The Arabidopsis JAZ2 Promoter Contains a G-Box and Thymidine-Rich Module that are Necessary and Sufficient for Jasmonate-Dependent Activation by MYC Transcription Factors and Repression by JAZ Proteins

The development of the endocrine pancreas is under the control of highly orchestrated, cross-interacting transcription factors. Pancreas genesis is initiated by the emergence of a Pdx1/Ptf1a marked territory at the foregut/midgut junction. A small fraction of pancreatic fated cells activates the expression of the bHLH transcription factor Ngn3 triggering the endocrine cell program, thus giving rise to beta-, alpha-, delta-, PP-, and epsilon-cells, producing insulin, glucagon, somatostatin, pancreatic polypeptide, and ghrelin, respectively. Two transcription factors, Pax4 and Arx, play a crucial role in differential endocrine cell subtype specification. They were shown to be necessary and sufficient to endow endocrine progenitors with either a beta- or alpha-cell destiny. Interestingly, whereas the forced expression of Arx in beta-cells converts these into cells exhibiting alpha- and PP-cell characteristics, the sole expression of Pax4 in alpha-cells promotes alpha-cell-neogenesis and the acquisition of beta-cell features, the resulting beta-like cells being capable of counteracting chemically induced diabetes. Gaining new insights into the molecular mechanisms controlling Pax4 and Arx expression in the endocrine pancreas may therefore pave new avenues for the therapy of diabetes.

Download Full-text

A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer

Nature Communications ◽

10.1038/s41467-021-27055-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yanli Liu ◽

Zhong Wu ◽

Jin Zhou ◽

Dinesh K. A. Ramadurai ◽

Katelyn L. Mortenson ◽

...

Keyword(s):

Transcription Factors ◽

Copy Number ◽

Noncoding Region ◽

Transcriptional Change ◽

Chromatin Looping ◽

Squamous Cancer ◽

Necessary And Sufficient ◽

Remarkable Reduction

AbstractAmplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3’ noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.

Download Full-text

Homolog of ELAC2 is a central regulator of the mitochondrial unfolded protein response

10.1101/2021.06.22.449331 ◽

2021 ◽

Author(s):

James P Held ◽

Benjamin R Saunders ◽

Claudia V Pereria ◽

Maulik R Patel

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Unfolded Protein Response ◽

Negative Regulation ◽

Mitochondrial Stress ◽

Trna Processing ◽

Unfolded Protein ◽

Necessary And Sufficient ◽

Protein Response ◽

Mitochondrial Unfolded Protein Response

The mitochondrial unfolded protein response (UPRmt) has emerged as a predominant mechanism that preserves mitochondrial function. Consequently, multiple pathways likely exist to modulate UPRmt. We unexpectedly discovered that the tRNA processing enzyme, homolog of ELAC2 (HOE-1), is central to UPRmt regulation in Caenorhabditis elegans. We find that nuclear HOE-1 is necessary and sufficient to robustly activate UPRmt. We show that HOE-1 acts via transcription factors ATFS-1 and DVE-1 that are crucial for UPRmt. Mechanistically, we show that HOE-1 likely mediates its effects via tRNAs, as blocking tRNA export prevents HOE-1-induced UPRmt. Interestingly, we find that HOE-1 does not act via the integrated stress response, which can be activated by uncharged tRNAs, pointing towards its reliance on a new mechanism. Finally, we show that the subcellular localization of HOE-1 is responsive to mitochondrial stress and is subject to negative regulation via ATFS-1. Together, we have discovered a novel RNA-based cellular pathway that modulates UPRmt.

Download Full-text

The transcription factors Elk-1 and serum response factor interact by direct protein-protein contacts mediated by a short region of Elk-1.

