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.m114.632109

Cited by 15 publications

(8 citation statements)

References 87 publications

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“…For instance, in clusters of very early expressed genes, we found an enrichment of motifs for the transcription factor Caudal (Cad) (cluster 1 and 2) and the Hox protein Fushi tarazu (Ftz) (cluster 1) ( Fig 2 ). Caudal is a downstream core promoter activator [ 102 ] and very recently it has been found that it cooperates with Nejire to promote the expression of the homeobox gene fushi tarazu ( ftz ) [ 103 ]. A Caudal-like transcription factor binding motif has been identified within Sine oculis (So) bound DNA fragments as identified by ChIP-seq [ 48 ], suggesting that So and Cad may co-regulate potential target genes in the eye-antennal disc.…”

Section: Resultsmentioning

confidence: 99%

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity

Torres-Oliva¹,

Schneider²,

Wiegleb³

et al. 2018

PLoS Genet

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Drosophila melanogaster head development represents a valuable process to study the developmental control of various organs, such as the antennae, the dorsal ocelli and the compound eyes from a common precursor, the eye-antennal imaginal disc. While the gene regulatory network underlying compound eye development has been extensively studied, the key transcription factors regulating the formation of other head structures from the same imaginal disc are largely unknown. We obtained the developmental transcriptome of the eye-antennal discs covering late patterning processes at the late 2nd larval instar stage to the onset and progression of differentiation at the end of larval development. We revealed the expression profiles of all genes expressed during eye-antennal disc development and we determined temporally co-expressed genes by hierarchical clustering. Since co-expressed genes may be regulated by common transcriptional regulators, we combined our transcriptome dataset with publicly available ChIP-seq data to identify central transcription factors that co-regulate genes during head development. Besides the identification of already known and well-described transcription factors, we show that the transcription factor Hunchback (Hb) regulates a significant number of genes that are expressed during late differentiation stages. We confirm that hb is expressed in two polyploid subperineurial glia cells (carpet cells) and a thorough functional analysis shows that loss of Hb function results in a loss of carpet cells in the eye-antennal disc. Additionally, we provide for the first time functional data indicating that carpet cells are an integral part of the blood-brain barrier. Eventually, we combined our expression data with a de novo Hb motif search to reveal stage specific putative target genes of which we find a significant number indeed expressed in carpet cells.

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Section: Resultsmentioning

confidence: 99%

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity

Torres-Oliva¹,

Schneider²,

Wiegleb³

et al. 2018

PLoS Genet

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“…It will be important to understand the molecular basis of enhancer-core promoter specificity. In this regard, it was found that the Drosophila Caudal protein, a sequence-specific transcription factor (ssTF) and a master developmental regulator, is a DPE-specific transcription factor that functions preferentially with DPE-dependent core promoters relative to TATA-dependent core promoters (Juven-Gershon et al 2008;Shir-Shapira et al 2015). In addition, the transcriptional cofactors NC2 (negative cofactor 2, also known as Dr1-Drap1) and Mot1 were observed to activate DPEdependent transcription and to inhibit TATA-dependent transcription (Willy et al 2000;Hsu et al 2008).…”

Section: Enhancer-core Promoter Specificitymentioning

confidence: 99%

The RNA Polymerase II Core Promoter in Drosophila

Ngoc¹,

Kassavetis²,

Kadonaga

2019

Genetics

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Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila. The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.

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“…Creb-binding protein (CBP) is a histone acetyl transferase (HAT) that is responsible for acetylating H3K27 in Drosophila ( 40 ). CBP is a coactivator of multiple transcription factors, including Cad, and also localizes to PREs, including gt PRE1 and PRE2 in wild-type embryos ( 41 , 42 ). In addition, it is a component of a Trithorax-group (TrxG) complex, TAC1, which also includes Trithorax (Trx) and dSbf1, that was isolated from Drosophila embryos ( 43 ).…”

Section: Discussionmentioning

confidence: 99%

Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator

Ghotbi

Ervin

et al. 2021

Sci. Adv.

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Polycomb-group (PcG) proteins are epigenetic regulators that maintain the transcriptional repression of target genes following their initial repression by transcription factors. PcG target genes are repressed in some cells, but active in others. Therefore, a mechanism must exist by which PcG proteins distinguish between the repressed and active states and only assemble repressive chromatin environments at target genes that are repressed. Here, we present experimental evidence that the repressed state of a Drosophila PcG target gene, giant (gt), is not identified by the presence of a repressor. Rather, de novo establishment of PcG-mediated silencing at gt is the default state that is prevented by the presence of an activator or coactivator, which may inhibit the catalytic activity of Polycomb-repressive complex 2 (PRC2).

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Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation

Cited by 15 publications

References 87 publications

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity

The RNA Polymerase II Core Promoter in Drosophila

Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator

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