scholarly journals A non-canonical histone acetyltransferase targets intragenic enhancers and regulates plant architecture

2020 ◽  
Author(s):  
Xueyong Yang ◽  
Jianbin Yan ◽  
Zhen Zhang ◽  
Tao Lin ◽  
Tongxu Xin ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Gene Activation ◽  
Sequence Divergence ◽  
Globular Domain ◽  
Intrinsically Disordered ◽  
Body Regions ◽  
Meristem Development ◽  
Canonical Histone

AbstractAxillary meristem development determines both plant architecture and crop yield; this critical process is regulated by the TCP transcription factor (TF) family, including the maize TB1 and Arabidopsis BRC1. Studies have shown that both TB1 and AtBRC1 can target the gene body regions of some target genes and activate their expression; however, the regulatory mechanisms remain largely unknown. Here, we show that a cucumber CYC/TB1 homologue, TEN, controls the identity and mobility of tendrils. Through its C-terminus, TEN binds at intragenic enhancers of target genes; its N-terminal domain functions as a novel, non-canonical histone acetyltransferase (HAT) to preferentially act on lysine 56 and 122, of the histone H3 globular domain. This HAT activity is responsible for chromatin loosening and host gene activation. The N-termini of all tested CYC/TB1-like proteins contain an intrinsically disordered region (IDR), and despite their sequence divergence, they have conserved HAT activity. This study discovered a non-canonical class of HATs, and as well, provides a mechanism by which modification at the H3 globular domain is integrated with the transcription process.

scholarly journals Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription

2021 ◽  
Author(s):  
Shasha Chong ◽  
Thomas G. W. Graham ◽  
Claire Dugast-Darzacq ◽  
Gina M. Dailey ◽  
Xavier Darzacq ◽  
...  
Keyword(s):  
Single Molecule ◽  
Target Genes ◽  
Gene Activation ◽  
Low Complexity ◽  
Intrinsically Disordered ◽  
Human Genes ◽  
Domain Interactions ◽  
Bona Fide ◽  
Liquid Liquid Phase Separation

Gene activation by mammalian transcription factors (TFs) requires dynamic, multivalent, and selective interactions of their intrinsically disordered low-complexity domains (LCDs), but how such interactions mediate transcription remains unclear. It has been proposed that extensive LCD-LCD interactions culminating in liquid-liquid phase separation (LLPS) of TFs is the dominant mechanism underlying transactivation. Here, we investigated how tuning the amount and localization of LCD-LCD interactions in vivo affects transcription of endogenous human genes. Quantitative single-cell and single-molecule imaging reveals that the oncogenic TF EWS/FLI1 requires a finely tuned range of LCD-LCD interactions to efficiently activate target genes. Modest or more dramatic increases in LCD-LCD interactions toward putative LLPS repress EWS/FLI1-driven transcription in patient cells. Likewise, ectopically creating LCD-LCD interactions to sequester EWS/FLI1 into a bona fide LLPS compartment, the nucleolus, inhibits EWS/FLI1-driven transcription and oncogenic transformation. Our findings reveal fundamental principles underlying LCD-mediated transcription and suggest mislocalizing specific LCD-LCD interactions as a novel therapeutic strategy for targeting disease-causing TFs.

scholarly journals Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response

2021 ◽  
Author(s):  
Surabhi Chowdhary ◽  
Amoldeep S. Kainth ◽  
Sarah Paracha ◽  
David S. Gross ◽  
David Pincus
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Target Genes ◽  
Gene Activation ◽  
Heat Shock Factor 1 ◽  
3D Genome ◽  
Intrinsically Disordered ◽  
Genome Reorganization ◽  
Shock Response ◽  
Disease Associated Genes

