Molecular Characterization of HOXA2 and HOXA3 Binding Properties

From MDPI via Jisc Publications RouterHistory: accepted 2021-11-30, pub-electronic 2021-12-03Publication status: PublishedFunder: SPARC (Scheme for Promotion of Academic and Research Collaboration) and UKIERI (United Kingdom India Research Initiative); Grant(s): project P657Funder: Biotechnology and Biological Sciences Research Council; Grant(s): BB/N00907X/1 and BB/T007761/1The highly conserved HOX homeodomain (HD) transcription factors (TFs) establish the identity of different body parts along the antero−posterior axis of bilaterian animals. Segment diversification and the morphogenesis of different structures is achieved by generating precise patterns of HOX expression along the antero−posterior axis and by the ability of different HOX TFs to instruct unique and specific transcriptional programs. However, HOX binding properties in vitro, characterised by the recognition of similar AT-rich binding sequences, do not account for the ability of different HOX to instruct segment-specific transcriptional programs. To address this problem, we previously compared HOXA2 and HOXA3 binding in vivo. Here, we explore if sequence motif enrichments observed in vivo are explained by binding affinities in vitro. Unexpectedly, we found that the highest enriched motif in HOXA2 peaks was not recognised by HOXA2 in vitro, highlighting the importance of investigating HOX binding in its physiological context. We also report the ability of HOXA2 and HOXA3 to heterodimerise, which may have functional consequences for the HOX patterning function in vivo

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation [preprint]

Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers

Functional abdominal pain disorders and patient- and parent- reported outcomes in children with inflammatory bowel disease in remission

BACKGROUND: Chronic abdominal pain occurs frequently in pediatric patients with inflammatory bowel disease (IBD) in remission. AIMS: To assess the prevalence and factors associated with Functional Abdominal Pain Disorders among IBD children in remission (IBD-FAPD). METHODS: Patients with IBD for > 1 year, in clinical remission for ≥ 3 months were recruited from a National IBD network. IBD-FAPDs were assessed using the Rome III questionnaire criteria. Patient- or parent- reported outcomes were assessed. RESULTS: Among 102 included patients, 57 (56%) were boys, mean age (DS) was 15.0 (± 2.0) years and 75 (74%) had Crohn's disease. Twenty-two patients (22%) had at least one Functional Gastrointestinal Disorder among which 17 had at least one IBD-FAPD. Past severity of disease or treatments received and level of remission were not significantly associated with IBD-FAPD. Patients with IBD-FAPD reported more fatigue (peds-FACIT-F: 35.9 ± 9.8 vs. 43.0 ± 6.9, p = 0.01) and a lower HR-QoL (IMPACT III: 76.5 ± 9.6 vs. 81.6 ± 9.2, p = 0.04) than patients without FAPD, and their parents had higher levels of State and Trait anxiety than the other parents. CONCLUSIONS: Prevalence of IBD-FAPD was 17%. IBD-FAPD was not associated with past severity of disease, but with fatigue and lower HR-QoL

Molecular and regulatory HOXA2 interactions : focus on KPC2 and RCHY1

Hox genes encode transcription factors which fulfill well-documented functions during embryonic development. Regarding the mode of action of these proteins, numerous studies identified Hox-regulated genes and, in some instances, characterized specific target enhancers. However, little data related to Hox-mediated interactions at the protein level is currently available. To better understand the mode of action of Hoxa2, our laboratory started characterizing protein-protein interactions which could be mediated by Hoxa2. During this thesis, nine of these potential Hoxa2 partners were under the scope with a particular focus on two of them, KPC2 and RCHY1. We identified KPC2 as a new HOXA2 regulator and showed that KPC2 modulates HOXA2’s subcellular distribution, relocalizing it to the cytoplasm. Moreover, this relocalization correlates with a decrease in Hoxa2 transcriptional activity. In addition, we demonstrated that the domains of expression of Hoxa2 and Kpc2 partially overlap during mouse embryogenesis which indicates that Hoxa2 might be regulated by Kpc2 in this context. Previous data from the laboratory and results obtained in the present work revealed that HOXA2 fulfills non-transcriptional activities by modulating the proteasomal degradation of RCHY1. Here, we dissected molecular aspects of the HOXA2-RCHY1 interaction, highlighting the mainly nuclear localization of the interaction and revealing the critical involvement of the Hoxa2 homeodomain in its ability to promote RCHY1 degradation. Furthermore, we demonstrated that this ability to modulate RCHY1 stability is evolutionarily conserved for HOXA2 and shared by several but not all HOX proteins. This function could therefore reflect an almost generic and possibly ancestral HOX protein activity.(SC - Sciences) -- UCL, 201

