Genomic features of BRDT binding sites in gene units suggest transcriptional partners and specific epigenetic landscapes to regulate transcriptional activity during spermatogenesis

AbstractBRDT, a member of the BET family of double bromodomain-containing proteins, is expressed uniquely in the male germ line, is essential for spermatogenesis in the mouse, and binds to acetylated transcription start sites of genes expressed in meiosis and spermiogenesis. It has thus been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in regulating gene expression, we characterized its genome-wide distribution, in particular the features of the BRDT binding sites within gene units, by ChIP-Seq analysis of enriched fractions of spermatocytes and spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exon, and introns of genes that are highly transcribed during meiosis and spermiogenesis. Furthermore, in promoters, BRDT binding sites overlapped with several histone modifications and histone variants associated with active transcription, and were also enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE and RFX in round spermatids. Our analysis further revealed that BRDT-bound genes play key roles in diverse biological processes that are essential for proper spermatogenesis. Taken together, our data suggest that BRDT is involved in the recruitment of different transcription factors to distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.

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lag-1, a gene required for lin-12 and glp-1 signaling in Caenorhabditis elegans, is homologous to human CBF1 and Drosophila Su(H)

Development ◽

10.1242/dev.122.5.1373 ◽

1996 ◽

Vol 122 (5) ◽

pp. 1373-1383 ◽

Cited By ~ 12

Author(s):

S. Christensen ◽

V. Kodoyianni ◽

M. Bosenberg ◽

L. Friedman ◽

J. Kimble

Keyword(s):

Caenorhabditis Elegans ◽

Binding Sites ◽

Feedback Loop ◽

Target Genes ◽

Sequence Similarity ◽

Nematode Caenorhabditis Elegans ◽

C Elegans ◽

Downstream Target ◽

Binding Factor ◽

Flanking Regions

The homologous receptors LIN-12 and GLP-1 mediate diverse cell-signaling events during development of the nematode Caenorhabditis elegans. These two receptors appear to be functionally interchangeable and have sequence similarity to Drosophila Notch. Here we focus on a molecular analysis of the lag-1 gene (lin-12 -and glp-1), which plays a central role in LIN-12 and GLP-1-mediated signal transduction. We find that the predicted LAG-1 protein is homologous to two DNA-binding proteins: human C Promoter Binding Factor (CBF1) and Drosophila Suppressor of Hairless (Su(H)). Furthermore, we show that LAG-1 binds specifically to the DNA sequence RTGGGAA, previously identified as a CBF-1/Su(H)-binding site. Finally, we report that the 5′ flanking regions and first introns of the lin-12, glp-1 and lag-1 genes are enriched for potential LAG-1-binding sites. We propose that LAG-1 is a transcriptional regulator that serves as a primary link between the LIN-12 and GLP-1 receptors and downstream target genes in C. elegans. In addition, we propose that LAG-1 may be a key component of a positive feedback loop that amplifies activity of the LIN-12/GLP-1 pathway.

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HOT or not: examining the basis of high-occupancy target regions

10.1101/107680 ◽

2017 ◽

Cited By ~ 3

Author(s):

Katarzyna Wreczycka ◽

Vedran Franke ◽

Bora Uyar ◽

Ricardo Wurmus ◽

Altuna Akalin

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Binding Sites ◽

Cell Types ◽

Data Sets ◽

Gene Promoters ◽

Quadruplex Dna ◽

Golden Standard ◽

Multiple Cell ◽

Multiple Species

AbstractHigh-occupancy target (HOT) regions are the segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and the associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solemnly defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed “hyper-ChIPable” regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers and enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies.

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Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome

10.1101/168419 ◽

2018 ◽

Cited By ~ 10

Author(s):

