Structure-function analysis of the Drosophila melanogaster Caudal transcription factor provides insights into core promoter-preferential activation.

Shir-Shapira, Hila; Sharabany, Julia; Filderman, Matan; Ideses, Diana; Ovadia-Shochat, Avital; Mannervik, Mattias; Juven‐Gershon, Tamar

doi:10.1074/jbc.a114.632109

Cited by 7 publications

(10 citation statements)

References 87 publications

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“…Dref (DNA replication-related element-binding factor) is a BED finger-type transcription factor shown to bind to the sequence 5′-TATCGATA ( Hirose et al, 1993 ), a highly conserved sequence in the core promoters of many Drosophila genes ( Ohler et al, 2002 ), whereas Cad encodes a homeobox transcription factor that is maternally provided and forms a concentration-gradient enriched at the posterior ( Mlodzik et al, 1985 ). Cad exhibits preferential activation of DPE-containing promoters ( Shir-Shapira et al, 2015 ). Trl/GAF is a transcriptional factor that regulates chromatin structure by promoting the open chromatin conformation in promoter gene regions, with optimal binding to the pentamer 5'-GAGAG-3' ( Chopra et al, 2008 ).…”

Section: Resultsmentioning

confidence: 99%

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Koromila

Iwasaki

et al. 2020

eLife

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Pioneer factors such as Zelda (Zld) help initiate zygotic transcription in Drosophila early embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls the transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates expression through enhancer sog_Distal along the dorso-ventral axis, we hypothesized Opa’s role is more general. Chromatin-immunoprecipitation (ChIP-seq) confirmed its in vivo binding to sog_Distal but also identified widespread binding throughout the genome, comparable to Zld. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zld, influences chromatin accessibility genome-wide at cellularization, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lacking opa exhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa is a general timing factor and likely late-acting pioneer factor that drives a secondary wave of zygotic gene expression.

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Section: Resultsmentioning

confidence: 99%

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Koromila

Iwasaki

et al. 2020

eLife

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“…Enhancer-core promoter specificity was further examined in the context of the homeotic (Hox) gene network in Drosophila (Juven-Gershon et al 2008b). Nearly all of the Drosophila Hox genes contain DPE-dependent core promoters, and Caudal, a sequence-specific DNA-binding transcription factor and key regulator of the Hox gene network, preferentially activates transcription from DPE-dependent promoters relative to some, but not all, TATAdependent promoters (Juven-Gershon et al 2008b;Shir-Shapira et al 2015). In addition, the presence of the BRE u motif suppresses the ability of Caudal to function in conjunction with the TATA box.…”

Section: Enhancer-core Promoter Specificitymentioning

confidence: 99%

The punctilious RNA polymerase II core promoter

et al. 2017

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The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.

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“…To verify whether Msx1 and Foxd3 are novel, direct Cdx targets, we looked for relevant regulatory elements in their proximal promoter region -through which many Cdx targets are known to be regulated (Shir-Shapira et al, 2015). As Cdx proteins can regulate gene expression by either DNA binding-dependent or -independent means (Beland et al, 2004;Sanchez-Ferras et al, 2014), binding sites for Cdx as well as for Cdx-interacting proteins with a key role in NC induction were both considered to be of interest.…”

Section: Sp/+mentioning

confidence: 99%

A direct role for murine Cdx proteins in the trunk neural crest-gene regulatory network

et al. 2016

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Numerous studies in chordates and arthropods currently indicate that Cdx proteins have a major ancestral role in the organization of posthead tissues. In urochordate embryos, Cdx loss-of-function has been shown to impair axial elongation, neural tube (NT) closure and pigment cell development. Intriguingly, in contrast to axial elongation and NT closure, a Cdx role in neural crest (NC)-derived melanocyte/ pigment cell development has not been reported in any other chordate species. To address this, we generated a new conditional pan-Cdx functional knockdown mouse model that circumvents Cdx functional redundancy as well as the early embryonic lethality of Cdx mutants. Through directed inhibition in the neuroectoderm, we provide in vivo evidence that murine Cdx proteins impact melanocyte and enteric nervous system development by, at least in part, directly controlling the expression of the key early regulators of NC ontogenesis Pax3, Msx1 and Foxd3. Our work thus reveals a novel role for Cdx proteins at the top of the trunk NC gene regulatory network in the mouse, which appears to have been inherited from their ancestral ortholog.

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Structure-function analysis of the Drosophila melanogaster Caudal transcription factor provides insights into core promoter-preferential activation.

Cited by 7 publications

References 87 publications

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

The punctilious RNA polymerase II core promoter

A direct role for murine Cdx proteins in the trunk neural crest-gene regulatory network

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