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Cited by 101Williams Syndrome ResearchCraniofacial Disorders and TreatmentsGenetics and Neurodevelopmental Disorders

Dosage analysis of the 7q11.23 Williams region identifies BAZ1B as a major human gene patterning the modern human face and underlying self-domestication

Open access
Zanella, Matteo, Vitriolo, Alessandro, Andirko, Alejandro, Martins, Pedro Tiago, Sturm, Stefanie, O’Rourke, Thomas, Laugsch, Magdalena, Malerba, Natascia +8 more·2019·Science Advances
DOI 10.1126/sciadv.aaw7908PMC PMC6892627

Published version of a preprint

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Abstract

Dissecting the BAZ1B genetic circuitry in the neural crest brings out its critical role in shaping the modern human face.

AI snapshot

Written from the paper’s full text.

TL;DR

The paper dissects BAZ1B dosage in patient-derived neural crest stem cells from Williams-Beuren syndrome, 7q11.23 duplication syndrome, atypical WBS, and controls, showing that BAZ1B controls neural crest migration, induction, and enhancer-centered transcriptional circuits. Integrating these BAZ1B-dependent circuits with paleogenomic datasets links BAZ1B to regulatory changes in modern humans and supports a neurocristopathic basis for self-domestication.

Key findings

  • BAZ1B knockdown in patient-derived neural crest stem cells reduced BAZ1B mRNA by about 40% with sh1 and 70% with sh2. BAZ1B dosage imbalance produced symmetrically opposite migration effects: 7dupASD knockdown lines were slower to close a wound, whereas WBS knockdown lines were faster; neural crest induction was delayed, with lower outgrowth and down-regulation of NR2F1, NR2F2, TFAP2A, and SOX9.
  • RNA-seq across 32 interfered NCSC lines identified 448 genes following BAZ1B dosage at FDR < 0.1 (1192 at P < 0.01 and FDR < 0.25), including 202 directly and 246 inversely correlated genes. The regression analysis captured about 90% of differentially expressed genes from the pairwise analysis (27 of 29, FDR < 0.1). Directly correlated genes enriched for histone phosphorylation, chromosome localization, RNA processing, and splicing; inversely correlated genes enriched for cell migration and cardiovascular and skeletal development.
  • ChIP-seq with CRISPR-Cas9–tagged BAZ1B showed preferential binding at enhancers: 75% of targets were bound at enhancers (6747 genes), with 2297 targets bound at promoters; 40% of genes expressed in neural crest were bound by BAZ1B. The analysis identified 81 regions quantitatively bound by BAZ1B depending on copy number and a core set of 30 bona fide direct targets.
  • Paleogenomic integration found the most significant overlap with the top 10% of genes showing an excess of nearly fixed regulatory mutations in modern humans compared with archaics, across both directly and inversely BAZ1B-dependent genes. The strongest overlaps mapped to genes inversely correlated with BAZ1B levels; no statistically significant overlap was found for archaic-specific mutations against genes directly correlated with BAZ1B.

Methods

  • The study used an iPSC-derived NCSC cohort from WBS, 7dupASD, atypical WBS, and control individuals, with BAZ1B knocked down by two shRNAs (sh1, sh2) plus scrambled control, yielding 32 interfered NCSC lines. Assays included qPCR, Western blot, wound-healing migration, embryoid body–based neural crest differentiation, RNA-seq, and ChIP-seq.
  • For ChIP-seq, endogenous BAZ1B was 3xFLAG-tagged by CRISPR-Cas9 in representative iPSC lines, differentiated to NCSCs, and profiled with anti-FLAG plus histone marks H3K27ac, H3K4me1, H3K4me3, and H3K27me3. RNA-seq and ChIP-seq differential analyses used edgeR with models accounting for individual genetic background (~individual + BAZ1B or ~individual + KD), followed by GO, master regulator, motif, and integrative overlap analyses.
  • Paleogenomic comparisons used high-coverage archaic genomes (one Denisovan, one Altai Neanderthal, one Vindija Neanderthal) and published modern-versus-archaic datasets, including high-frequency changes, missense mutations, regulatory-region mutations, and positive-selection signals in modern humans and domesticated species.

Limitations

  • The paper does not include a dedicated limitations section. It states that the obviously very limited number of high-quality coverage archaic genomes results in many more nearly fixed changes identified in archaics than in modern humans, setting a comparatively higher threshold for identifying nearly fixed modern changes.
  • Evident from the text: the experimental work relies on in vitro patient-derived iPSC/NCSC lines and BAZ1B knockdown rather than in vivo human craniofacial development, and the evolutionary interpretation depends on overlap with paleogenomic datasets that the authors describe as previously correlative.
  • Evident from the text: the NCSC cohort is described as the largest of its kind but remains small, and PCA showed a significant impact of individual genetic backgrounds on transcriptional variability, which the analyses attempted to model statistically.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1126/sciadv.aaw7908

Cites

93 of 93 references verified0 citation errors · 0 not checkable

Statistics

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Claims the paper makes

0 of 57 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    7dupASD NCSC BAZ1B knockdown lines took longer to fill the wound than their respective control scr lines at 8 and 16 hours.