Mehran Karimzadeh ◽

Michael M. Hoffman

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Binding Sites ◽

Cell Types ◽

Transcription Factor Binding ◽

Regulatory Function ◽

Factor Binding ◽

Link Type ◽

Genomic Regions ◽

Factor Sequence

AbstractMotivationIdentifying transcription factor binding sites is the first step in pinpointing non-coding mutations that disrupt the regulatory function of transcription factors and promote disease. ChIP-seq is the most common method for identifying binding sites, but performing it on patient samples is hampered by the amount of available biological material and the cost of the experiment. Existing methods for computational prediction of regulatory elements primarily predict binding in genomic regions with sequence similarity to known transcription factor sequence preferences. This has limited efficacy since most binding sites do not resemble known transcription factor sequence motifs, and many transcription factors are not even sequence-specific.ResultsWe developed Virtual ChIP-seq, which predicts binding of individual transcription factors in new cell types using an artificial neural network that integrates ChIP-seq results from other cell types and chromatin accessibility data in the new cell type. Virtual ChIP-seq also uses learned associations between gene expression and transcription factor binding at specific genomic regions. This approach outperforms methods that predict TF binding solely based on sequence preference, pre-dicting binding for 36 transcription factors (Matthews correlation coefficient > 0.3).AvailabilityThe datasets we used for training and validation are available at https://virchip.hoffmanlab.org. We have deposited in Zenodo the current version of our software (http://doi.org/10.5281/zenodo.1066928), datasets (http://doi.org/10.5281/zenodo.823297), predictions for 36 transcription factors on Roadmap Epigenomics cell types (http://doi.org/10.5281/zenodo.1455759), and predictions in Cistrome as well as ENCODE-DREAM in vivo TF Binding Site Prediction Challenge (http://doi.org/10.5281/zenodo.1209308).

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The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry

Cells ◽

10.3390/cells9122690 ◽

2020 ◽

Vol 9 (12) ◽

pp. 2690

Author(s):

Mónica Fernández-Cortés ◽

Eduardo Andrés-León ◽

Francisco Javier Oliver

Keyword(s):

Transcription Factors ◽

Binding Sites ◽

Regulatory Networks ◽

Target Genes ◽

Parp Inhibitor ◽

Vasculogenic Mimicry ◽

Transcriptome Profiling ◽

Key Species ◽

Non Coding Rnas ◽

The Impact

In highly metastatic tumors, vasculogenic mimicry (VM) involves the acquisition by tumor cells of endothelial-like traits. Poly-(ADP-ribose) polymerase (PARP) inhibitors are currently used against tumors displaying BRCA1/2-dependent deficient homologous recombination, and they may have antimetastatic activity. Long non-coding RNAs (lncRNAs) are emerging as key species-specific regulators of cellular and disease processes. To evaluate the impact of olaparib treatment in the context of non-coding RNA, we have analyzed the expression of lncRNA after performing unbiased whole-transcriptome profiling of human uveal melanoma cells cultured to form VM. RNAseq revealed that the non-coding transcriptomic landscape differed between olaparib-treated and non-treated cells: olaparib significantly modulated the expression of 20 lncRNAs, 11 lncRNAs being upregulated, and 9 downregulated. We subjected the data to different bioinformatics tools and analysis in public databases. We found that copy-number variation alterations in some olaparib-modulated lncRNAs had a statistically significant correlation with alterations in some key tumor suppressor genes. Furthermore, the lncRNAs that were modulated by olaparib appeared to be regulated by common transcription factors: ETS1 had high-score binding sites in the promoters of all olaparib upregulated lncRNAs, while MZF1, RHOXF1 and NR2C2 had high-score binding sites in the promoters of all olaparib downregulated lncRNAs. Finally, we predicted that olaparib-modulated lncRNAs could further regulate several transcription factors and their subsequent target genes in melanoma, suggesting that olaparib may trigger a major shift in gene expression mediated by the regulation lncRNA. Globally, olaparib changed the lncRNA expression landscape during VM affecting angiogenesis-related genes.

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Cell transformation mediated by homodimeric E2A-HLF transcription factors.

Molecular and Cellular Biology ◽

10.1128/mcb.17.3.1417 ◽

1997 ◽

Vol 17 (3) ◽

pp. 1417-1424 ◽

Cited By ~ 24

Author(s):

T Inukai ◽

T Inaba ◽

T Yoshihara ◽

A T Look

Keyword(s):

