Biology subjects

Mitchell, Z. H.

Publications and source records attributed to Mitchell, Z. H..

4 recordsLinked to original sources

bioRxiv2026

Human-specific retrotransposons encode the regulatory logic of two lineages in a bipotent neural crest and central nervous system precursor

Transposable elements are sources of cis-regulatory innovation, and the youngest families are particularly interesting because only recent insertions can account for species-specific regulatory divergence. SVAs (subfamilies -E, F), LTR5Hs and L1HS are human-specific retroelements. They are polymorphic, and in some cases still mobile. Regulatory activity in these families has been surveyed mainly in pluripotent cells and differentiated tissues, leaving the early embryonic precursors in which lineage decisions are made largely unexplored. We profiled chromatin accessibility and gene expression in human iPSC-derived bipotent neuroectodermal aggregates harvested at a stage that precedes lineage commitment and retains competence for both the neural crest and the central nervous system. Transcriptional profiling confirmed this dual competence: neural plate border, neural crest and forebrain programs were concurrently active, and definitive neural crest specifiers not yet induced. Of ~4,300 annotated human-specific transposons, 289 were reproducibly accessible in the aggregates. Relative to inaccessible elements, these were closer to genes, occupied gene-dense neighborhoods, and had more highly expressed neighboring transcripts. They were enriched for transcription factor binding motifs drawn from both neural crest and neuronal programs, mirroring the dual competence of the cells. Co-option was strongly family-biased in both extent and content, with SVA-F and LTR5Hs over-represented among accessible elements and each family carrying a distinct motif repertoire. Interestingly, protein interaction analysis of the genes near accessible elements recovered a module built around TRIM28 and multiple KRAB zinc-finger proteins, the machinery that silences transposons through H3K9me3 suggesting a potential feedback loop. These data identify human-specific elements as candidate regulatory substrates at a bipotent developmental stage.

developmental biology↗

bioRxiv2025

Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancers

Neural crest induction begins early during neural plate formation, requiring precise transcriptional control to activate lineage-specific enhancers. Here, we demonstrate that SALL4, a transcription factor associated with syndromes featuring craniofacial anomalies, plays a critical role in early cranial neural crest (CNCC) specification. Using SALL4-het-KO human iPSCs to model clinical haploinsufficiency, we show that SALL4 directly recruits BAF to CNCC-lineage specific enhancers at the neuroectodermal stage, specifically when neural crest gene expression is induced at the neural plate border. Without functional SALL4, BAF is not loaded at chromatin, leaving CNCC enhancers inaccessible. Consequently, the cells cannot undergo proper CNCC induction and specification due to persistent enhancer repression, despite normal neuroectodermal and neural plate progression. Moreover, by performing SALL4 isoform-specific depletion, we demonstrate that the SALL4A is the isoform essential for CNCC induction and specification, and that SALL4B cannot compensate for SALL4A loss in this developmental process. In summary, our findings reveal SALL4 as essential regulator of BAF-dependent enhancer activation during early stages of neural crest development, providing molecular insights into SALL4-associated craniofacial anomalies.

developmental biology↗

bioRxiv2025

Human-specific transposable elements shaped the evolution of craniofacial development through regulation of neural crest migration

Craniofacial development is evolutionarily conserved, yet subtle changes in its regulatory network drive species-specific traits. Transposable elements (TEs) contribute to genome evolution, but their role in cranial neural crest cells (CNCCs) remains unclear. Here, we investigate the domestication of hominoid-specific TEs (LTR5Hs and SVAs) as enhancers during human CNCC specification, a process critical for vertebrate craniofacial development. Using human iPSC-derived CNCCs, we identified [~]550 hominoid-specific TEs functioning as enhancers, including [~]250 human-specific, predominantly LTR5Hs. These elements are enriched for CNCC coordinator motifs, are bound by the CNCC signature factor TWIST1, and their enhancer activity appears largely CNCC-specific. CRISPR-interference targeting [~]75% of these active TEs led to widespread transcriptional dysregulation of genes involved in neural crest migration, and two orthogonal functional assays confirmed that CNCC migration is impaired upon TE repression. Finally, genes near human-specific TEs showed higher expression in human CNCCs compared to chimpanzee CNCCs, but TE repression restored gene expression to chimpanzee levels. These findings highlight how young TEs were domesticated to fine-tune CNCC regulatory networks, potentially contributing to lineage-specific craniofacial evolution.

genomics↗

bioRxiv2025

CHD3 regulates BMP signalling response during cranial neural crest cell specification

CHD3 is a component of the NuRD chromatin remodeling complex. Pathogenic CHD3 variants cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder with variable features including developmental delays, intellectual disability, speech/language difficulties, and craniofacial anomalies. To unveil the role of CHD3 in craniofacial development, we differentiated CHD3-KO induced pluripotent stem cells into cranial neural crest cells (CNCCs). CHD3 expression is low in wild-type iPSCs and neuroectoderm, but upregulated during CNCC specification, where it opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and an imbalance between BMP and Wnt signalling, ultimately resulting in aberrant mesodermal fate. Consequently, CNCC specification fails, replaced by early-mesoderm identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as a pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development.

developmental biology↗