    “The 7dupASD NCSC KD lines took longer to fill the wound when compared to the respective control lines (scr), as indicated by images taken at 8 and 16 hours after a gap was created on the plate surface (Fig. 1C and fig. S1F).”
    Quote in the paperSubstantial claim
  • Findingown data

    BAZ1B knockdown caused a minor delay in neural crest induction.

    “In contrast to the previous observations from X. laevis (10), we also observed a minor delay in NC induction as a consequence of BAZ1B KD (Fig. 1D and fig. S1D)”
    Quote in the paperNot a substantial claim
  • Findingown data

    There is major convergence between BAZ1B control and the genes harboring regulatory changes in the modern human lineage.

    “We find major convergence between the BAZ1B control and the genes harboring regulatory changes in the modern human lineage.”
    Quote in the paperSubstantial claim
  • Findingown data

    WBS BAZ1B knockdown lines were faster than their respective scr lines in closing the gap.

    “We instead observed an opposite behavior for the WBS BAZ1B KD lines, which were faster than the respective scr lines in closing the gap (Fig. 1C and fig. S1F).”
    Quote in the paperSubstantial claim
  • Findingown data

    The delay in neural crest formation upon BAZ1B knockdown was associated with down-regulation of NR2F1, NR2F2, TFAP2A, and SOX9.

    “In addition, the delay in NC formation was associated with a down-regulation of well-established critical regulators of NC migration and maintenance, including NR2F1, NR2F2, TFAP2A, and SOX9 (Fig. 1E).”
    Quote in the paperSubstantial claim
  • May combine two claims. 26
  • Classified as probably not a substantial claim. 14

  • May combine two claims.

    Findingown data

    BAZ1B knockdown resulted in a lower number of outgrowing cells at days 7 and 10 and evidently higher cell mortality.

    “In particular, starting from 2 to 3 days after attachment of EBs, we observed a lower number of outgrowing cells in the KD line (Fig. 1D, days 7 and 10), coupled with an evidently higher cell mortality.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    BAZ1B knockdown cells eventually acquired typical neural crest morphology but with lower differentiation efficiency at day 12.

    “Cells were eventually able to acquire the typical NC morphology, although lower differentiation efficiency was evident, as shown by images taken at day 12.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Principal component analysis corroborated a significant impact of individual genetic backgrounds on transcriptional variability, with most knockdown lines clustering with their respective control scr line.

    “Confirming our previous observations in the two largest cohorts of iPSC lines (29), a principal component analysis (PCA) corroborated the significant impact of individual genetic backgrounds on transcriptional variability, with most “KD lines” clustering with their respective control “scr line.””
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [29] Germain P.-L., Testa G., Taming human genetic variability: Transcriptomic meta-analysis guides the experimental design and interpretation of iPSC-based disease modeling. Stem Cell Rep. 8, 1784– 1796 (2017). PMC5470233 28591656 source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    There was a globally stronger transcriptional impact for samples targeted by sh2 and a milder but clearly distinguishable effect of sh1, resulting in a gradient of dosages over scr control lines.

    “Consistent with the differential efficiency of the two short hairpins, we found a globally stronger transcriptional impact for the group of samples targeted by sh2 (fig. S2C) and a milder but nevertheless clearly distinguishable effect of sh1, resulting in particularly informative gradient of dosages over the scr control lines.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Chromatin remodeling was the most prominently enriched group within the overall domain of transcriptional regulation.

    “Chromatin remodeling was indeed the most prominently enriched group within the overall domain of transcriptional regulation.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    MXI1 is itself found among genes inversely correlated with BAZ1B and is itself a regulator of BAZ1B, pointing to cross-talk between the two.

    “which is itself found among the genes inversely correlated with BAZ1B and is itself a regulator of BAZ1B, pointing to a cross-talk between the two (fig. S2C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Among 1192 DEGs, 21.3% (257 of 1192) are associated to enhancers that are both bound by BAZ1B and differentially H3K27-acetylated concordantly with BAZ1B levels, with a stronger overlap for genes inversely correlated with BAZ1B (160 versus 97).

    “This enabled the overlay of epigenomic and transcriptomic profiles, uncovering that among the 1192 DEGs identified in the regression RNA-seq analysis, 21.3% (257 of 1192) are associated to enhancers that are both bound by BAZ1B and differentially H3K27-acetylated in a manner concordant with BAZ1B levels (fig. S4E), with a stronger overlap for genes whose expression is inversely correlated with BAZ”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    BAZ1B binds 75% of its targets at enhancer regions (6747 genes), with the remaining 2297 targets bound at promoters.

