# Sox2 levels regulate the chromatin occupancy of WNT mediators in epiblast progenitors responsible for vertebrate body formation

**Authors:** Robert Blassberg, Harshil Patel, Thomas Watson, Mina Gouti, Vicki Metzis, M. Joaquina Delás, James Briscoe

PMC · DOI: 10.1038/s41556-022-00910-2 · Nature Cell Biology · 2022-05-12

## TL;DR

This paper shows how SOX2 protein levels control how cells respond to WNT signals during early development, influencing whether cells stay pluripotent or differentiate into mesoderm.

## Contribution

The study reveals that SOX2 expression levels dynamically regulate chromatin occupancy of WNT mediators, enabling distinct developmental outcomes in epiblast progenitors.

## Key findings

- High SOX2 levels maintain pluripotency by displacing nucleosomes and recruiting TCF/β-catenin to high-affinity sites.
- Reduced SOX2 levels shift TCF/β-catenin occupancy to caudal epiblast genes, co-occupied by T/Bra and CDX.
- Lower SOX2 allows WNT-induced mesodermal differentiation by reconfiguring chromatin interactions.

## Abstract

WNT signalling has multiple roles. It maintains pluripotency of embryonic stem cells, assigns posterior identity in the epiblast and induces mesodermal tissue. Here we provide evidence that these distinct functions are conducted by the transcription factor SOX2, which adopts different modes of chromatin interaction and regulatory element selection depending on its level of expression. At high levels, SOX2 displaces nucleosomes from regulatory elements with high-affinity SOX2 binding sites, recruiting the WNT effector TCF/β-catenin and maintaining pluripotent gene expression. Reducing SOX2 levels destabilizes pluripotency and reconfigures SOX2/TCF/β-catenin occupancy to caudal epiblast expressed genes. These contain low-affinity SOX2 sites and are co-occupied by T/Bra and CDX. The loss of SOX2 allows WNT-induced mesodermal differentiation. These findings define a role for Sox2 levels in dictating the chromatin occupancy of TCF/β-catenin and reveal how context-specific responses to a signal are configured by the level of a transcription factor.

Blassberg et al. report that SOX2 levels determine the chromatin occupancy of TCF/β-catenin, thus orchestrating the WNT response and epiblast progenitor fate.

## Linked entities

- **Genes:** SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657], HNF4A (hepatocyte nuclear factor 4 alpha) [NCBI Gene 3172], ctnnb1.S (catenin beta 1 S homeolog) [NCBI Gene 380441], cdx (transcription factor protein) [NCBI Gene 778562]
- **Proteins:** SOX2 (SRY-box transcription factor 2), cdx (transcription factor protein)

