Biology subjects

Bonefas, K. M.

Publications and source records attributed to Bonefas, K. M..

3 recordsLinked to original sources

bioRxiv2026

POGZ safeguards neuronal gene chromatin architecture and transcription

Disruption of chromatin organization is a common pathogenic mechanism in neurodevelopmental disorders, yet how changes in 3D genome architecture relate to transcriptional dysfunction in the developing brain remains unclear. POGZ, a transposase-derived chromatin regulator mutated in White-Sutton syndrome and autism spectrum disorder (ASD) has been linked to both heterochromatin and accessible regulatory DNA, but its in vivo function in the brain is unresolved. Using immunoprecipitation-mass spectrometry in embryonic day 13.5 (E13.5) mouse cortex, we identify the H3K9 methyltransferases G9a/GLP as principal POGZ interactors, placing POGZ within the core H3K9 methylation machinery in vivo. We find that POGZ loss in embryonic mouse cortex drives bidirectional, megabase-scale redistribution of H3K9me3, with ectopic losses and gains over discrete neuronal gene loci. In developing Pogz-/-cortex, regions with H3K9me3 gains are repositioned to the nuclear lamina and exhibit strengthened B-compartment scores by Micro-C, locus-restricted erosion of TAD architecture, weakened boundary insulation, and reduced CTCF occupancy. Within these domains, nascent RNA synthesis at neuronal genes is markedly diminished. These results identify POGZ as a G9a/GLP-associated chromatin regulator that protects neurodevelopmental gene domains from heterochromatinization and perinuclear sequestering, preserving 3D architecture and transcription during cortical development. Major PointsO_LIPOGZ interacts with the G9a/GLP H3K9 methyltransferase complex in the developing mouse cortex, identified by IP-mass spectrometry. C_LIO_LILoss of POGZ drives megabase-scale redistribution of H3K9me3 and increases compartmentalization and nuclear-lamina association of neurodevelopmental gene loci, shown by ChIP-seq, Micro-C, and DNA FISH. C_LIO_LIMicro-C reveals disrupted TAD architecture at specific neuronal gene loci in Pogz-/-.PRO-seq shows POGZ is required to maintain nascent RNA synthesis of neurodevelopmental genes within disrupted chromatin domains. C_LI

neuroscience↗

bioRxiv2024

KDM5C is a sex-biased brake against germline gene expression programs in somatic lineages

The division of labor among cellular lineages is a pivotal step in the evolution of multicellularity. In mammals, the soma-germline boundary is formed during early embryogenesis, when genes that drive germline identity are repressed in somatic lineages through DNA and histone modifications at promoter CpG islands (CGIs). Somatic misexpression of germline genes is a signature of cancer and observed in select neurodevelopmental disorders. However, it is currently unclear if all germline genes use the same repressive mechanisms and if factors like development and sex influence their dysregulation. Here, we examine how cellular context influences the formation of somatic tissue identity in mice lacking lysine demethylase 5c (KDM5C), an X chromosome eraser of histone 3 lysine 4 di and tri-methylation (H3K4me2/3). We found male Kdm5c knockout (-KO) mice aberrantly express many tissue-specific genes within the brain, the majority of which are unique to the germline. By developing a comprehensive list of mouse germline-enriched genes, we observed Kdm5c-KO cells aberrantly express key drivers of germline fate during early embryogenesis but late-stage spermatogenesis genes within the mature brain. KDM5C binds CGIs within germline gene promoters to facilitate DNA CpG methylation as embryonic stem cells differentiate into epiblast-like cells (EpiLCs). However, the majority of late-stage spermatogenesis genes expressed within the Kdm5c-KO brain did not harbor promoter CGIs. These CGI-free germline genes were not bound by KDM5C and instead expressed through ectopic activation by RFX transcription factors. Furthermore, germline gene repression is sexually dimorphic, as female EpiLCs require a higher dose of KDM5C to maintain germline silencing. Altogether, these data revealed distinct regulatory classes of germline genes and sex-biased silencing mechanisms in somatic cells.

molecular biology↗

bioRxiv2023

A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A

How cell-type-specific chromatin landscapes emerge and progress during metazoan ontogenesis remains an important question. Transcription factors are expressed in a cell-type-specific manner and recruit chromatin-regulatory machinery to specific genomic loci. In contrast, chromatin-regulatory proteins are expressed broadly and are assumed to exert the same intrinsic function across cell types. However, human genetics studies have revealed an unexpected vulnerability of neurodevelopment to chromatin factor mutations with unknown mechanisms. Here, we report that 14 chromatin regulators undergo evolutionary-conserved neuron-specific splicing events involving microexons. Of the 14 chromatin regulators, two are integral components of a histone H3K4 demethylase complex; the catalytic subunit LSD1 and an H3K4me0-reader protein PHF21A adopt neuron-specific forms. We found that canonical PHF21A (PHF21A-c) binds to DNA by AT-hook motif, and the neuronal counterpart PHF21A-n lacks this DNA-binding function yet maintains H3K4me0 recognition intact. In-vitro reconstitution of the canonical and neuronal PHF21A-LSD1 complexes identified the neuronal complex as a hypomorphic H3K4 demethylating machinery with reduced nucleosome engagement. Furthermore, an autism-associated PHF21A missense mutation, 1285 G>A, at the last nucleotide of the common exon immediately upstream of the neuronal microexon led to impaired splicing of PHF21A-n. Thus, ubiquitous chromatin regulatory complexes exert unique intrinsic functions in neurons via alternative splicing of their subunits and potentially contribute to faithful human brain development.

molecular biology↗