Mammalian developmental and disease-associated genes concentrate large quantities of the transcriptional machinery by forming membrane-less compartments known as transcriptional condensates. However, it is unknown whether these structures are evolutionarily conserved, capable of stress-inducible gene activation or involved in 3D genome reorganization. Here, we identify inducible transcriptional condensates in the yeast heat shock response (HSR). HSR condensates are biophysically dynamic spatiotemporal clusters of the sequence-specific transcription factor Heat shock factor 1 (Hsf1) with Mediator and RNA Pol II. Uniquely, HSR condensates drive the coalescence of multiple Hsf1 target genes, even those located on different chromosomes. Binding of the chaperone Hsp70 to a site on Hsf1 represses clustering, while an intrinsically disordered region on Hsf1 promotes condensate formation and intergenic interactions. Mutation of both Hsf1 determinants reprograms HSR condensates to become mammalian-like: constitutively active without intergenic coalescence. These results suggest that transcriptional condensates are ancient and flexible compartments of eukaryotic gene control.

scholarly journals Pygo2 Associates with MLL2 Histone Methyltransferase and GCN5 Histone Acetyltransferase Complexes To Augment Wnt Target Gene Expression and Breast Cancer Stem-Like Cell Expansion

2010 ◽  
Vol 30 (24) ◽  
pp. 5621-5635 ◽  
Author(s):  
Jiakun Chen ◽  
Qicong Luo ◽  
Yuanyang Yuan ◽  
Xiaoli Huang ◽  
Wangyu Cai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Transcriptional Activation ◽  
Cell Expansion ◽  
Breast Cancer Cells ◽  
Target Gene ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Gene Activation ◽  
Histone Methyltransferase ◽  
T Cell Factor

ABSTRACT Resent studies have identified Pygopus as a core component of the β-catenin/T-cell factor (TCF)/lymphoid-enhancing factor 1 (LEF) transcriptional activation complex required for the expression of canonical Wg/Wnt target genes in Drosophila. However, the biochemical involvement of mammalian Pygopus proteins in β-catenin/TCF/LEF gene activation remains controversial. In this study, we perform a series of molecular/biochemical experiments to demonstrate that Pygo2 associates with histone-modifying enzymatic complexes, specifically the MLL2 histone methyltransferase (HMT) and STAGA histone acetyltransferase (HAT) complexes, to facilitate their interaction with β-catenin and to augment Wnt1-induced, TCF/LEF-dependent transcriptional activation in breast cancer cells. We identify a critical domain in Pygo2 encompassing the first 47 amino acids that mediates its HMT/HAT interaction. We further demonstrate the importance of this domain in Pygo2's ability to transcriptionally activate both artificial and endogenous Wnt target genes and to expand breast cancer stem-like cells in culture. This work now links mechanistically Pygo2's role in histone modification to its enhancement of the Wnt-dependent transcriptional program and cancer stem-like cell expansion.

scholarly journals Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130018 ◽  
Author(s):  
Andrea I. Ramos ◽  
Scott Barolo
Keyword(s):  
Transcription Factor ◽  
Binding Affinity ◽  
Binding Sites ◽  
Target Genes ◽  
Gene Activation ◽  
Transcriptional Response ◽  
Morphogen Gradients ◽  
Weak Binding ◽  
Initial Hypothesis

In the era of functional genomics, the role of transcription factor (TF)–DNA binding affinity is of increasing interest: for example, it has recently been proposed that low-affinity genomic binding events, though frequent, are functionally irrelevant. Here, we investigate the role of binding site affinity in the transcriptional interpretation of Hedgehog (Hh) morphogen gradients . We noted that enhancers of several Hh-responsive Drosophila genes have low predicted affinity for Ci, the Gli family TF that transduces Hh signalling in the fly. Contrary to our initial hypothesis, improving the affinity of Ci/Gli sites in enhancers of dpp , wingless and stripe , by transplanting optimal sites from the patched gene, did not result in ectopic responses to Hh signalling. Instead, we found that these enhancers require low-affinity binding sites for normal activation in regions of relatively low signalling. When Ci/Gli sites in these enhancers were altered to improve their binding affinity, we observed patterning defects in the transcriptional response that are consistent with a switch from Ci-mediated activation to Ci-mediated repression. Synthetic transgenic reporters containing isolated Ci/Gli sites confirmed this finding in imaginal discs. We propose that the requirement for gene activation by Ci in the regions of low-to-moderate Hh signalling results in evolutionary pressure favouring weak binding sites in enhancers of certain Hh target genes.

