Table 1.
Genes encoding transcription factors of the bHLH family in the ascidian Ciona robusta.
| Gene Name | Alternative Names | Human Hits * | Gene Models KH2013 KY2019 |
Expression at Mid/Late Tailbud | Reference | scRNA-Seq Data from Larvae | |
|---|---|---|---|---|---|---|---|
| [27] | [31] | ||||||
| Ascl.a (achaete-scute family bHLH transcription factor.a) | Achaete-Scute a-like2 | ASCL1; ASCL3; ASCL5 | KH.L9.13 KY.Chr2.2314 |
Epid., palps | [50] | ||
| Ascl.b (achaete-scute family bHLH transcription factor.b) | Achaete-Scute b | ASCL3; ASCL4; ASCL5 | KH.C2.880 KY.Chr2.2022 |
ESNs | [163] | ||
| Ascl.c (achaete-scute family bHLH transcription factor.c) | Achaete-Scute a-like1 | ASCL3; ASCL5; NEUROD1 | KH.C2.560 KY.Chr2.1484 |
Anterior SV, weak mesench. and palps | [50]; Figure 3 | ||
| Atoh8 (Atonal bHLH transcription factor 8) | Net; NeuroD-like | ATOH1; ATOH8; NEUROD4 | KH.C9.872 KY.Chr9.174 |
Anterior SV, MG, cESNs, trunk endod. | [50,84] Figure 3 |
aSV | Ventral SV |
| Atonal | ATOH1; ATOH7; NEUROD1 | KH.C8.175 KY.Chr8.248 |
ESNs, palps | [50] | cESNs rTENs |
||
| Bhlha15 (basic helix-loop-helix family member a15) | Mist | BHLHA15; NEUROG1; NEUROG2 | KH.C3.308 KY.Chr3.1309 |
Mesench. | [50] | ||
| Hand (heart and neural crest derivatives expressed) | HAND1; HAND2; TCF15 | KH.C14.604 KY.Chr14.359 |
Mesench. | [50] | |||
| Hand-r (heart and neural crest derivatives expressed-related) | NoTrlc | HAND1; HAND2; SCX | KH.C1.1116 KY.Chr1.2070 |
Mesench., TVCs, SV | [164]; Figure 3 | ||
| Mesp (mesoderm posterior bHLH transcription factor) | MESP2; MSGN1; PTF1A | KH.C3.100 KY.Chr3.993 |
Anterior ventral primary muscle, TVCs | [159] | |||
| Mrf (Myogenic regulatory factor) | MyoD; CiMDFa | MYF5; MYF6; MYOD1 | KH.C14.307 KY.Chr14.1058 |
Muscle | [156] | ||
| Neurog (Neurogenin) | NEUROG1; NEUROG2; NEUROG3 | KH.C6.129 KY.Chr6.427 |
SV, MG, NC Atrial ectoderm |
[50,147,208] Figure 3 |
aATENs, aSV, MHB, SV, MG, Epend. | Dorsolat. SV; SV wall | |
| Ptf1a (pancreas associated transcription factor 1a) | Ptfa | not determined | KH.C3.967 KY.Chr3.526 |
SV | [165]; Figure 3 | ||
| Ptf1a-r (pancreas associated transcription factor 1a-related) | Ptfb | not determined | KH.L116.39 KY.Chr11.543 |
SV | [50]; Figure 3 | Coronet cells | Ventral SV |
|
Tcf3
(transcription factor 3) |
E12/E47 E2A | not determined | KH.C3.480 KY.Chr3.781 |
Diffuse signal, predominant in SV # | [50]; Figure 3 | ||
| Tcf15-r (transcription factor 15-related) | Paraxis-like | SCX; TAL2; TCF15 | KH.S781.11 KY.Chr11.73 |
No expression | [160] | ||
| Twist-r.a (twist family bHLH transcription factor-related.a) | Twist-like-1a | ATOH1; NEUROD6; PTF1A | KH.C5.416 KY.Chr5.356 |
TLCs | [164] | ||
| Twist-r.b (twist family bHLH transcription factor-related.b) | Twist-like-1b | ATOH1; NEUROD6; NEUROG2 | KH.C5.554 KY.Chr5.355 |
Mesench. | [124] | ||