    “Notably, BAZ1B binds 75% of its targets at their enhancer regions (6747 genes), with the remaining 2297 targets bound at promoters (Fig. 3C).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    40% of genes expressed in neural crest are bound by BAZ1B, either exclusively at enhancers (27.4%), exclusively at promoters (3.5%), or at both regions (9%).

    “In addition, 40% of genes expressed in NC are bound by BAZ1B, either exclusively at enhancers (27.4%) or exclusively at promoters (3.5%) or at both regions (9%).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    176 and 25 regions are differentially bound preferentially in WBS and 7dupASD, respectively (FDR < 0.1).

    “and 176 and 25 regions differentially bound preferentially in WBS (fig. S4B) and 7dupASD (FDR < 0.1) (fig. S4C), respectively.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    A total of 30,8470 putative enhancer regions were identified.

    “identifying a total of 30,8470 putative enhancer regions.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    H3K27ac was the most affected histone mark, with 7254 genes differentially acetylated at their enhancers, followed by differential distribution of H3K4me1 (4048) and H3K27me3 (2136) marks.

    “We thus performed a regression analysis on BAZ1B levels for the distribution of the three histone marks in the aforementioned regions and found H3K27ac to be the most affected, with 7254 genes differentially acetylated at their enhancers, followed by a differential distribution of the H3K4me1 (4048) and H3K27me3 (2136) marks (fig. S4D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Among the key neural crest hubs affected by BAZ1B dosage, EDN3, MAGOH, and ZEB2 are additional critical genes that had also been predicted in the same model because they are associated with behavioral changes found in domesticates.

    “Among the key NC hubs affected by BAZ1B dosage, we uncovered three additional critical genes—EDN3, MAGOH, and ZEB2—that had also been predicted in the same model because they are associated with behavioral changes found in domesticates”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The most parsimonious hypothesis posits that the same core mechanisms underlie both domestication and self-domestication.

    “Thus, as self-domestication represents a special case of domestication, the most parsimonious hypothesis must posit the same core mechanisms to underlie both.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Modern humans went through a domestication process in the course of their evolution, according to the self-domestication hypothesis.

    “This has led to the formulation of a self-domestication hypothesis according to which modern humans (3) went through a domestication process in the course of their evolution.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [3] R. W. Wrangham, The Goodness Paradox: How Evolution Made Us Both More and Less Violent (Profile Books Ltd., 2019).

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    BAZ1B has an established role in neural crest maintenance and migration in Xenopus laevis, and knockout mice show craniofacial defects.

    “(i) its established role in NC maintenance and migration in Xenopus laevis and the craniofacial defects observed in knockout mice (10, 11);”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [10] Barnett C., Yazgan O., Kuo H. C., Malakar S., Thomas T., Fitzgerald A., Harbour W., Henry J. J., Krebs J. E., Williams syndrome transcription factor is critical for neural crest cell function in Xenopus laevis. Mech. Dev. 129, 324– 338 (2012). 22691402 PMC3459152 source

      Not checked in the free run.

    • cites [11] Ashe A., Morgan D. K., Whitelaw N. C., Bruxner T. J., Vickaryous N. K., Cox L. L., Butterfield N. C., Wicking C., Blewitt M. E., Wilkins S. J., Anderson G. J., Cox T. C., Whitelaw E., A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development. Genome Biol. 9, R182 (2008). 19099580 PMC2646286 source

      Not checked in the free run.

  • May combine two claims.

    Premisenone given

    Williams-Beuren syndrome and Williams-Beuren region duplication syndrome are caused respectively by hemideletion or hemiduplication of 28 genes at the 7q11.23 region (WBSCR).

    “Williams-Beuren syndrome [WBS; OMIM (Online Mendelian Inheritance in Man) 194050] and Williams-Beuren region duplication syndrome (7dupASD; OMIM 609757), caused respectively by the hemideletion or hemiduplication of 28 genes at the 7q11.23 region [WBS critical region (WBSCR)]”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The most detailed study systematically exploring high-frequency (>90%) changes in modern humans for which archaic humans carry the ancestral state found BAZ1B enriched for mutations in modern humans, most of which fall in regulatory regions of the gene.

    “(v) the thus far most detailed study systematically exploring high-frequency (HF) (>90%) changes in modern humans for which archaic humans carry the ancestral state, which found BAZ1B enriched for mutations in modern humans (most of which fall in the regulatory regions of the gene) (15).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [15] Kuhlwilm M., Boeckx C., A catalog of single nucleotide changes distinguishing modern humans from archaic hominins. Sci. Rep. 9, 8463 (2019). 31186485 PMC6560109 source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    BAZ1B knockdown achieved an overall reduction of about 40% for sh1 and 70% for sh2 at the RNA level, as well as reduction at the protein level.