Molecular and Cellular Biology ◽

10.1128/mcb.14.5.3283 ◽

1994 ◽

Vol 14 (5) ◽

pp. 3283-3291 ◽

Cited By ~ 103

Author(s):

P Shore ◽

A D Sharrocks

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Protein Interactions ◽

Serum Response Factor ◽

Specific Protein ◽

Response Factor ◽

Protein Protein Interactions ◽

Amino Acid Peptide ◽

Necessary And Sufficient ◽

Serum Response

Transcriptional induction of the c-fos gene in response to epidermal growth factor stimulation is mediated in part by a ternary nucleoprotein complex within the promoter consisting of serum response factor (SRF), p62TCF/Elk-1 and the serum response element (SRE). Both SRF and p62TCF/Elk-1 contact the DNA and bind in a cooperative manner to the SRE. In this study, we demonstrate that SRF and Elk-1 interact directly in the absence of the SRE. A 30-amino-acid peptide from Elk-1 (B-box) is both necessary and sufficient to mediate protein-protein contacts with SRF. Moreover, the Elk-1 B-box is necessary to enable SRF-dependent binding of an alternative ETS domain (from the transcription factor PU.1) to the c-fos SRE. Mutations in either the Elk-1 B-box or the C-terminal half of the SRF DNA-binding domain (coreSRF) which show reduced ability to form ternary complexes also show greatly reduced protein-protein interactions in the absence of the SRE. Our results clearly demonstrate that direct protein-protein interactions between the transcription factors Elk-1 and SRF, in addition to DNA contacts, contribute to the formation of a ternary complex on the c-fos SRE. We discuss the wider applicability of our results in describing specific protein-protein interactions between short well-defined transcription factor domains.

Download Full-text

Cement gland-specific activation of the Xag1 promoter is regulated by co-operation of putative Ets and ATF/CREB transcription factors

Development ◽

10.1242/dev.129.19.4387 ◽

2002 ◽

Vol 129 (19) ◽

pp. 4387-4397

Author(s):

Fiona C. Wardle ◽

Daniel H. Wainstock ◽

Hazel L. Sive

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Transcription Factors ◽

Binding Site ◽

Reporter Gene ◽

Binding Sites ◽

Cement Gland ◽

Specific Expression ◽

Necessary And Sufficient ◽

Do So

The cement gland marks the extreme anterior ectoderm of the Xenopus embryo, and is determined through the overlap of several positional domains. In order to understand how these positional cues activate cement gland differentiation, the promoter of Xag1, a marker of cement gland differentiation, was analyzed. Previous studies have shown that Xag1 expression can be activated by the anterior-specific transcription factor Otx2, but that this activation is indirect. 102 bp of upstream genomic Xag1 sequence restricts reporter gene expression specifically to the cement gland. Within this region, putative binding sites for Ets and ATF/CREB transcription factors are both necessary and sufficient to drive cement gland-specific expression, and cooperate to do so. Furthermore, while the putative ATF/CREB factor is activated by Otx2, a factor acting through the putative Ets-binding site is not. These results suggest that Ets-like and ATF/CREB-like family members play a role in regulating Xag1 expression in the cement gland, through integration of Otx2 dependent and independent pathways.

Download Full-text

Retinoic acid blocks adipogenesis by inhibiting C/EBPbeta-mediated transcription.

Molecular and Cellular Biology ◽

10.1128/mcb.17.3.1552 ◽

1997 ◽

Vol 17 (3) ◽

pp. 1552-1561 ◽

Cited By ~ 213

Author(s):

E J Schwarz ◽

M J Reginato ◽

D Shao ◽

S L Krakow ◽

M A Lazar

Keyword(s):

Transcription Factors ◽

Retinoic Acid ◽

Transcriptional Activation ◽

Adipocyte Differentiation ◽

Ectopic Expression ◽

Transient Transfection ◽

Peroxisome Proliferator ◽

Peroxisome Proliferator Activated Receptor ◽

Necessary And Sufficient ◽

Sequential Induction

Adipocyte differentiation is thought to involve sequential induction of the transcription factors C/EBPbeta, peroxisome proliferator-activated receptor gamma (PPARgamma), and C/EBPalpha. C/EBPalpha expression is both necessary and sufficient for adipocyte differentiation. Here we report that ectopic expression of either C/EBPalpha or C/EBPbeta induces PPARgamma expression and adipogenesis and that retinoic acid (RA) completely inhibits adipogenesis by either form of C/EBP. In studies of normal preadipocytes, RA does not prevent C/EBPbeta induction but blocks induction of PPARgamma, C/EBPalpha, and adipogenesis. In transient transfection studies, liganded RA receptor (RAR) specifically blocks transcriptional activation by either C/EBPalpha or C/EBPbeta. These results strongly suggest that C/EBPalpha substitutes for C/EBPbeta to induce adipocyte differentiation and that liganded RAR inhibits adipogenesis by blocking C/EBPbeta-mediated induction of downstream genes.

