Regulatory integration of Hox factor activity with Tbox factors in limb development

Abstract

In tetrapods, , and Hox cluster genes are crucial for forelimb and hindlimb development and mutations in these genes are responsible for congenital limb defects. The molecular basis of their integrated mechanisms of action in the context of limb development remains poorly understood. We studied Tbx4 and Hoxc10 owing to their overlapping loss-of-function phenotypes and colocalized expression in mouse hindlimb buds. We report an extensive overlap between Tbx4 and Hoxc10 genome occupancy and their putative target genes. Tbx4 and Hoxc10 interact directly with each other, have the ability to bind to a previously unrecognized T-box-Hox composite DNA motif and show synergistic activity when acting on reporter genes. Pitx1, the master regulator for hindlimb specification, also shows extensive genomic colocalization with Tbx4 and Hoxc10. Genome occupancy by Tbx4 in hindlimb buds is similar to Tbx5 occupancy in forelimbs. By contrast, another Hox factor, Hoxd13, also interacts with Tbx4/Tbx5 but antagonizes Tbx4/Tbx5-dependent transcriptional activity. Collectively, the modulation of Tbx-dependent activity by Hox factors acting on common DNA targets may integrate different developmental processes for the balanced formation of proportionate limbs.

Hoxa13 regulates expression of common Hox target genes involved in cartilage development to coordinate the expansion of the autopodal anlage

“…The number of independent HOXA11 and HOXA13 ChIP peaks was 2,953 and 143,460, respectively (Supporting Information Table a). The number of HOXA11 peak is comparable to that of recently reported HOXC10 ChIP‐Seq peak in the E11.5 limb bud (Jain et al., ). Figure a–c and Supporting Information Figure A–C show the integrative genome viewer (IGV) representation of HOXA11, HOXA13 and other homeodomain transcription factor binding sites in the representative gene loci.…”

“…ChIP-Seq peak in the E11.5 limb bud (Jain et al, 2018). the intron of Hoxa11 (arrowhead) (Figure 2a).…”

“…Hoxc10 is expressed in the mesenchyme of the stylopodal and zeugopodal anlagen of the hindlimb bud. Using deposited ChIP-Seq data (Jain et al, 2018), we found that HOXC10 also binds to the Hoxa7 intron and Hoxa9 5′-UTR but binding to the Hoxa11 intron was significantly lower or indistinguishable from background (Supporting Information Figure S10). Interestingly, non-HOX homeodomain transcription factors SHOX2 and PBX also exhibited similar binding profiles to the Hoxa11 intron (Figure 2a).…”

‘Building a perfect body’: control of vertebrate organogenesis by PBX-dependent regulatory networks

“…During development, HOX proteins can bind similar AT-rich DNA sequences in vitro (for reviews, see McGinnis and Krumlauf 1992;Gehring et al 1994;Lemons and McGinnis 2006). HOX proteins can heterodimerize with PBX/ Exd proteins (see Saadaoui et al 2011;Ladam and Sagerström 2014;Merabet and Mann 2016;Ortiz-Lombardia et al 2017) and can also pair with other classes of TFs for function; for example T-box factors, as recently described in limb development (Jain et al 2018). Through the years, heterodimerization with PBX/Exd has been proposed as a mechanism through which HOX proteins acquire DNA-binding selectivity and specificity.…”

Identification of a deletion containing TBX4 in a neonate with acinar dysplasia by rapid exome sequencing

“…TBX4 belongs to the T‐box family of transcription factors, which govern multiple processes in early embryonic development (Bertolessi, Linta, Seufferlein, Kleger, & Liebau, ; Ghosh, Brook, & Wilsdon, ; Jain et al, ). Tbx4 is expressed in early lung mesenchyme as well as the limbs (primarily hindlimb), mandible, heart and body wall (Ghosh et al, ).…”