    “confirming the attainment of the desired gradient with an overall reduction of about 40% for sh1 and 70% for sh2, as well as reduction at the protein level, as detected by Western blot (fig. S1E).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    Previous work established the largest cohort of 7q11.23 patient-derived iPSC lines and revealed major disease-relevant transcriptional dysregulation apparent at the pluripotent state and exacerbated upon differentiation.

    “Our previous work had established the largest cohort of 7q11.23 patient-derived induced pluripotent stem cell (iPSC) lines and revealed major disease-relevant transcriptional dysregulation that was already apparent at the pluripotent state and became further exacerbated upon differentiation (16).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [16] Adamo A., Atashpaz S., Germain P. L., Zanella M., D'Agostino G., Albertin V., Chenoweth J., Micale L., Fusco C., Unger C., Augello B., Palumbo O., Hamilton B., Carella M., Donti E., Pruneri G., Selicorni A., Biamino E., Prontera P., McKay R., Merla G., Testa G., 7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages. Nat. Genet. 47, 132– 141 (2015). 25501393 source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    A manually curated signature from an extensive literature review validated the cranial identity of the NCSC lines, and clustering by Pearson correlation excluded genotype- or hairpin-specific expression changes.

    “As shown in fig. S2A, a manually curated signature from an extensive literature review (23–28) validated the cranial identity of our NCSC lines, while clustering by Pearson correlation excluded the presence of any genotype- or hairpin-specific expression change.”
    Quote in the paperSubstantial claim0 of 6 sources checked
    • cites [23] Wilderman A., VanOudenhove J., Kron J., Noonan J. P., Cotney J., High-resolution epigenomic atlas of human embryonic craniofacial development. Cell Rep. 23, 1581– 1597 (2018). 29719267 PMC5965702 source

      Not checked in the free run.

    • cites [24] Spokony R. F., Aoki Y., Saint-Germain N., Magner-Fink E., Saint-Jeannet J.-P., The transcription factor Sox9 is required for cranial neural crest development in Xenopus. Development 129, 421– 432 (2002). 11807034 source

      Not checked in the free run.

    • cites [25] Santagati F., Rijli F. M., Cranial neural crest and the building of the vertebrate head. Nat. Rev. Neurosci. 4, 806– 818 (2003). 14523380 source

      Not checked in the free run.

    • cites [26] Bhatt S., Diaz R., Trainor P. A., Signals and switches in mammalian neural crest cell differentiation. Cold Spring Harb. Perspect. Biol. 5, a008326 (2013). 23378583 PMC3552505 source

      Not checked in the free run.

    • cites [27] Ko S. O., Chung I. H., Xu X., Oka S., Zhao H., Cho E. S., Deng C., Chai Y., Smad4 is required to regulate the fate of cranial neural crest cells. Dev. Biol. 312, 435– 447 (2007). 17964566 PMC2704603 source

      Not checked in the free run.

    • cites [28] Mishina Y., Snider T. N., Neural crest cell signaling pathways critical to cranial bone development and pathology. Exp. Cell Res. 325, 138– 147 (2014). 24509233 PMC4072849 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Several master regulators are themselves causative genes of intellectual disability syndromes with neurocristopathic involvement, as in Gabriele-de Vries syndrome caused by YY1 haploinsufficiency.

    “several of which are themselves causative genes of intellectual disability syndromes with neurocristopathic involvement, as in the case of our recently identified Gabriele–de Vries syndrome caused by YY1 haploinsufficiency (31, 32).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [31] Gabriele M., Vulto-van Silfhout A. T., Germain P. L., Vitriolo A., Kumar R., Douglas E., Haan E., Kosaki K., Takenouchi T., Rauch A., Steindl K., Frengen E., Misceo D., Pedurupillay C. R. J., Stromme P., Rosenfeld J. A., Shao Y., Craigen W. J., Schaaf C. P., Rodriguez-Buritica D., Farach L., Friedman J., Thulin P., McLean S. D., Nugent K. M., Morton J., Nicholl J., Andrieux J., Stray-Pedersen A., Chambon P., Patrier S., Lynch S. A., Kjaergaard S., Tørring P. M., Brasch-Andersen C., Ronan A., van Haeringen A., Anderson P. J., Powis Z., Brunner H. G., Pfundt R., Schuurs-Hoeijmakers J. H. M., van source

      Not checked in the free run.

    • cites [32] Gabriele M., Lopez Tobon A., D’Agostino G., Testa G., The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog. Neuropsychopharmacol. Biol. Psychiatry 84, 306– 327 (2018). 29309830 source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    EGR1 is implicated in cranial development in animal models, and its promoter has been shown to feature a bivalent state in human embryonic cranial neural crest.

