Identification of candidate enhancers controlling the transcriptome during the formation of interphalangeal joints

Karol Nowosad, Rutger W.W. Brouwer, Adrian Odrzywolski, Anne L. Korporaal, Bartłomiej Gielniewski, Bartosz Wojtaś, Wilfred F.J. van IJcken, Frank Grosveld, Danny Huylebroeck, Przemko Tylzanowski*

*Corresponding author for this work

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Abstract

The formation of the synovial joint begins with the visible emergence of a stripe of densely packed mesenchymal cells located between distal ends of the developing skeletal anlagen called the interzone. Recently the transcriptome of the early synovial joint was reported. Knowledge about enhancers would complement these data and lead to a better understanding of the control of gene transcription at the onset of joint development. Using ChIP-sequencing we have mapped the H3-signatures H3K27ac and H3K4me1 to locate regulatory elements specific for the interzone and adjacent phalange, respectively. This one-stage atlas of candidate enhancers (CEs) was used to map the association between these respective joint tissue specific CEs and biological processes. Subsequently, integrative analysis of transcriptomic data and CEs identified new putative regulatory elements of genes expressed in interzone (e.g., GDF5, BMP2 and DACT2) and phalange (e.g., MATN1, HAPLN1 and SNAI1). We also linked such CEs to genes known as crucial in synovial joint hypermobility and osteoarthritis, as well as phalange malformations. These analyses show that the CE atlas can serve as resource for identifying, and as starting point for experimentally validating, putative disease-causing genomic regulatory regions in patients with synovial joint dysfunctions and/or phalange disorders, and enhancer-controlled synovial joint and phalange formation.

Original languageEnglish
Article number12835
JournalScientific Reports
Volume12
Issue number1
DOIs
Publication statusPublished - 27 Jul 2022

Bibliographical note

Acknowledgements:
We thank the members of the Center for Biomics-Genomics at the Erasmus University Medical Center for technical support. We also thank all the members of the Cell Biology Department for fruitful discussion. This work was supported by Polish National Science Centre (UMO-2015/19/B/NZ4/03184) and primary funding to the Department of Cell Biology at Erasmus University Medical Center.

Publisher Copyright:
© 2022, The Author(s).

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