| Twist-r.c (twist family bHLH transcription factor-related.c) | Twist-like-2 | TAL2; TWIST1; TWIST2 | KH.C5.202 KY.Chr5.357 |
Mesench., TLCs | [50] | Mesench. | |
| AP4 (transcription factor AP-4) | SREBF1; TFAP4; TWIST1 | KH.C14.448 KY.Chr14.930 |
Mesench., SV | [50]; Figure 3 | |||
| Figla-r (Folliculogenesis specific bHLH transcription factor-related) | FIGLA; NHLH1; TAL2 | KH.C2.1152 KY.Chr2.2108 |
Not analyzed | ||||
| Mad (Mothers against dpp) | Noto7 | MXD1; MXD4; MXI1 | KH.C1.661 KY.Chr1.761 |
SV, MG, palps, notochord, tail epid., tail muscles | [50,179] | Neurons, notochord | Dorsolat. SV, ventral SV, Endod., Epid. |
| Max (Myc associated factor X) | Not determined | KH.C5.373 KY.Chr5.121 |
Mesench. | [50] | ANB, aSV, MG | Epid., Mesench., Endod. | |
| Mitf (Microphthalmia-associated transcription factor) | MITF; TFE3; TFEB | KH.C10.106 KY.Chr10.837 |
Mesench., pigmented cells (otolith, ocellus), MG |
[50,120]; Figure 3 | Collocytes aATENs |
Epid. | |
| Mlx (Max-like protein x) | MLXIP; MLXIPL | KH.C11.706 KY.Chr11.477 |
Mesench. | [50] | |||
| Mnt-r (Max network transcriptional repressor-related) | Mnt-like | MNT; MXD1; MXD3 | KH.L20.34 KY.Chr6.608 |
No expression; a faint signal in SV, palps and mesench. might be present in late tailbuds | [50] | ||
| Myc (Myelocytomatosis) | MNT; MYC; MYCN | KH.L24.23 KY.Chr1.686 |
Mesench., anterior SV, trunk endod.; in juveniles: endostyle pharyngeal gills, heart, intestine, body wall muscle, neural gland epidermis, stomach, esophagus | [50,145] Figure 3 |
ANB | Endod., Epid. | |
| Srebp (Sterol regulatory element-binding transcription factor 1) | SREBF1; SREBF2 | KH.L99.12 KY.Chr9.7 |
SV, palps; epid. (in larvae) | [50,141] Figure 3 |
NC | SV wall, ventral SV | |
| Usf (Upstream transcription factor) | USF1; USF2; USF3 | KH.C3.624 KY.Chr3.1438 |
Mesench., faint signal in SV and NC | [50]; Figure 3 | Dorsolat. SV, Mesench., Epid. | ||
| AHR (Aryl hydrocarbon receptor) | AHR; AHRR; SIM2 | KH.C12.93 KY.Chr12.869 |
Mesench., palps, NC | [50] | Collocytes aATENs |
Epid. | |
| ARNT (Aryl hydrocarbon receptor nuclear translocator) | ARNT; ARNT2; ARNTL | KH.C5.213 KY.Chr5.617 |
Weak mesench., notochord, unclear signal in epidermis; in juveniles: endostyle pharyngeal gills, neural gland, stomach, esophagus | [50,136,180] | |||
| Hif (Hypoxia inducible factor) | EPAS1; HIF1A; HIF3A | KH.C4.83 KY.Chr4.583 |
Mesench., anterior SV, palps, ventral midline, tail epid.; in juveniles: endostyle pharyngeal gills, heart, intestine, body wall muscle, neural gland epidermis, stomach, esophagus | [30,50]; Figure 3 |
aSV | ||
| Sim (Single-minded) | Not determined | KH.L20.56 KY.Chr6.618 |
Not analyzed | ||||
| Trh (Trachealess) | NPAS1; NPAS3; SIM2 | KH.L154.23 KY.Chr11.674 |
Mesench., very weak SV | [50] | |||
| Id.a (inhibitor of DNA binding.a) | Emc | ID2; ID3 | KH.C7.692 KY.Chr7.1153 |