    “which is implicated in cranial development (in animal models) (33, 34) and whose promoter has been recently shown to feature a bivalent state in human embryonic cranial NC (23, 35).”
    Quote in the paperNot a substantial claim0 of 4 sources checked
    • cites [33] McMahon A. P., Champion J. E., McMahon J. A., Sukhatme V. P., Developmental expression of the putative transcription factor Egr-1 suggests that Egr-1 and c-fos are coregulated in some tissues. Development 108, 281– 287 (1990). 2351070 source

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    • cites [34] Dalcq J., Pasque V., Ghaye A., Larbuisson A., Motte P., Martial J. A., Muller M., RUNX3, EGR1 and SOX9B form a regulatory cascade required to modulate BMP-signaling during cranial cartilage development in zebrafish. PLOS ONE 7, e50140 (2012). 23209659 PMC3507947 source

      Not checked in the free run.

    • cites [23] Wilderman A., VanOudenhove J., Kron J., Noonan J. P., Cotney J., High-resolution epigenomic atlas of human embryonic craniofacial development. Cell Rep. 23, 1581– 1597 (2018). 29719267 PMC5965702 source

      Not checked in the free run.

    • cites [35] Werner A., Iwasaki S., McGourty C. A., Medina-Ruiz S., Teerikorpi N., Fedrigo I., Ingolia N. T., Rape M., Cell-fate determination by ubiquitin-dependent regulation of translation. Nature 525, 523– 527 (2015). 26399832 PMC4602398 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    BAZ1B binding regions are enriched for target sites of major regulators of neural crest and its neural derivatives, among which TFAP2A stands out given its core role in neural border formation and neural crest induction and differentiation through binding and stabilization of neural-crest-specific enhancers with NR2F1, NR2F2, and EP300.

    “Thus, BAZ1B binding regions are enriched for target sites of major regulators of NC and its neural derivatives (38, 39), among which TFAP2A stands out given its core role in neural border formation and NC induction and differentiation (40) through the binding and stabilization of NC-specific enhancers, in concert with NR2F1, NR2F2, and EP300 (41).”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [38] Wapinski O. L., Vierbuchen T., Qu K., Lee Q. Y., Chanda S., Fuentes D. R., Giresi P. G., Ng Y. H., Marro S., Neff N. F., Drechsel D., Martynoga B., Castro D. S., Webb A. E., Südhof T. C., Brunet A., Guillemot F., Chang H. Y., Wernig M., Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell 155, 621– 635 (2013). 24243019 PMC3871197 source

      Not checked in the free run.

    • cites [39] Hong S. J., Choi H. J., Hong S., Huh Y., Chae H., Kim K. S., Transcription factor GATA-3 regulates the transcriptional activity of dopamine beta-hydroxylase by interacting with Sp1 and AP4. Neurochem. Res. 33, 1821– 1831 (2008). 18338249 PMC2712938 source

      Not checked in the free run.

    • cites [40] de Crozé N., Maczkowiak F., Monsoro-Burq A. H., Reiterative AP2a activity controls sequential steps in the neural crest gene regulatory network. Proc. Natl. Acad. Sci. U.S.A. 108, 155– 160 (2011). 21169220 PMC3017139 source

      Not checked in the free run.

    • cites [41] Rada-Iglesias A., Prescott S. L., Wysocka J., Human genetic variation within neural crest enhancers: molecular and phenotypic implications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20120360 (2013). 23650634 PMC3682725 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    This first dosage-faithful analysis of BAZ1B occupancy in a diverse cohort of human NCSCs establishes its pervasive and mostly distal targeting of the neural-crest-specific epigenome, with a preferential activator role on critical transcriptional circuits that define neural crest fate and function.

    “Together, this first dosage-faithful analysis of BAZ1B occupancy in a diverse cohort of human NCSCs establishes its pervasive and mostly distal targeting of the NC-specific epigenome, with a preferential activator role on the critical transcriptional circuits that define NC fate and function.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The list of genes harboring (nearly) fixed mutations in moderns versus archaics contains three classes: genes harboring high-frequency changes, genes harboring high-frequency missense mutations, and genes enriched for high-frequency mutations in regulatory regions.

    “the list of genes harboring (nearly) fixed mutations in moderns versus archaics contains three classes: (i) genes harboring high-frequency changes (15), (ii) genes harboring high-frequency missense mutations (red barplot), and (iii) genes enriched for high-frequency mutations in regulatory regions (green barplot) [data based on (15)]”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [15] Kuhlwilm M., Boeckx C., A catalog of single nucleotide changes distinguishing modern humans from archaic hominins. Sci. Rep. 9, 8463 (2019). 31186485 PMC6560109 source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    Mild neural crest deficits have been put forth as a unifying explanatory framework for the defining features of domestication syndrome, with BAZ1B listed among putative underlying genes because of its previously reported role in the neural crest of model organisms.