Download Full-text

Recognition of Phosphorylated-Smad2-Containing Complexes by a Novel Smad Interaction Motif

Molecular and Cellular Biology ◽

10.1128/mcb.24.3.1106-1121.2004 ◽

2004 ◽

Vol 24 (3) ◽

pp. 1106-1121 ◽

Cited By ~ 41

Author(s):

Rebecca A. Randall ◽

Michael Howell ◽

Christopher S. Page ◽

Amanda Daly ◽

Paul A. Bates ◽

...

Keyword(s):

Transcription Factors ◽

Growth Factor ◽

Transforming Growth Factor ◽

Transforming Growth Factor Β ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Hydrophobic Pocket ◽

Winged Helix ◽

The Common ◽

Necessary And Sufficient

ABSTRACT Transforming growth factor β (TGF-β) superfamily members signal via complexes of activated Smads, comprising phosphorylated receptor-regulated Smads, such as Smad2 and Smad3, and Smad4. These complexes are recruited to DNA by specific transcription factors. The forkhead/winged-helix transcription factors, XFast-1/XFoxH1a and XFast-3/XFoxH1b, bind an activated Smad heterotrimer comprising two Smad2s and one Smad4. Here we identify a novel Smad2 interaction motif, the Fast/FoxH1 motif (FM), present in all known Fast/FoxH1 family members, N-terminal to the common Smad interaction motif (SIM). The FM is necessary and sufficient to bind active Smad2/Smad4 complexes. The FM differs from the SIM since it discriminates between Smad2 and Smad3, and moreover only binds phosphorylated Smad2 in the context of activated Smad complexes. It is the first Smad interaction motif with this property. Site-directed mutagenesis indicates that the binding site for the FM on a Smad2/Smad4 heterotrimer is a hydrophobic pocket that incorporates the Smad/Smad interface. We demonstrate that the presence of an FM and SIM in the Fast/FoxH1 proteins allows them to compete efficiently for activated Smad2/Smad4 complexes with transcription factors such as Mixer that only contain a SIM. This establishes a hierarchy of Smad-interacting transcription factors, determined by their affinity for active Smad complexes.

Download Full-text

A combination of transcription factors mediates inducible interchromosomal pairing

10.1101/385047 ◽

2018 ◽

Author(s):

Seungsoo Kim ◽

Maitreya J Dunham ◽

Jay Shendure

Keyword(s):

Transcription Factors ◽

Binding Site ◽

Molecular Mechanism ◽

Dna Sequences ◽

Three Dimensional ◽

Chromosome Conformation ◽

Homolog Pairing ◽

A Genome ◽

Repressor Complex ◽

Necessary And Sufficient

SummaryRemodeling of the three-dimensional organization of a genome has been previously described (e.g. condition-specific pairing or looping), but it remains unknown which factors specify and mediate such shifts in chromosome conformation. Here we describe an assay, MAP-C (Mutation Analysis in Pools by Chromosome conformation capture), that enables the simultaneous characterization of hundreds of cis or trans-acting mutations for their effects on a chromosomal contact or loop. As a proof of concept, we applied MAP-C to systematically dissect the molecular mechanism of inducible interchromosomal pairing between HAS1pr-TDA1pr alleles in Saccharomyces yeast. We identified three transcription factors, Leu3, Sdd4 (Ypr022c), and Rgt1, whose collective binding to nearby DNA sequences is necessary and sufficient for inducible pairing between binding site clusters. Rgt1 contributes to the regulation of pairing, both through changes in expression level and through its interactions with the Tup1/Ssn6 repressor complex. HAS1pr-TDA1pr is the only locus with a cluster of binding site motifs for all three factors in both S. cerevisiae and S. uvarum genomes, but the promoter for HXT3, which contains Leu3 and Rgt1 motifs, also exhibits inducible homolog pairing. Altogether, our results demonstrate that specific combinations of transcription factors can mediate condition-specific interchromosomal contacts, and reveal a molecular mechanism for interchromosomal contacts and mitotic homolog pairing.