HOX Protein Activity Regulation by Cellular Localization

While the functions of HOX genes have been and remain extensively studied in distinct model organisms from flies to mice, the molecular biology of HOX proteins remains poorly documented. In particular, the mechanisms involved in regulating the activity of HOX proteins have been poorly investigated. Nonetheless, based on data available from other well-characterized transcription factors, it can be assumed that HOX protein activity must be finely tuned in a cell-type-specific manner and in response to defined environmental cues. Indeed, records in protein–protein interaction databases or entries in post-translational modification registries clearly support that HOX proteins are the targets of multiple layers of regulation at the protein level. In this context, we review here what has been reported and what can be inferred about how the activities of HOX proteins are regulated by their intracellular distribution

The homeodomain transcription factor Hoxa2 interacts with and promotes the proteasomal degradation of the E3 ubiquitin protein ligase RCHY1.

Hox proteins are conserved homeodomain transcription factors known to be crucial regulators of animal development. As transcription factors, the functions and modes of action (co-factors, target genes) of Hox proteins have been very well studied in a multitude of animal models. However, a handful of reports established that Hox proteins may display molecular activities distinct from gene transcription regulation. Here, we reveal that Hoxa2 interacts with 20S proteasome subunits and RCHY1 (also known as PIRH2), an E3 ubiquitin ligase that targets p53 for degradation. We further show that Hoxa2 promotes proteasome-dependent degradation of RCHY1 in an ubiquitin-independent manner. Correlatively, Hoxa2 alters the RCHY1-mediated ubiquitination of p53 and promotes p53 stabilization. Together, our data establish that Hoxa2 can regulate the proteasomal degradation of RCHY1 and stabilization of p53

HOX Protein Activity Regulation by Cellular Localization

While the functions of HOX genes have been and remain extensively studied in distinct model organisms from flies to mice, the molecular biology of HOX proteins remains poorly documented. In particular, the mechanisms involved in regulating the activity of HOX proteins have been poorly investigated. Nonetheless, based on data available from other well-characterized transcription factors, it can be assumed that HOX protein activity must be finely tuned in a cell-type-specific manner and in response to defined environmental cues. Indeed, records in protein-protein interaction databases or entries in post-translational modification registries clearly support that HOX proteins are the targets of multiple layers of regulation at the protein level. In this context, we review here what has been reported and what can be inferred about how the activities of HOX proteins are regulated by their intracellular distribution

Post-translational modifications of HOX proteins, an underestimated issue.

Post-translational modifications (PTMs) are important determinants which contribute to modulating the turn-over, intracellular localisation, molecular interactions and activity of most eukaryotic proteins. Such modifications and their consequences have been extensively examined for some proteins or classes of proteins. This is not the case for the HOX transcription factors which are crucial regulators of animal development. In this review, we provide a survey of the literature and data repositories pertaining to HOX-associated PTMs. This highlights that HOX proteins are also likely widely post-translationally modified, and defines HOX PTMs as an under-valued facet of their biology

HOX genes are expressed in bovine and mouse oocytes and early embryos.

HOX proteins are transcription factors that play a major role in patterning the body axis of vertebrates from the gastrulation stage. While nothing has been reported so far about their roles at earlier stages, there is evidence that some HOX genes are expressed before gastrulation. The objective of this work was to study the pattern of expression of several HOX genes during oocyte maturation and early embryonic development up to the blastocyst stage. Using nested PCR, HOXD1, HOXA3, HOXD4, HOXB7, HOXB9, and HOXC9 transcripts were detected in bovine oocytes and early embryos at various frequencies depending on the stage of development. Quantitative PCR was performed on bovine oocytes and early embryos: relative expression of HOXD1, HOXA3, and HOXC9 decreased sharply after the 5-8 cell stage. HOXB9 relative expression increased between the oocyte and the morula stage. All transcripts seemed to be of maternal origin before the maternal to embryonic transition, as demonstrated by blocking transcription with α-amanitin. Reverse transcription was performed with either hexamers or oligo-dT, allowing for the determination that HOXC9 transcripts were slightly deadenylated during oocyte maturation; HOXD1, HOXA3, and HOXB9 transcripts were not, indicating that they could be translated. Hoxd1, Hoxa3, Hoxb9, and Hoxc9 expression was also detected in mouse oocytes and early embryos. A similar pattern of expression was found in the two species. In conclusion, mammalian HOX genes might be implicated in the control of oocyte maturation, the maternal-to-embryonic transition or the first steps of embryo differentiation