Chromatin architecture and cis-regulatory landscape of the DACT2-SMOC2 locus in the developing synovial joint.
Nowosad, K.; Hordyjewska-Kowalczyk, E.; Malesa, A.; Odrzywolski, A.; Brouwer, R. W. W.; Kolovos, P.; Boltsis, I.; Birkhoff, J. C.; van IJcken, W. F. J.; Grosveld, F. G.; Conidi, A.; Huylebroeck, D.; Tylzanowski, P.
Show abstract
BackgroundSynovial joints form in several steps, starting with the formation of an interzone, a condensation of mesenchymal cells at the sites of prospective joints. Despite the identification of multiple factors essential for formation of interzone, little is known about the regulation of their spatio-temporal gene expression during that process in limb development. Here, we investigated the cis- regulatory landscape of the Wnt-modulator encoding genes DACT2 and SMOC2, both expressed in the forming joint interzone. ResultsMechanically collected interzone and phalange samples, respectively, from chick embryos were found to express acknowledged marker genes (GDF5 and MATN1), as well as DACT2 and SMOC2. Using Targeted Chromatin Capture (T2C) we characterized the 3D chromatin structure of a ~3.45 Mb-long region encompassing DACT2 and SMOC2, which revealed differences at sub-TAD level between interzones and phalange. We identified candidate enhancers (CEs) based on H3-histone marks (H3K427ac and H3K4me1) located in close proximity to the promoters of DACT2 and SMOC2, and further documented these CEs in a zebrafish enhancer assay. ConclusionsOur approach yields new insight into the regulation, in dynamic chromatin context, of two Wnt-signaling modulatory genes during synovial joint induction.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation 95%
- Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive inter- and intra-enhancer redundancy 95%
- TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene 95%
Similar papers in this journal
- Active regulatory elements recruit cohesin to establish cell-specific chromatin domains. 95%
- Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L 94%
- Pseudotime analysis reveals novel regulatory factors for multigenic onset and monogenic transition of odorant receptor expression 94%
Similar papers in this journal
Similar papers in this journal
- Detection of new pioneer transcription factors as cell-type specific nucleosome binders 94%
- Functional characteristics and computational model of abundant hyperactive loci in the human genome 94%
- Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors 94%
Similar papers in this journal
- Chromatin Environment-Dependent Effects of DOT1L on Gene Expression in Male Germ Cells 93%
- Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing 93%
- smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.