# Foxi2 and Sox3 are master transcription regulators that control ectoderm germ layer specification in Xenopus

## TL;DR

The study identifies Foxi2 and Sox3 as key regulators that control how cells in Xenopus become part of the ectoderm germ layer.

## Contribution

The novel contribution is identifying Foxi2 and Sox3 as master transcription regulators of ectoderm specification in Xenopus.

## Key findings

- Foxi2 and Sox3 co-expression induces ectodermal markers and suppresses mesendodermal markers.
- Foxi2 and Sox3 bind to cis-regulatory modules, shaping the epigenetic landscape of the ectoderm genome.
- Ectodermal super-enhancers are enriched with cis-regulatory modules regulated by Foxi2 and Sox3.

## Abstract

Germ layer specification represents a critical transition where pluripotent cells acquire lineage-specific identities. We identify the maternal transcription factors Foxi2 and Sox3 to be pivotal master regulators of ectodermal germ layer specification in Xenopus. Ectopic co-expression of Foxi2 and Sox3 in prospective endodermal tissue induces the expression of ectodermal markers while suppressing mesendodermal markers. Transcriptomic analyses reveal that Foxi2 and Sox3 jointly and independently regulate hundreds of ectodermal target genes. During early cleavage stages, Foxi2 and Sox3 pre-bind to key cis-regulatory modules (CRMs), marking sites that later recruit Ep300 and facilitate H3K27ac deposition, thereby shaping the epigenetic landscape of the ectodermal genome. These CRMs are highly enriched within ectoderm-specific super-enhancers (SEs). Our findings highlight the pivotal role of ectodermal SE-associated CRMs in precise and robust ectodermal gene activation, establishing Foxi2 and Sox3 as central architects of ectodermal lineage specification.

Pluripotent cells acquire lineage-specific identities during germ layer specification, but the mechanisms underlying this process remain unclear. This study shows that the maternal transcription factors Foxi2 and Sox3 act as master regulators of ectodermal germ layer specification in Xenopus, ensuring the robust and precise expression of target genes.