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Table 6 Genes dysregulated after late RAR inhibition associated with organ development and differentiation. Genes shown in Fig. 6 along with their general function (adapted from genecards.org)

From: Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function

Gene

Gene Name

General Protein Function

Decreased

 ALX1

Alx Homeobox 1

Unknown in humans, in rodents it is necessary for survival of forebrain mesenchyme and possibly neural tube development.

 BGN

Biglycan

Small, leucine-rich proteoglycan that plays a role in bone growth, muscle development, and collagen fibril assembly.

 BMP2

Bone Morphogenetic Protein 2

Secreted ligand of the TGF-beta family that is important in bone and cartilage development.

 BMP5

Bone Morphogenetic Protein 5

TGF-beta family ligand that binds to BMP receptors and activates Smad signaling. Important for bone and cartilage development.

 COL9A1

Collagen Type IX Alpha 1 Chain

Essential for assembly of type IX collagen a minor component of hyaline cartilage and found in tissues containing type II collagen which forms cartilage

 COL9A2

Collagen Type IX Alpha 2 Chain

Essential for assembly of type IX collagen a minor component of hyaline cartilage and found in tissues containing type II collagen which forms cartilage

 COL9A3

Collagen Type IX Alpha 3 Chain

Essential for assembly of type IX collagen a minor component of hyaline cartilage and found in tissues containing type II collagen which forms cartilage

 HMGA2

High Mobility Group AT-Hook 2

A member of the non-histone chromosomal high mobility group protein family that acts as a transcription regulator.

 RARB

Retinoic Acid Receptor Beta

Ligand-dependent transcription regulator important for embryonic morphogenesis, cell growth, and differentiation.

 RARG

Retinoic Acid Receptor Gamma

Ligand-dependent transcription regulator implicated in embryonic growth, limb bud development, and differentiation.

 SIX2

SIX Homeobox 2

A member of the sine oculis family of proteins that are transcription factors involved in limb and eye development.

 TGFB1

Transforming Growth Factor Beta 1

Ligand for TGF-beta superfamily of signaling molecules, activates Smad signaling to regulate cellular proliferation and differentiation.

 WNT1

Wnt Family Member 1

Soluble transcription regulator that binds to frizzled receptors and plays several roles in development.

Increased

 DLX2

Distal-Less Homeobox 2

Transcription factor expressed in the developing head and limbs; important for the terminal differentiation of neurons and craniofacial patterning.

 FRZB

Frizzled Related Protein

Modulator of Wnt signaling important for the regulation of bone development.

 SLC39A8

Solute Carrier Family 39 Member 8

Manganese and zinc influx transporter.

 COL2A1

Collagen Type II Alpha 1 Chain

Fibrillar collagen found in cartilage and the vitreous of the eye, essential for normal embryonic development of the skeleton

Unchanged

 ACAN

Aggrecan

Integral extracellular matrix proteoglycan in cartilaginous tissue

 CHRDL2

Chordin Like 2

Chordin family member that interacts with TGF-beta signaling and may play a role in myoblast and osteoblast differentiation.

 SIX5

SIX Homeobox 5

Transcription factor involved in the regulation of organogenesis.

 SNAI1

Snail Family Transcriptional Repressor 1

Zinc finger transcriptional repressor that downregulates the expression of ectodermal genes in the mesoderm.

 TGFB2

Transforming Growth Factor Beta 2

Ligand for TGF-beta superfamily of signaling molecules, activates Smad signaling.