News & Events

Data release: SHH expression in the Frontonasal Ectodermal Zone (21 May 2025)

We are excited to announce a new data release from a PLOS Genetics paper on SHH expression in the Frontonasal Ectodermal Zone that depicts a new enhancer element!

PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms Principal Investigators: Licia Selleri and Ralph S. Marcucio (University of California, San Francisco)

Citation: 

Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS (2025) PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. PLoS Genet 21(5): e1011315. https://doi.org/10.1371/journal.pgen.1011315

FaceBase Dataset:

• ATAC-seq and ChIP-seq targeting PBX1 and PBX3 in the normal chick FEZ at HH22 (https://doi.org/10.25550/5G-BBG8)

Description:

Facial development is orchestrated by complex molecular interactions among signaling molecules and transcription factors, a class of proteins that regulate gene expression. Disruption of these interactions can lead to congenital facial malformations, affecting the lives of patients and their families. Understanding the molecular basis of these interactions during embryonic facial development will provide key insights into the origin of these disorders and may ultimately provide novel therapeutic targets. SHH is one of the key genes encoding a signaling molecule that regulates facial development. During early embryonic development, SHH is expressed in a signaling center in the surface cell layer that covers part of the face. This signaling center regulates proliferation to control proper outgrowth of the upper jaw. In the present study, we demonstrated that PBX1 and PBX3 transcription factors control expression of SHH at the molecular level. We identified a DNA element, SFE1, located in a regulatory region of the SHH locus. SFE1 induces SHH transcription when associated with PBX1 and represses transcription when associated with PBX3. These findings highlight the intricate molecular mechanisms underlying regulation of SHH expression and advance current knowledge of the regulatory pathways that control midfacial development.

This figure was generated from the ChIP-seq and ATAC-seq data in this study, submitted to FaceBase, and it shows the location of SFE1, a new enhancer element that we identified from this study.

Data release: TGF-β Signaling and Craniofacial Morphogenesis (20 May 2025)

We are excited to announce new data releases from a Nature Communications paper on TGF-β Signaling and Craniofacial Morphogenesis featuring high resolution spatial genomics data!

High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development (2 datasets) Principal Investigator: Yang Chai (University of Southern California)

Citation: 

Feng, Jifan & Janeckova, Eva & Guo, Tingwei & Ziaei, Heliya & Zhang, Mingyi & Geng, Jessica & Cha, Sa & Araujo-Villalba, Angelita & Liu, Mengmeng & Ho, Thach-Vu & Chai, Yang. (2025). High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development. Nature Communications. 16. 10.1038/s41467-025-59206-2. 

The authors employed scRNA-seq analysis alongside a seqFISH-based spatial genomics approach for high-resolution visualization of spatially resolved gene expression profiles for the developing palate and other craniofacial regions in the mouse embryos. The raw and processed scRNA-seq data from embryonic palatal tissue at different developmental stages (E12.5, E13.5, E14.5, E15.5, and E18.5) generated in this study has been deposited in FaceBase under the DOI 10.25550/62-QZ1A. The raw and processed sequencing-FISH data for anterior and posterior embryonic heads at E12.5, E13.5, and E15.5 are available in the FaceBase database under the DOI 10.25550/62-Y0VT.

FaceBase Achieves CoreTrustSeal Certification (26 March 2025)

FaceBase has officially been awarded the CoreTrustSeal certification. This recognition affirms our commitment to maintaining a trusted, sustainable, and FAIR (Findable, Accessible, Interoperable, Reusable) data repository for the dental, oral, and craniofacial research community.

The CoreTrustSeal is an internationally recognized certification that evaluates data repositories based on 16 rigorous requirements related to sustainability, data integrity, and long-term accessibility.

This milestone reflects our ongoing efforts to support open science, facilitate data sharing, and enhance research reproducibility.

To learn more about the CoreTrustSeal certification and what it means for FaceBase, visit CoreTrustSeal or read our CoreTrustSeal application.

Join us at AADOCR in New York City this week! (11 March 2025)

If you’re at AADOCR conference in New York City at the Javits Center this week, come say Hi!

Exhibit Hall: Booth #124: March 13-15, 9am to 5pm We’ll have new merch and FaceBase team members who would love to answer your questions, give demos and talk about your data.

Also:

NIDCR Trainee Poster session: Room 1A08 - March 12, 9am to 12pm Alejandro Bugacov will have a poster and a table where he can talk one on one with postdocs and give demos

Registration is open for the FaceBase 2025 Community Forum! (07 March 2025)

Join this us this summer for one-and-a-half days of advances in data science, cutting-edge technologies, and cross-disciplinary collaborations in dental, oral, craniofacial, and related research in beautiful Marina del Rey, CA! We’ll convene at the USC Information Sciences Institute (ISI) on June 3 & 4.

Register today!

This year’s theme is Enabling and Expanding the Reach of Craniofacial Research: Building Connections and Supporting Reuse. We will explore how data sharing and integration can enhance dental, oral and craniofacial research, with a focus on maximizing data reuse, bridging preclinical and clinical research, and expanding interdisciplinary collaborations into related regions such as the inner ear and related domains such as pain management.

Call for Posters!

There will be in-person poster presentations this year. Use the registration form to indicate that you want to present a poster.

Submission abstracts are due by May 16.

Topics for posters:

• We encourage submissions of clinical/translational cases, ML/AI and training scenarios as well as basic science that indicate scientific progress or accomplishments that advance FaceBase aims.

• Demonstration of how FaceBase data is used or reused for new scientific insights.

• Posters should include data/research that has been or will be submitted to FaceBase.

You can find full poster information on this PDF.

Learn more and register here!

We are looking forward to seeing you in Marina del Rey! Click to download the flyer below and share!! And if you have any questions, please send them to help@facebase.org.