappears as it is surrounded by vertebral bodies)
Structures formed from sclerotome:
- Vertebral bodies and arches
- Ribs (from thoracic sclerotomes)
- Sternum (from sternal bars of lateral plate mesoderm - not directly from somites)
- Intervertebral discs
B. Dermomyotome → Myotome and Dermatome
The dorsolateral portion of the somite - the dermomyotome - remains epithelial and then further divides:
Myotome (muscle precursors)
The myotome divides into:
| Division | Name | Innervation | Muscles Formed |
|---|
| Dorsal (medial) | Epimere / Epaxial | Dorsal (posterior) ramus of spinal nerve | Intrinsic (deep) back muscles (erector spinae, multifidus, rotatores, interspinales, intertransverse muscles); keep segmental arrangement |
| Ventral (lateral) | Hypomere / Hypaxial | Ventral (anterior) ramus of spinal nerve | Anterolateral chest wall, abdominal wall muscles (intercostals, external/internal oblique, transversus abdominis, rectus abdominis); diaphragm; limb musculature |
Figure: Transverse sections through a 6-week embryo showing the epaxial musculature (posterior, supplied by dorsal ramus) and hypaxial musculature (anterior/lateral, supplied by ventral ramus). At limb levels (a), myotome cells migrate into the limb bud to form limb muscles. At abdominal levels (b), hypaxial muscle forms the abdominal wall. (Thieme Atlas of Anatomy)
Limb muscles: At limb bud levels, myotome cells with replicative capacity migrate from the hypomere into the developing limb bud. They differentiate into a dorsal blastema (extensor muscles) and a ventral blastema (flexor muscles). Limb muscles are innervated by ventral rami through the brachial plexus (upper limb) and lumbosacral plexus (lower limb).
Fate of segmental arrangement: The original metameric (segmental) pattern:
- Persists in: deep intrinsic back muscles (rotatores, interspinales, intertransverse muscles), intercostal muscles
- Disappears (polymerization) in: superficial back muscles (which span multiple segments); but the segmental neurovascular supply remains as evidence of origin
Dermatome (dermis of back)
The dermatome gives rise to the dermis and subcutaneous tissue of the back. Note: the dermis of the ventral body wall and limbs is derived from lateral plate mesoderm, not somites. The dermis of the face and scalp is derived from neural crest cells.
8. Complete Summary of Somite Derivatives
PARAXIAL MESODERM (presomitic → somites)
│
├── SCLEROTOME (ventromedial)
│ ├── Vertebral bodies (via resegmentation)
│ ├── Vertebral arches (pedicles, laminae, spinous/transverse processes)
│ ├── Ribs (thoracic levels)
│ └── Nucleus pulposus contribution (notochordal remnant encased by sclerotome)
│
└── DERMOMYOTOME (dorsolateral)
│
├── MYOTOME
│ ├── Epaxial → intrinsic back muscles (dorsal ramus)
│ └── Hypaxial → body wall muscles, diaphragm, limb muscles (ventral ramus)
│
└── DERMATOME → dermis of the back
(The Developing Human; Fischer's Mastery of Surgery; Thieme Atlas of Anatomy)
9. Clinical Correlations
Spondylocostal Dysostosis (Jarcho-Levin Syndrome)
Mutations in the Notch-Delta segmentation clock genes disrupt orderly somite boundary formation → irregular, fused, "butterfly" vertebrae and rib fusions. Caused by recessive mutations in:
- DLL3 (Delta-like-3)
- MESP2 (Mesoderm posterior-2)
- LFNG (Lunatic fringe)
- HES7
- TBX6 (also dominant forms)
Hemivertebra
Failure of one half of a sclerotome to develop → asymmetric vertebra → congenital scoliosis.
Spina Bifida
Failure of the neural arches (vertebral arch components from sclerotome) to fuse posteriorly. Ranges from spina bifida occulta (hidden, no neural protrusion) to myelomeningocele (herniation of spinal cord + meninges).
Klippel-Feil Syndrome
Failure of normal segmentation of cervical somites → fusion of two or more cervical vertebrae. Clinically: short neck, limited neck movement, low posterior hairline.
Nucleus Pulposus Herniation (Disc Prolapse)
The nucleus pulposus is the notochordal remnant within each intervertebral disc. It retains high water content and viscoelastic properties. With age or trauma, the annulus fibrosus (sclerotomal fibrocartilage) can rupture, allowing the nucleus pulposus to herniate and compress spinal nerve roots.
Alagille Syndrome
Mutations in JAGGED1 (a Notch ligand) or NOTCH2 → variable features including butterfly vertebrae, congenital heart disease, cholestasis, and renal anomalies - demonstrating that Notch signaling operates far beyond somitogenesis.
Presenilin-1 Mutations
Presenilin-1 is a γ-secretase component essential for Notch processing during somitogenesis - but it is better known as the most common cause of early-onset familial Alzheimer's disease (autosomal dominant), illustrating the same molecular machinery is reused in adult neuronal function.
(Emery's Elements of Medical Genetics and Genomics)
10. Quick Reference Summary
| Feature | Detail |
|---|
| First somites appear | Day 20, caudal to otic placode |
| Final number | 42-44 pairs |
| Direction of formation | Craniocaudal |
| Origin | Paraxial mesoderm (flanking notochord) |
| Molecular clock | Notch-Delta oscillation; FGF8 wavefront; WNT |
| Somite boundary genes | Notch receptor, Delta-like-1/3, Mesp2, Lunatic fringe |
| Somite identity genes | HOX genes (along entire axis) |
| PSM specification | T-box (Tbx6), Fgf8 |
| Sclerotome inducer | Sonic Hedgehog (SHH) from notochord |
| Myotome inducer | Wnt from dorsal neural tube |
| Sclerotome → | Vertebrae, ribs (via resegmentation) |
| Myotome epaxial → | Intrinsic back muscles (dorsal ramus) |
| Myotome hypaxial → | Body wall, limb, diaphragm muscles (ventral ramus) |
| Dermatome → | Dermis of the back |
| Notochord remnant → | Nucleus pulposus of intervertebral disc |