    “Mild NC deficits have been put forth as a unifying explanatory framework for the defining features of the so-called domestication syndrome, with BAZ1B listed among the putative underlying genes because of its previously reported role in the NC of model organisms (5, 10, 11).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [5] Wilkins A. S., Wrangham R. W., Fitch W. T., The “domestication syndrome” in mammals: A unified explanation based on neural crest cell behavior and genetics. Genetics 197, 795– 808 (2014). 25024034 PMC4096361 source

      Not checked in the free run.

    • cites [10] Barnett C., Yazgan O., Kuo H. C., Malakar S., Thomas T., Fitzgerald A., Harbour W., Henry J. J., Krebs J. E., Williams syndrome transcription factor is critical for neural crest cell function in Xenopus laevis. Mech. Dev. 129, 324– 338 (2012). 22691402 PMC3459152 source

      Not checked in the free run.

    • cites [11] Ashe A., Morgan D. K., Whitelaw N. C., Bruxner T. J., Vickaryous N. K., Cox L. L., Butterfield N. C., Wicking C., Blewitt M. E., Wilkins S. J., Anderson G. J., Cox T. C., Whitelaw E., A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development. Genome Biol. 9, R182 (2008). 19099580 PMC2646286 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Neanderthal face displays derived characteristics.

    “given the evidence that the Neanderthal face also displays derived characteristics (42)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [42] Lacruz R. S., Stringer C. B., Kimbel W. H., Wood B., Harvati K., O’Higgins P., Bromage T. G., Arsuaga J.-L., The evolutionary history of the human face. Nat. Ecol. Evol. 3, 726– 736 (2019). 30988489 source

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  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing).

    Premisecitation

    COL11A1 lies in a region of the human genome that resisted archaic introgression.

    “which lies in a region of the human genome that resisted archaic introgression (13)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [13] Peyrégne S., Boyle M. J., Dannemann M., Prüfer K., Detecting ancient positive selection in humans using extended lineage sorting. Genome Res. 2017, 1563– 1572 (2017). PMC5580715 28720580 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Mild neural crest deficits are a central and unifying functional layer underlying domestication.

    “The first problem was tackled by the recent proposition of mild NC deficits as a central and unifying functional layer underlying domestication (5).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [5] Wilkins A. S., Wrangham R. W., Fitch W. T., The “domestication syndrome” in mammals: A unified explanation based on neural crest cell behavior and genetics. Genetics 197, 795– 808 (2014). 25024034 PMC4096361 source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    BAZ1B plays a pivotal role in neural crest stem cell enhancer regulation, consistent with its preferential binding of distal regulatory regions.

    “we were able to define a pivotal role for BAZ1B in NCSC enhancer regulation, consistent with its preferential binding of distal regulatory regions”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    FOXP2, ROBO1, and ROBO2 have long been implicated in brain wiring processes critical for vocal learning in several species, including humans.

    “Among the genes downstream of BAZ1B that we uncovered in this study, FOXP2, ROBO1, and ROBO2 have long been implicated in brain wiring processes critical for vocal learning in several species (50, 51), including humans”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [50] Vernes S. C., Oliver P. L., Spiteri E., Lockstone H. E., Puliyadi R., Taylor J. M., Ho J., Mombereau C., Brewer A., Lowy E., Nicod J., Groszer M., Baban D., Sahgal N., Cazier J. B., Ragoussis J., Davies K. E., Geschwind D. H., Fisher S. E., Foxp2 regulates gene networks implicated in neurite outgrowth in the developing brain. PLOS Genet. 7, e1002145 (2011). 21765815 PMC3131290 source

      Not checked in the free run.

    • cites [51] Wang R., Chen C. C., Hara E., Rivas M. V., Roulhac P. L., Howard J. T., Chakraborty M., Audet J. N., Jarvis E. D., Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners. J. Comp. Neurol. 523, 892– 906 (2015). 25424606 PMC4329046 source

      Not checked in the free run.

  • May combine two claims.

    Study design and conductown data

    The study used a large set of samples (11 individuals) and two short hairpins that robustly reduced BAZ1B expression levels by ~40 and ~70% in all individuals lines.

    “We were able to do this because of the availability of a large set of samples (11 individuals) and because of the two short hairpins robustly respectively reducing BAZ1B expression levels, respectively by ~40 and ~70% in all individuals lines.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The atypical BAZ1B-sparing deletion patient served as a particularly informative control, as confirmed by clustering of atypical NCSC lines with controls when probed for BAZ1B occupancy.

    “Notably, our cohort also included NCSCs from a patient with rare WBS featuring a much milder WBS gestalt and harboring an atypical, BAZ1B-sparing deletion that served as a particularly informative control, as confirmed by the clustering of atypical NCSC lines with controls when probed for BAZ1B occupancy.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    Our findings establish the heuristic power of neurodevelopmental disease modeling for the study of human evolution.