Download Full-text

Homeodomain and winged-helix transcription factors recruit activated Smads to distinct promoter elements via a common Smad interaction motif

Genes & Development ◽

10.1101/gad.14.4.435 ◽

2000 ◽

Vol 14 (4) ◽

pp. 435-451 ◽

Cited By ~ 7

Author(s):

Stéphane Germain ◽

Michael Howell ◽

Graeme M. Esslemont ◽

Caroline S. Hill

Keyword(s):

Transcription Factors ◽

Target Genes ◽

Expression Patterns ◽

Common Mechanism ◽

Homeodomain Proteins ◽

Promoter Elements ◽

Winged Helix ◽

Effector Domain ◽

Dna Binding Specificity ◽

Necessary And Sufficient

We have investigated the regulation of the activin-inducible distal element (DE) of the Xenopus goosecoid promoter. The results show that paired-like homeodomain transcription factors of the Mix family, Mixer and Milk, but not Mix.1, mediate activin/TGF-β-induced transcription through the DE by interacting with the effector domain of Smad2, thereby recruiting active Smad2/Smad4 complexes to the Mixer/Milk-binding site. We identify a short motif in the carboxyl termini of Mixer and Milk, which is demonstrated to be both necessary and sufficient for interaction with the effector domain of Smad2 and is required for mediating activin/TGF-β-induced transcription. This motif is not confined to these homeodomain proteins, but is also present in the Smad2-interacting winged-helix proteins Xenopus Fast-1, human Fast-1, and mouse Fast-2. We demonstrate directly that transcription factors of different DNA-binding specificity recruit activated Smads to distinct promoter elements via a common mechanism. These observations, together with the temporal and spatial expression patterns ofMixer and Milk, lead us to propose a model for mesoendoderm formation in Xenopus in which these homeodomain transcription factor/Smad complexes play a role in initiating and maintaining transcription of target genes in response to endogenous activin-like signals.

Download Full-text

Ordering promoter binding of class III transcription factors TFIIIC1 and TFIIIC2.

Molecular and Cellular Biology ◽

10.1128/mcb.8.8.3017 ◽

1988 ◽

Vol 8 (8) ◽

pp. 3017-3025 ◽

Cited By ~ 40

Author(s):

N Dean ◽

A J Berk

Keyword(s):

Transcription Factor ◽

Drosophila Melanogaster ◽

Transcription Factors ◽

Transcription Initiation ◽

Class Iii ◽

High Affinity ◽

Necessary And Sufficient ◽

Functional Components ◽

Competition Assays

The separation of the mammalian class III transcription factor TFIIIC into two functional components, termed TFIIIC1 and TFIIIC2, enabled an analysis of their functions in transcription initiation. Template competition assays were used to define the order with which these factors interact in vitro to form stable preinitiation complexes on the adenovirus VAI and Drosophila melanogaster tRNA(Arg) genes. The interaction between these genes and TFIIIC2, the factor that binds with high affinity to the B block, was both necessary and sufficient for template commitment. When either the VAI or tRNA(Arg) gene was preincubated with TFIIIC2 alone, transcription of a second gene added subsequently was excluded, indicating that TFIIIC2 bound stably to the first template. Furthermore, the interaction between TFIIIC2 and these genes must occur prior to that of TFIIIC1 or TFIIIB. Once TFIIIC2 was bound, TFIIIC1 could bind to the tRNA(Arg) and VAI genes, although its interaction with the VAI gene was less stable than that with the tRNA(Arg) gene. TFIIIB activity bound stably to the complex of both genes with TFIIIC2. These results demonstrate that TFIIIC2 is the first transcription factor to bind to these genes and that TFIIIB and TFIIIC1 can then interact in either order to form a preinitiation complex.

Download Full-text