Biology subjects

Lencer, E.

Publications and source records attributed to Lencer, E..

6 recordsLinked to original sources

bioRxiv2026

PRDM3 and PRDM16 define cranial neural crest cell states in zebrafish development

Cartilage and bone that comprise craniofacial structures as well as neurons and glia of the peripheral nervous system are derived from a multipotent population of cranial neural crest cells, that respond to both cell intrinsic and extrinsic cues to differentiate into precise cell states. Both a genetic and epigenetic regulatory network are required for each step in the differentiation process, involving transcription factors, histone modifiers and chromatin remodelers. Here, we examined the direct transcriptional targets of two histone methyltransferases, Prdm3 and Prdm16 in zebrafish neural crest cells at 48 hours post fertilization in zebrafish. Using CUT&RUN, we examined both direct DNA binding and nucleosome association. At this stage of development, CUT&RUN fragment size analysis indicated that Prdm3 and Prdm16 are largely associated with nucleosomes. We further analyzed these nucleosome peak sets to identify 6 clusters where differential binding of Prdm3 and Prdm16 and differential enrichment of gene ontology terms for target genes was observed. We validated gene expression in each cluster by in situ hybridization chain reaction (HCR) at 48 hpf demonstrating that prdm3 and prdm16 mutants exhibit corresponding changes in gene expression of the putative gene targets identified. Finally, we performed CUT&RUN-qPCR in prdm3 and prdm16 mutant zebrafish embryos and demonstrated reduced binding at putative target loci. Together these data suggest that Prdm3 and Prdm16 regulate their transcriptional targets primarily by binding nucleosomes around their putative target loci to control downstream gene expression. HighlightsPrdm3 and Prdm16 associate with nucleosomes for regulation of gene expression Gene targets are altered in prdm3 and prdm16 mutant zebrafish Reduced binding is observed in respective mutants

developmental biology↗

bioRxiv2023

SPLIT HAND/FOOT VARIANTS FAIL TO RESCUE PRDM1A MUTANT CRANIOFACIAL DEFECTS

BackgroundSplit Hand/Foot Malformation (SHFM) is a congenital limb disorder presenting with limb anomalies, such as missing, hypoplastic, or fused digits, and often craniofacial defects, including a cleft lip/palate, microdontia, micrognathia, or maxillary hypoplasia. We previously identified three novel variants in the transcription factor, PRDM1, that are associated with SHFM phenotypes. One individual also presented with a high arch palate. Studies in vertebrates indicate that PRDM1 is important for development of the skull; however, prior to our study, human variants in PRDM1 had not been associated with craniofacial anomalies. MethodsUsing transient mRNA overexpression assays in prdm1a-/- mutant zebrafish, we tested whether the PRDM1 SHFM variants were functional and could lead to a rescue of the craniofacial defects observed in prdm1a-/- mutants. We also mined a CUT&RUN and RNA-seq dataset to examine Prdm1a binding and the effect of Prdm1a loss on craniofacial genes. Resultsprdm1a-/- mutants exhibit craniofacial defects including a hypoplastic neurocranium, a loss of posterior ceratobranchial arches, a shorter palatoquadrate, and an inverted ceratohyal. Injection of wildtype hPRDM1 in prdm1a-/- mutants partially rescues these structures. However, injection of each of the three SHFM variants fails to rescue the skeletal defects. Loss of prdm1a leads to a decreased expression of important craniofacial genes, such as dlx5a/dlx6a, hand2, sox9b, col2a1a, and hoxb genes. ConclusionThese data suggest that the three SHFM variants are not functional and may have led to the craniofacial defects observed in the humans. Finally, they demonstrate how Prdm1a can directly bind and regulate craniofacial gene expression.

developmental biology↗

bioRxiv2022

cdon and boc affect trunk neural crest cell migration through a non-cell autonomous reduction of hedgehog signaling in zebrafish slow-twitch muscle

The transmembrane proteins cdon and boc are implicated in regulating hedgehog signaling during vertebrate development. Recent work showing roles for these genes in axon guidance and neural crest cell migration suggest that cdon/boc may play additional functions in regulating directed cell movements. We use novel and existing mutants to investigate a role for cdon and boc in zebrafish neural crest cell migration. We find that single mutant embryos exhibit normal neural crest phenotypes, but that neural crest migration is strikingly disrupted in double cdon;boc mutant embryos. We further show that this migration phenotype is associated with defects to the differentiation of slow-twitch muscle cells, and the loss of a Col1a1a containing extracellular matrix, suggesting that neural crest defects are a secondary consequence to defects in mesoderm development. Combined, our data add to a growing literature showing that cdon and boc act synergistically to promote hedgehog signaling during vertebrate development, and provide a foundation for using zebrafish to study the function of hedgehog receptor paralogs.