    “In conclusion, our findings establish the heuristic power of neurodevelopmental disease modeling for the study of human evolution.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Ethics approvals for the original iPSC cohort also apply to the additional samples included in this study.

    “Ethics approvals were reported in the study that established the original iPSC cohort (16) and also apply to the additional samples included in this study (7dupASD3 and CTL4R).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [16] Adamo A., Atashpaz S., Germain P. L., Zanella M., D'Agostino G., Albertin V., Chenoweth J., Micale L., Fusco C., Unger C., Augello B., Palumbo O., Hamilton B., Carella M., Donti E., Pruneri G., Selicorni A., Biamino E., Prontera P., McKay R., Merla G., Testa G., 7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages. Nat. Genet. 47, 132– 141 (2015). 25501393 source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    BAZ1B knockdown was performed using validated pLKO.1 TRC vectors TRCN0000013338 and TRCN0000013341.

    “BAZ1B KD was performed using validated pLKO.1 TRC vector TRCN0000013338 (referred to as sh1) and TRCN0000013341 (referred to as sh2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    The quality of the numerical differential expression analysis was validated using HipSci data and iPSCpoweR tools, and all analyses identified very low number of spurious DEGs.

    “To validate the quality of our numerical differential expression analysis, we took advantage of HipSci data (55, 56) and iPSCpoweR tools (29).”
    • Also stated in: § RNA-seq analysis · plain
      “All analyses identified very low number of spurious DEGs (fig. S2E).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [55] Streeter I., Harrison P. W., Faulconbridge A.; The HipSci Consortium, Flicek P., Parkinson H., Clarke L., The human-induced pluripotent stem cell initiative-data resources for cellular genetics. Nucleic Acids Res. 45, D691– D697 (2017). 27733501 PMC5210631 source

      Not checked in the free run.

    • cites [56] Kilpinen H., Goncalves A., Leha A., Afzal V., Alasoo K., Ashford S., Bala S., Bensaddek D., Casale F. P., Culley O. J., Danecek P., Faulconbridge A., Harrison P. W., Kathuria A., McCarthy D., McCarthy S. A., Meleckyte R., Memari Y., Moens N., Soares F., Mann A., Streeter I., Agu C. A., Alderton A., Nelson R., Harper S., Patel M., White A., Patel S. R., Clarke L., Halai R., Kirton C. M., Kolb-Kokocinski A., Beales P., Birney E., Danovi D., Lamond A. I., Ouwehand W. H., Vallier L., Watt F. M., Durbin R., Stegle O., Gaffney D. J., Common genetic variation drives molecular heterogeneity in human i source

      Not checked in the free run.

    • cites [29] Germain P.-L., Testa G., Taming human genetic variability: Transcriptomic meta-analysis guides the experimental design and interpretation of iPSC-based disease modeling. Stem Cell Rep. 8, 1784– 1796 (2017). PMC5470233 28591656 source

      Not checked in the free run.

38 of 38

  • The paper relies on this without support.

    The neurocristopathic basis of domestication and its extension to the evolution of anatomically modern humans had not been experimentally tested.

    “However, both the neurocristopathic basis of domestication and its extension to the evolution of AMHs remain to be tested experimentally.”

  • The paper relies on this without support.

    Phenomena such as odontogenesis and endochondral bone morphogenesis are linked to recent changes in the bone structure of modern versus archaic humans, with Homo sapiens having characteristically smaller teeth than its extinct relatives.

    “Many of the phenomena captured by these GO categories (e.g., odontogenesis and endochondral bone morphogenesis) are linked to recent changes in the bone structure of modern (versus archaic) humans, with Homo sapiens having characteristically smaller teeth than its extinct relatives.”

  • The paper relies on this without support.

    There is an obvious lack of gene expression data from archaic hominins.

    “For humans, given the obvious lack of gene expression data from archaic hominins, we reasoned that this hypothesis could be verified by examining the genetic changes between archaic and modern humans in light of the gene regulatory networks directly inferred from human neurocristopathies.”
3 of 3

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • GTF2I is deleted in Williams-Beuren syndrome, a complex condition characterized by craniofacial, hyper-vocalization, and hyper-sociability.

    “a transcription factor deleted in Williams–Beuren syndrome, a complex condition characterized by craniofacial, hyper-vocalization, and hyper-sociability (fig. 7), signs which has been considered an entry point to understand the evolution of the modern human face and prosociability (Zanella, et al. 2019).”