Dpp signaling thresholds in the dorsal ectoderm of the Drosophila embryo

Development ◽  
2000 ◽  
Vol 127 (15) ◽  
pp. 3305-3312 ◽  
Author(s):  
H.L. Ashe ◽  
M. Mannervik ◽  
M. Levine
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Cell Types ◽  
Drosophila Embryo ◽  
Present Evidence ◽  
Drosophila Homolog ◽  
Dorsal Ectoderm ◽  
Transgenic Embryos ◽  
Different Cell Types

The dorsal ectoderm of the Drosophila embryo is subdivided into different cell types by an activity gradient of two TGF(β) signaling molecules, Decapentaplegic (Dpp) and Screw (Scw). Patterning responses to this gradient depend on a secreted inhibitor, Short gastrulation (Sog) and a newly identified transcriptional repressor, Brinker (Brk), which are expressed in neurogenic regions that abut the dorsal ectoderm. Here we examine the expression of a number of Dpp target genes in transgenic embryos that contain ectopic stripes of Dpp, Sog and Brk expression. These studies suggest that the Dpp/Scw activity gradient directly specifies at least three distinct thresholds of gene expression in the dorsal ectoderm of gastrulating embryos. Brk was found to repress two target genes, tailup and pannier, that exhibit different limits of expression within the dorsal ectoderm. These results suggest that the Sog inhibitor and Brk repressor work in concert to establish sharp dorsolateral limits of gene expression. We also present evidence that the activation of Dpp/Scw target genes depends on the Drosophila homolog of the CBP histone acetyltransferase.

scholarly journals The HOX Homeodomain Proteins Block CBP Histone Acetyltransferase Activity

2001 ◽  
Vol 21 (21) ◽  
pp. 7509-7522 ◽  
Author(s):  
Wei-fang Shen ◽  
Keerthi Krishnan ◽  
H. J. Lawrence ◽  
Corey Largman
Keyword(s):  
Dna Binding ◽  
Protein Function ◽  
Histone Acetyltransferase ◽  
Gene Activation ◽  
Homeodomain Proteins ◽  
Hox Proteins ◽  
Reporter Assays ◽  
Hox Protein

ABSTRACT Despite the identification of PBC proteins as cofactors that provide DNA affinity and binding specificity for the HOX homeodomain proteins, HOX proteins do not demonstrate robust activity in transient-transcription assays and few authentic downstream targets have been identified for these putative transcription factors. During a search for additional cofactors, we established that each of the 14 HOX proteins tested, from 11 separate paralog groups, binds to CBP or p300. All six isolated homeodomain fragments tested bind to CBP, suggesting that the homeodomain is a common site of interaction. Surprisingly, CBP-p300 does not form DNA binding complexes with the HOX proteins but instead prevents their binding to DNA. The HOX proteins are not substrates for CBP histone acetyltransferase (HAT) but instead inhibit the activity of CBP in both in vitro and in vivo systems. These mutually inhibitory interactions are reflected by the inability of CBP to potentiate the low levels of gene activation induced by HOX proteins in a range of reporter assays. We propose two models for HOX protein function: (i) HOX proteins may function without CBP HAT to regulate transcription as cooperative DNA binding molecules with PBX, MEIS, or other cofactors, and (ii) the HOX proteins may inhibit CBP HAT activity and thus function as repressors of gene transcription.

scholarly journals Enhancing c-MYC degradation via 20S proteasome activation induces in vivo anti-tumor efficacy