Transcription Factors ◽

Target Genes ◽

Fusion Gene ◽

Dominant Negative ◽

Fusion Product ◽

3T3 Cells ◽

Par Proteins ◽

Downstream Target ◽

Nih 3T3 ◽

Nih 3T3 Cells

The E2A-HLF fusion gene, created by the t(17;19)(q22;p13) chromosomal translocation in pro-B lymphocytes, encodes an oncogenic protein in which the E2A trans-activation domain is linked to the DNA-binding and protein dimerization domain of hepatic leukemia factor (HLF), a member of the proline- and acidic amino acid-rich (PAR) subfamily of bZIP transcription factors. This fusion product binds to its DNA recognition site not only as a homodimer but also as a heterodimer with HLF and two other members of the PAR bZIP subfamily, thyrotroph embryonic factor (TEF) and albumin promoter D-box binding protein (DBP). Thus, E2A-HLF could transform cells by direct regulation of downstream target genes, acting through homodimeric or heterodimeric complexes, or by sequestering normal PAR proteins into nonfunctional heterocomplexes (dominant-negative interference). To distinguish among these models, we constructed mutant E2A-HLF proteins in which the leucine zipper domain of HLF was extended by one helical turn or altered in critical charged amino acids, enabling the chimera to bind to DNA as a homodimer but not as a heterodimer with HLF or other PAR proteins. When introduced into NIH 3T3 cells in a zinc-inducible vector, each of these mutants induced anchorage-independent growth as efficiently as unaltered E2A-HLF, indicating that the chimeric oncoprotein can transform cells in its homodimeric form. Transformation also depended on an intact E2A activator region, providing further support for a gain-of-function contribution to oncogenesis rather than one based on a dominant-interfering or dominant-negative mechanism. Thus, the tumorigenic effects of E2A-HLF and its mutant forms in NIH 3T3 cells favor a straightforward model in which E2A-HLF homodimers bind directly to promoter/enhancer elements of downstream target genes and alter their patterns of expression in early B-cell progenitors.

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Potential Downstream Target Genes of Aberrant ETS Transcription Factors Are Differentially Affected in Ewing’s Sarcoma and Prostate Carcinoma

PLoS ONE ◽

10.1371/journal.pone.0049819 ◽

2012 ◽

Vol 7 (11) ◽

pp. e49819 ◽

Cited By ~ 12

Author(s):

Maria J. Camões ◽

Paula Paulo ◽

Franclim R. Ribeiro ◽

João D. Barros-Silva ◽

Mafalda Almeida ◽

...

Keyword(s):

Transcription Factors ◽

Prostate Carcinoma ◽

Target Genes ◽

Ewing’S Sarcoma ◽

Ewing's Sarcoma ◽

Ets Transcription Factors ◽

Downstream Target

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Regulation and function of homeodomain proteins in the embryonic and adult vascular systemsThis paper is one of a selection of papers published in this Special Issue, entitled Young Investigators' Forum.

Canadian Journal of Physiology and Pharmacology ◽

10.1139/y06-091 ◽

2007 ◽

Vol 85 (1) ◽

pp. 55-65 ◽

Cited By ~ 15

Author(s):

Josette M. Douville ◽

Jeffrey T. Wigle

Keyword(s):

Transcription Factors ◽

Target Genes ◽

Vascular System ◽

Homeobox Genes ◽

Tube Formation ◽

Binding Motif ◽

Homeodomain Proteins ◽

Downstream Target ◽

Endothelial Tube Formation ◽

And Function

During embryonic development, the cardiovascular system first forms and then gives rise to the lymphatic vascular system. Homeobox genes are essential for both the development of the blood and lymphatic vascular systems, as well as for their maintenance in the adult. These genes all encode proteins that are transcription factors that contain a well conserved DNA binding motif, the homeodomain. It is through the homeodomain that these transcription factors bind to the promoters of target genes and regulate their expression. Although many homeodomain proteins have been found to be expressed within the vascular systems, little is known about their downstream target genes. This review highlights recent advances made in the identification of novel genes downstream of the homeodomain proteins that are necessary for regulating vascular cellular processes such as proliferation, migration, and endothelial tube formation. Factors known to regulate the functions of vascular cells via modulating the expression of homeobox genes will be discussed. We will also review current methods used to identify and characterize downstream target genes of homeodomain proteins.

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Differential developmental expression of transcription factors GATA-4 and GATA-6, their cofactor FOG-2 and downstream target genes in testicular carcinoma in situ and germ cell tumors

Acta Endocrinologica ◽

10.1530/eje-09-0734 ◽

2010 ◽

Vol 162 (3) ◽

pp. 625-631 ◽

Cited By ~ 10

Author(s):

Jonna Salonen ◽

Ewa Rajpert-De Meyts ◽

Susanna Mannisto ◽

John E Nielsen ◽

Niels Graem ◽

...