    From <i>DLX5/6</i> GABAergic Expression Affects Social Vocalization: Implications for Human Evolution (2021) · cites this paper as Zanella, et al. 2019

    The Introduction (page not available) describes WBS as a deletion of genes in the 7q11.23 region, names GTF2I among WBS genes, and connects WBS craniofacial and social traits to the study of modern human evolution. The Discussion mentions a distinctive linguistic profile in WBS, but neither passage identifies hyper-vocalization as a characteristic of the syndrome. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • In comparison with high-frequency mutations and selective sweep studies in archaic humans, modern humans, and domesticated species, the only significant intersection was between Lidia DEGs and genes with high frequency regulatory mutations in archaic compared to modern humans.

    “In the comparison with the high-frequency mutations and selective sweep studies in archaic humans, modern humans, and domesticated species (thirteen gene sets in total, compiled in [42], the only significant intersection was between the Lidia DEGs and genes with high frequency regulatory mutations in archaic compared to modern humans.”

    From Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle (2021) · cites this paper as [42]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

  • HipSci sample count conflicts with individuals and clones per individual

    Minor

    Thirteen individuals with two clones per individual would provide 26 samples, not the reported 22.

    Reported 22 · recomputed 26

  • Interfered-line total does not match the stated cohort and conditions

    Minor

    The paper describes 11 NCSC lines, each assigned two BAZ1B-targeting hairpins and a scrambled control. That gives 33 lines, not 32, even before counting the additional atWBS line.

    Reported 32 · recomputed 33

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 2

  1. C. Barnett, J. E. Krebs, WSTF does it all: A multifunctional protein in transcription, repair, and replication. Biochem. Cell Biol. 89, 12–23 (2011).
  2. T. O’Rourke C. Boeckx Converging roles of glutamate receptors in domestication and prosociality. bioRxiv 439869 [ Preprint ]. https://doi.org/10.1101/439869. · DOI

Cited by

Sorted by citations

Related

Authors
Zanella, M., Vitriolo, A., Andirko, A., Martins, P. T., Sturm, S., O’Rourke, T., Laugsch, M., Malerba, N., Skaros, A., Trattaro, S., Germain, P.-L., Mihailovic, M., Merla, G., Rada-Iglesias, A., Boeckx, C., & Testa, G.
Affiliations
  • University of Milan (IT)
  • University of Barcelona, Barcelona, Spain.
  • Universitat de Barcelona (ES)
  • University of Cologne (DE)
  • Casa Sollievo della Sofferenza (IT)
  • Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
  • Institució Catalana de Recerca i Estudis Avançats (ES)
Corresponding author
Testa, Giuseppe
ORCID
Venue
Science Advances
Publisher
American Association for the Advancement of Science (AAAS)
Published
2019-12-06
Volume
5
Issue
12
Pages
eaaw7908-eaaw7908
ISSN
2375-2548 (ISSN-L)
DOI
10.1126/sciadv.aaw7908
PMC
PMC6892627
OpenAlex
W2993685839
Semantic Scholar
a33599b15701dd0f38894b3f4bcfe6d3ef5f5d2f
Cited by
101
References
92
Citations by year
2026: 8 · 2025: 11 · 2024: 9 · 2023: 15 · 2022: 17 · 2021: 22 · 2020: 16 · 2019: 2 · 2018: 1
FWCI
5.37
Type
journal article
Language
en
Open access
Licence
cc-by-sa
Locations
  • Science Advances (publishedVersion, cc-by-sa)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
  • Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by-nc)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc)
  • ETH Zürich Research Collection
Funders
  • Ministry of Health
  • European Research Council (616441-DISEASEAVATARS)
  • Fondazione Telethon (GGP14265)
  • Generalitat de Catalunya (2017-SGR-341)
  • Fondazione Umberto Veronesi
  • European Social Fund (BES-2017-080366)
  • Spanish Ministry of Economy and Competitiveness (FFI2016-78034-C2-1-P)
  • MEXT/JSPS Grant-in-Aid for Scientific Research on Innovative Areas 4903 (JP17H06379)
  • Marie Curie International Reintegration Grant from the European Union (PIRG-GA-2009-256413)
  • EPIGEN Flagship Project of the Italian National Research Council
  • Horizon 2020
  • Ricerca Corrente granted by the Italian Ministry of Health
  • IEO Foundation
  • Portuguese Foundation for Science and Technology (SFRH/BD/131640/2017)
Topics
  • Life Sciences › Neuroscience › Developmental Neuroscience › Williams Syndrome Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Craniofacial Disorders and Treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Keywords
BAZ1B, Williams syndrome, neural crest stem cells, chromatin remodeling, paleogenomics, craniofacial development, prosocial behavior, neural crest migration, transcriptional regulation
MeSH terms
Domestication, Epigenome, Bromodomain Containing Proteins, Cell Line, Cell Movement, Chromosomes, Human, Pair 7, Face, Humans, Transcription Factors, Gene Dosage, Williams Syndrome, Evolution, Molecular, Databases, Genetic, Histone Code, Gene Regulatory Networks, Induced Pluripotent Stem Cells, Neural Stem Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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