Not analyzed | SV wall, mesench., epid. | ||
| Id.b (inhibitor of DNA binding.b) | Emc2 | ID1; ID2; ID3 | KH.C7.157 KY.Chr7.1157 |
SV, MG, NC; palps, tail epid., ESNs | [50] | NC, aSV | SV wall, ventral SV, Endod., Mesench. |
| Hes.a (hairy and enhancer of split.a) | E(spl)/hairy-a | HES1; HES2; HES4 | KH.C1.159 KY.Chr1.28 |
Muscle, SV, epid. | [50]; Figure 3 | NC | Epid., Mesench., Endod., SV wall, dorsolat. SV |
| Hes.b (hairy and enhancer of split.b) | E(spl)/hairy-b | HES1; HES4; HES6 | KH.C3.312 KY.Chr3.580 |
Patchy SV, trunk epid., rows of tail epid.; in juveniles: body wall muscle, stigmatal cells | [50,137,187] | Epend., NC, aSV, MHB, SV | Dorsolat. SV, Epid., SV wall, Endod. |
| Hes.c (hairy and enhancer of split.c) | E(spl)/hairy-c | HES1; HES2; HES4 | KH.L34.9 KY.Chr1.1234 |
No distinct zygotic signal, ubiquitous staining throughout embryogenesis | [50] | Collocytes | Endod., epid. |
| Hey (hes related family bHLH transcription factor with YRPW motif) | HEY1; HEY2; HEYL | KH.L130.6 KY.Chr10.1431 |
No distinct zygotic signal | [50] | Endod., epid., mesench. | ||
| Ebf (Ebf transcription factor) | COE | EBF1; EBF2; EBF3 | KH.L24.10 KY.Chr1.724 |
SV, MG; neurohypophysis primordium; tail epid. | [50]; Figure 3 | Epend., Eminens cell, pSV aSV, MG |
Dorsolat. SV |
| bHLH-like1 | CCDC169-SOHLH2; SOHLH1; SOHLH2 | KH.C9.380 KY.Chr9.350 |
Not analyzed | ||||
|
Bhlh-tun1
(Tunicate bhlh 1) |
Orphan bHLH-1 | Not determined | KH.C7.269 KY.Chr7.1158 |
SV, palps, notochord, epid. | [50,166]; Figure 3 | NC, aSV, PSCs related, pigment cells, MHB, SV, pSV, Epend., Notochord | SV wall, ESNs, ventral SV, epid., endod., mesench. |
|
Bhlh-tun2
(Tunicate bhlh 2) |
Orphan bHLH-2 | NHLH1; NHLH2; TAL2 | KH.C4.649 KY.Chr4.1008 |
SV, BTNs, mesench. | [50,108]; Figure 3 | aSV, MG, Eminens cell | Dorsolat. SV |
|
Bhlh-tun3
(Tunicate bhlh 3) |
Orphan bHLH-3 | Not determined | KY.Chr10.1238 | Not analyzed | |||
|
Bhlh-tun4
(Tunicate bhlh 4) |
Orphan bHLH-4 | Not determined | KH.L41.39 KY.Chr4.1211 |
No distinct zygotic signal | [50] | ||
|
Tcf4
(transcription factor 4) |
TFDP1; TFDP2; TFDP3 | KH.L60.12 KY.Chr1.10 |
No distinct zygotic signal; weak mesench. throughout embryogenesis | [50] | |||
* Retrieved from the Aniseed database [209]. # From the Ghost database [210]. Abbreviations: aATENs, anterior apical trunk epidermal neurons; ANB, anterior neural boundary; aSV, anterior sensory vesicle; BTNs, bipolar tail neurons; cESNs, caudal epidermal sensory neurons; DEGs, differentially expressed genes; dorsolat., dorsolateral; endod., endoderm; epend., ependymal cells; epid., epidermis; ESNs, epidermal sensory neurons; mesench., mesenchyme; MG, motor ganglion; MHB, midbrain–hindbrain boundary; NC, nerve cord; rTENs, rostral trunk epidermal neurons; SV, sensory vesicle; TLCs, trunk lateral cells; TVCs, trunk ventral cells.