2020 ◽  
Author(s):  
Evert Njomen ◽  
Theresa A. Lansdell ◽  
Allison Vanecek ◽  
Vanessa Benham ◽  
Matt P. Bernard ◽  
...  
Keyword(s):  
Therapeutic Strategy ◽  
Target Genes ◽  
Intrinsically Disordered Proteins ◽  
Therapeutic Potential ◽  
Human Cancer ◽  
Disordered Proteins ◽  
20S Proteasome ◽  
Intrinsically Disordered

SUMMARYEnhancing proteasome activity is a potential new therapeutic strategy to prevent the accumulation of aberrant high levels of protein that drive the pathogenesis of many diseases. Herein, we examine the use of small molecules to activate the 20S proteasome to reduce aberrant signaling by the undruggable oncoprotein c-MYC, to treat c-MYC driven oncogenesis. Overexpression of c-MYC is found in more than 50% of all human cancer but remains undruggable because of its highly dynamic intrinsically disordered 3-D conformation, which renders traditional therapeutic strategies largely ineffective. We demonstrate herein that small molecule activation of the 20S proteasome targets dysregulated intrinsically disordered proteins (IDPs), including c-MYC, and reduces cancer growth in vitro and in vivo models of multiple myeloma, and is even effective in bortezomib resistant cells and unresponsive patient samples. Genomic analysis of various cancer pathways showed that proteasome activation results in downregulation of many c-MYC target genes. Moreover, proteasome enhancement was well tolerated in mice and dogs. These data support the therapeutic potential of 20S proteasome activation in targeting IDP-driven proteotoxic disorders, including cancer, and demonstrate that this new therapeutic strategy is well tolerated in vivo.

Regulation of plant architecture by a new histone acetyltransferase targeting gene bodies

Nature Plants ◽  
2020 ◽  
Vol 6 (7) ◽  
pp. 809-822 ◽  
Author(s):  
Xueyong Yang ◽  
Jianbin Yan ◽  
Zhen Zhang ◽  
Tao Lin ◽  
Tongxu Xin ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Histone Acetyltransferase

scholarly journals Transgenic Analysis Reveals that Thyroid Hormone Receptor Is Sufficient To Mediate the Thyroid Hormone Signal in Frog Metamorphosis

2004 ◽  
Vol 24 (20) ◽  
pp. 9026-9037 ◽  
Author(s):  
Daniel R. Buchholz ◽  
Akihiro Tomita ◽  
Liezhen Fu ◽  
Bindu D. Paul ◽  
Yun-Bo Shi
Keyword(s):  
Thyroid Hormone ◽  
Hormone Receptor ◽  
Target Genes ◽  
Thyroid Hormone Receptor ◽  
Gene Activation ◽  
Inducible Promoter ◽  
Vertebrate Development ◽  
Transcription System

ABSTRACT Thyroid hormone (T3) has long been known to be important for vertebrate development and adult organ function. Whereas thyroid hormone receptor (TR) knockout and transgenic studies of mice have implicated TR involvement in mammalian development, the underlying molecular bases for the resulting phenotypes remain to be determined in vivo, especially considering that T3 is known to have both genomic, i.e., through TRs, and nongenomic effects on cells. Amphibian metamorphosis is an excellent model for studying the role of TR in vertebrate development because of its total dependence on T3. Here we investigated the role of TR in metamorphosis by developing a dominant positive mutant thyroid hormone receptor (dpTR). In the frog oocyte transcription system, dpTR bound a T3-responsive promoter and activated the promoter independently of T3. Transgenic expression of dpTR under the control of a heat shock-inducible promoter in premetamorphic tadpoles led to precocious metamorphic transformations. Molecular analyses showed that dpTR induced metamorphosis by specifically binding to known T3 target genes, leading to increased local histone acetylation and gene activation, similar to T3-bound TR during natural metamorphosis. Our experiments indicated that the metamorphic role of T3 is through genomic action of the hormone, at least on the developmental parameters tested. They further provide the first example where TR is shown to mediate directly and sufficiently these developmental effects of T3 in individual organs by regulating target gene expression in these organs.

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