Keyword(s):

Transcription Factors ◽

Germ Cell ◽

Germ Cells ◽

Target Genes ◽

Developmental Expression ◽

Human Testis ◽

Testicular Development ◽

Downstream Target ◽

Germ Cell Differentiation

ObjectiveTesticular germ cell cancer is the most common malignancy among young males. The pre-invasive precursor, carcinoma in situ testis (CIS), presumably originates from arrested and transformed fetal gonocytes. Given that GATA transcription factors have essential roles in embryonic and testicular development, we explored the expression of GATA-4, GATA-6, cofactor friend of GATA (FOG)-2, and downstream target genes during human testis development and addressed the question whether changes in this pathway may contribute to germ cell neoplasms.MethodsFetal testis, testicular CIS, and overt tumor samples were analyzed by immunohistochemistry for GATA-4, GATA-6, FOG-2, steroidogenic factor 1 (NR5A1/SF1), anti-Müllerian hormone/Müllerian-inhibiting substance (AMH), and inhibin-α (INHα).ResultsGATA-4 was not expressed in normal germ cells, except for a subset of gonocytes at the 15th gestational week. The CIS cells expressed GATA-4 and GATA-6 heterogeneously, whereas most of the CIS cells expressed GATA-4 cofactor FOG-2. GATA target gene SF-1 was expressed heterogeneously in CIS cells, whereas INHα and AMH were mostly negative. Seminomas and yolk sac tumors were positive for GATA-4 and GATA-6, but mostly negative for FOG-2 and the GATA target genes. In contrast, pluripotent embryonal carcinomas and choriocarcinomas were GATA-4 and GATA-6 negative.ConclusionsDifferential expression of the GATA-4 target genes suggested cell-specific functions of GATA-4 in the germ and somatic cells. The GATA-4 expression in early fetal gonocytes, CIS, and seminoma cells but the absence in more mature germ cells is consistent with the early fetal origin of CIS cells and suggests that GATA-4 is involved in early germ cell differentiation.

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The Proneural Proteins Atonal and Scute Regulate Neural Target Genes through Different E-Box Binding Sites

Molecular and Cellular Biology ◽

10.1128/mcb.24.21.9517-9526.2004 ◽

2004 ◽

Vol 24 (21) ◽

pp. 9517-9526 ◽

Cited By ~ 56

Author(s):

Lynn M. Powell ◽

Petra I. zur Lage ◽

David R. A. Prentice ◽

Biruntha Senthinathan ◽

Andrew P. Jarman

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Sites ◽

Tandem Repeats ◽

Target Genes ◽

Expression Patterns ◽

Sense Organ ◽

Ample Evidence ◽

E Box ◽

Bhlh Transcription Factors

ABSTRACT For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct EAto and ESc sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing EAto and ESc sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging EAto and ESc sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.

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Probing transcription factor combinatorics in different promoter classes and in enhancers

10.1101/197418 ◽

2017 ◽

Author(s):

Jimmy Vandel ◽

Océane Cassan ◽

Sophie Lèbre ◽

Charles-Henri Lecellier ◽

Laurent Bréhélin

Keyword(s):

Binding Sites ◽

Target Genes ◽

Cell Types ◽

Model Parameters ◽

Binding Motif ◽

Cell Type ◽

Regulatory Regions ◽

New Approach ◽

Cell Type Specific ◽

Common Target

In eukaryotic cells, transcription factors (TFs) are thought to act in a combinatorial way, by competing and collaborating to regulate common target genes. However, several questions remain regarding the conservation of these combina-tions among different gene classes, regulatory regions and cell types. We propose a new approach named TFcoop to infer the TF combinations involved in the binding of a tar-get TF in a particular cell type. TFcoop aims to predict the binding sites of the target TF upon the binding affinity of all identified cooperating TFs. The set of cooperating TFs and model parameters are learned from ChIP-seq data of the target TF. We used TFcoop to investigate the TF combina-tions involved in the binding of 106 TFs on 41 cell types and in four regulatory regions: promoters of mRNAs, lncRNAs and pri-miRNAs, and enhancers. We first assess that TFcoop is accurate and outperforms simple PWM methods for pre-dicting TF binding sites. Next, analysis of the learned models sheds light on important properties of TF combinations in different promoter classes and in enhancers. First, we show that combinations governing TF binding on enhancers are more cell-type specific than that governing binding in pro-moters. Second, for a given TF and cell type, we observe that TF combinations are different between promoters and en-hancers, but similar for promoters of mRNAs, lncRNAs and pri-miRNAs. Analysis of the TFs cooperating with the dif-ferent targets show over-representation of pioneer TFs and a clear preference for TFs with binding motif composition similar to that of the target. Lastly, our models accurately dis-tinguish promoters associated with specific biological processes.

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