## Full-text entities

- **Genes:** Sox3 (SRY (sex determining region Y)-box 3) [NCBI Gene 20675] {aka Sox-3}, Fgf5 (fibroblast growth factor 5) [NCBI Gene 14176] {aka Fgf-5, Fgf3a, HBGF-5, angora, go}, Eomes (eomesodermin) [NCBI Gene 13813] {aka TBR-2, Tbr2}, Fgf2 (fibroblast growth factor 2) [NCBI Gene 14173] {aka Fgf-2, Fgf2a, Fgfb, bFGF}, Meis3 (Meis homeobox 3) [NCBI Gene 17537] {aka Mrg2}, LIF (LIF interleukin 6 family cytokine) [NCBI Gene 280840], Hprt1 (hypoxanthine phosphoribosyltransferase 1) [NCBI Gene 15452] {aka HPGRT, Hprt}, Qsox1 (quiescin Q6 sulfhydryl oxidase 1) [NCBI Gene 104009] {aka 1300003H02Rik, QSOX, Qscn6, SOx, b2b2673Clo}, Hspa1a (heat shock protein family A (Hsp70) member 1A) [NCBI Gene 193740] {aka Hsp70-3, Hsp70.3, Hsp72, hsp68, hsp70A1}, Tcf7l1 (transcription factor 7 like 1 (T cell specific, HMG box)) [NCBI Gene 21415] {aka Tcf-3, Tcf3, bHLHb21}, Ppme1 (protein phosphatase methylesterase 1) [NCBI Gene 72590] {aka 1110069N17Rik, 2700017M01Rik, PME-1, Pme1}, Hoxb (homeobox B cluster) [NCBI Gene 15406] {aka Hox-2}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Hoxb9 (homeobox B9) [NCBI Gene 15417] {aka Hox-2.5}, Cdx2 (caudal type homeobox 2) [NCBI Gene 12591] {aka Cdx-2}, Asc1 (anterior suture cataract 1) [NCBI Gene 104385] {aka Asc-1}, T (brachyury, T-box transcription factor T) [NCBI Gene 20997] {aka Bra, D17Mit170, Low, Lr, T1, Tbxt}, Gsk3b (glycogen synthase kinase 3 beta) [NCBI Gene 56637] {aka 7330414F15Rik, 8430431H08Rik, GSK-3, GSK-3beta, GSK3}, Sox2 (SRY (sex determining region Y)-box 2) [NCBI Gene 20674] {aka Sox-2, lcc, ysb}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, Lif (leukemia inhibitory factor) [NCBI Gene 16878], Cdx4 (caudal type homeobox 4) [NCBI Gene 12592] {aka Cdx-3, Cdx-4, Cdx3}, Ctnnb1 (catenin beta 1) [NCBI Gene 12387] {aka Bfc, Catnb, Mesc}, Lef1 (lymphoid enhancer binding factor 1) [NCBI Gene 16842] {aka 3000002B05, Lef-1}, Itpr3 (inositol 1,4,5-triphosphate receptor 3) [NCBI Gene 16440] {aka IP3R 3, IP3R-3, Ip3r3, Itpr-3, tf}, Tcf7l2 (transcription factor 7 like 2, T cell specific, HMG box) [NCBI Gene 21416] {aka TCF4B, TCF4E, Tcf-4, Tcf4}, Sox1 (SRY (sex determining region Y)-box 1) [NCBI Gene 20664] {aka Sox-1}, Tbx6 (T-box 6) [NCBI Gene 21389] {aka rv}, Hoxb8 (homeobox B8) [NCBI Gene 15416] {aka Hox-2.4}, Klf2 (Kruppel-like transcription factor 2 (lung)) [NCBI Gene 16598] {aka Lklf}, Meox1 (mesenchyme homeobox 1) [NCBI Gene 17285] {aka D330041M02Rik, Mox-1, Mox1, squig}, Mixl1 (Mix paired-like homeobox) [NCBI Gene 27217] {aka Mm1, Mml}, Pou5f1 (POU domain, class 5, transcription factor 1) [NCBI Gene 18999] {aka NF-A3, Oct-3, Oct-3/4, Oct-4, Oct3, Oct3/4}, P9Ehs1 (protein, Chr 9, NIEHS 1) [NCBI Gene 109957], Cdx1 (caudal type homeobox 1) [NCBI Gene 12590] {aka Cdx, Cdx-1}, CTNNB1 (catenin beta 1) [NCBI Gene 1499] {aka CTNNB, EVR7, MRD19, NEDSDV, armadillo}, Nanog (Nanog homeobox) [NCBI Gene 71950] {aka 2410002E02Rik, ENK, Stm1, ecat4}, Foxh1 (forkhead box H1) [NCBI Gene 14106] {aka Fast1, Fast2, fast-1, fast-2}, Nodal (nodal growth differentiation factor) [NCBI Gene 18119] {aka Tg.413d}, Nr5a2 (nuclear receptor subfamily 5, group A, member 2) [NCBI Gene 26424] {aka D1Ertd308e, Ftf, LRH-1, UF2-H3B, mFTF}, Alk (anaplastic lymphoma kinase) [NCBI Gene 11682] {aka CD246, Tcrz}, Dnase1 (deoxyribonuclease I) [NCBI Gene 13419] {aka DNaseI, Dnl1}, HNF4A (hepatocyte nuclear factor 4 alpha) [NCBI Gene 3172] {aka FRTS4, HNF4, HNF4a7, HNF4a8, HNF4a9, HNF4alpha}, Scgb1b27 (secretoglobin, family 1B, member 27) [NCBI Gene 11354] {aka Abp, Abpa, Abpa27, Sal-1, Tcp}
- **Diseases:** mycoplasma (MESH:D009175), T (MESH:D001260), O (MESH:C535508), CEpiLC (MESH:C537221), EpiLC (MESH:D002292), S (MESH:D018455), N (MESH:C536108)
- **Chemicals:** HCl (MESH:D006851), F12 (MESH:C007782), streptomycin (MESH:D013307), CO2 (MESH:D002245), SYBR-Green (MESH:C098022), MgCl2 (MESH:D015636), SB (MESH:D000965), penicillin (MESH:D010406), AlexaFluor 647 (MESH:C569686), N2 (MESH:D009584), FLC medium (-), PBS (MESH:D007854), 2-mercaptoethanol (MESH:D008623), NaCl (MESH:D012965), DOX (MESH:D004317), AlexaFluor 488 (MESH:C000711379), Triton X-100 (MESH:D017830), puromycin (MESH:D011691), PD0325901 (MESH:C506614), LGK974 (MESH:C586458), DAPI (MESH:C007293), FL (MESH:D005459), glycerine (MESH:D005990), SB-431542 (MESH:C459179), Oligonucleotide (MESH:D009841), paraformaldehyde (MESH:C003043), SDS (MESH:D012967), doxycycline (MESH:D004318), EDTA (MESH:D004492), l-glutamine (MESH:D005973), CHIR99021 (MESH:C473711)
- **Species:** Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** G > A, C with 0, 54G > A
- **Cell lines:** N2B27 — Rattus norvegicus (Rat), Transformed cell line (CVCL_D584), E-MTAB-2958 — Homo sapiens (Human), Finite cell line (CVCL_9L74), ES — Homo sapiens (Human), Embryonic stem cell (CVCL_C769), E-MTAB-2268 — Homo sapiens (Human), Hunter syndrome, Finite cell line (CVCL_W662), HM1 — Mus musculus (Mouse), Embryonic stem cell (CVCL_C315), E-MTAB-6337 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z894), ESCs — Mus musculus (Mouse), Embryonic stem cell (CVCL_9108), ESC — Homo sapiens (Human), Embryonic stem cell (CVCL_9771)

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## Figures

17 figures with captions in the complete paper: https://tomesphere.com/paper/PMC9106585/full.md

## References

90 references — full list in the complete paper: https://tomesphere.com/paper/PMC9106585/full.md

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Source: https://tomesphere.com/paper/PMC9106585