A misplaced lncRNA causes brachydactyly in humans
Philipp G. Maass, Andreas Rump, Herbert Schulz, Sigmar Stricker, Lisanne Schulze, Konrad Platzer, Atakan Aydin, Sigrid Tinschert, Mary B. Goldring, Friedrich C. Luft, Sylvia Bähring
Philipp G. Maass, Andreas Rump, Herbert Schulz, Sigmar Stricker, Lisanne Schulze, Konrad Platzer, Atakan Aydin, Sigrid Tinschert, Mary B. Goldring, Friedrich C. Luft, Sylvia Bähring
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Research Article

A misplaced lncRNA causes brachydactyly in humans

Abstract

Translocations are chromosomal rearrangements that are frequently associated with a variety of disease states and developmental disorders. We identified 2 families with brachydactyly type E (BDE) resulting from different translocations affecting chromosome 12p. Both translocations caused downregulation of the parathyroid hormone-like hormone (PTHLH) gene by disrupting the cis-regulatory landscape. Using chromosome conformation capturing, we identified a regulator on chromosome 12q that interacts in cis with PTHLH over a 24.4-megabase distance and in trans with the sex-determining region Y-box 9 (SOX9) gene on chromosome 17q. The element also harbored a long noncoding RNA (lncRNA). Silencing of the lncRNA, PTHLH, or SOX9 revealed a feedback mechanism involving an expression-dependent network in humans. In the BDE patients, the human lncRNA was upregulated by the disrupted chromosomal association. Moreover, the lncRNA occupancy at the PTHLH locus was reduced. Our results document what we believe to be a novel in cis– and in trans–acting DNA and lncRNA regulatory feedback element that is reciprocally regulated by coding genes. Furthermore, our findings provide a systematic and combinatorial view of how enhancers encoding lncRNAs may affect gene expression in normal development.

Authors

Philipp G. Maass, Andreas Rump, Herbert Schulz, Sigmar Stricker, Lisanne Schulze, Konrad Platzer, Atakan Aydin, Sigrid Tinschert, Mary B. Goldring, Friedrich C. Luft, Sylvia Bähring

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Figure 1

The translocation t(4;12)(q13.2-13.3;p11.2) and scheme of the 6C method.

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The translocation t(4;12)(q13.2-13.3;p11.2) and scheme of the 6C method....
(A) Translocation with der(4) and der(12). The hand roentgenogram, especially the shortened metacarpals of digits 4 and 5, are diagnostic of BDE. (B) 6C. Formaldehyde-crosslinked chromatin of C28/I2 chondrocytes was sonicated. After ChIP, the chromatin was blunt-end repaired and ligated at ultra-high dilution to favor intramolecular ligation events. Chromatin loops were PCR amplified with inverse oligos, and the amplicons were subcloned and sequenced. PTHLH and SOX9 promoters were the bait sequences. (C) Example of PTHLH 6C. Several bp were inserted due to the end repair of chromatin fragments. The interacting sequence was located at 52,431,496 bp on chromosome 12 (positions in bp; UCSC assembly hg18). In trans event in SOX9 6C. The interacting element on chromosome 12 was identified next to the bait sequence of the SOX9 promoter. (D) Restrictive classification of the 6C sequence reads. Either the promoter (bait) or the promoter interaction with any sequence was counted. (E) PTHLH and SOX9 mRNA expression in human C28/I2 and LCL.