developmental biology↗

bioRxiv2021

PRDM proteins control Wnt/β-catenin activity to regulate craniofacial chondrocyte differentiation

Cranial neural crest (NCC)-derived chondrocyte precursors undergo a dynamic differentiation and maturation process to establish a scaffold for subsequent bone formation, alterations in which contribute to congenital birth defects. Here, we demonstrate that transcription factor and histone methyltransferase proteins Prdm3 and Prdm16 control the differentiation switch of cranial NCCs to craniofacial cartilage. Loss of either results in hypoplastic and unorganized chondrocytes due to impaired cellular orientation and polarity. We show that PRDMs regulate cartilage differentiation by controlling the timing of Wnt/{beta}-catenin activity in strikingly different ways: prdm3 represses while prdm16 activates global gene expression, though both by regulating Wnt enhanceosome activity and chromatin accessibility. Finally, we show that manipulating Wnt/{beta}-catenin signaling pharmacologically or generating prdm3-/-;prdm16-/- double mutants rescues craniofacial cartilage defects. Our findings reveal upstream regulatory roles for Prdm3 and Prdm16 in cranial NCCs to control Wnt/{beta}-catenin transcriptional activity during chondrocyte differentiation to ensure proper development of the craniofacial skeleton. HighlightsO_LIPrdm3 and Prdm16 are required for chondrocyte organization in vertebrate craniofacial cartilage C_LIO_LILoss of Prdm3 and Prdm16 alters expression of Wnt/{beta}-catenin signaling components C_LIO_LIPrdm3 and Prdm16 oppositely control global chromatin accessibility C_LIO_LIPrdm3 and Prdm16 cartilage defects can be rescued pharmacologically or genetically C_LI

developmental biology↗

bioRxiv2020

Single cell RNA analysis of trunk neural crest cells in zebrafish identifies pre-migratory populations expressing markers of differentiated derivatives

The neural crest is a migratory population of stem-like cells that contribute to multiple traits including the bones of the skull, peripheral nervous system, and pigment. How neural crest cells differentiate into diverse cell types is a fundamental question in the study of vertebrate biology. Here, we use single cell RNA sequencing to characterize transcriptional changes associated with neural crest cell development in the zebrafish trunk during the early stages of migration. We show that neural crest cells are transcriptionally diverse, and identify pre-migratory populations already expressing genes associated with differentiated derivatives. Further, we identify a population of Rohon-Beard neurons that are shown to be sources of Fgf signaling in the zebrafish trunk. The data presented identify novel genetic markers for multiple trunk neural crest cell populations and Rohon-Beard neurons providing insight into previously uncharacterized genes critical for vertebrate development.

developmental biology↗

bioRxiv2020

The role of KMT2D and KDM6A in cardiac development: A cross-species analysis in humans, mice, and zebrafish

KMT2D and KDM6A are epigenetic regulators that have been implicated in Kabuki Syndrome, a rare congenital birth defect with multiple tissue and organ abnormalities, including craniofacial and heart defects. Our previous study identified human families with mutations in the epigenetic modifiers KMT2D and KDM6A, which is implicated in 32% and 10% of Kabuki Syndrome patients respectively. To understand the connection to Kabuki syndrome patients, and the transcriptional targets of KMT2D and KDM6A in humans, we performed RNA sequencing (seq) of lymphoblastoid cells from Kabuki Syndrome patients carrying mutations in KMT2D and KDM6A. We identified 1995 significant changes in transcriptional targets for KMT2D and 1917 for KDM6A, as compared to control. When compared with RNA-seq datasets obtained from other mouse and zebrafish studies, our analysis revealed KMT2D mutations affect the expression of 76 orthologous genes across all three datasets. Similarliy, KDM6A afftects the expprssion of 7 orthologous genes across three datasets. Despite the differences in cell types, stages, and species in the comparison between the transcriptomic datasets, there are common gene expression changes associated with KMT2D and KDM6A mutations. qPCR on novel zebrafish mutants confirmed the differentially expression in KMT2D or KDM6A mutant backgrounds. Taken together, our results show that KMT2D and KDM6A regulate common and unique genes across humans, mice, and zebrafish for early craniofacial and cardiac development and this information contributes to the understanding of epigenetic dysregulation during development of Kabuki syndrome.

developmental biology↗