scholarly journals KAT7 is a therapeutic vulnerability of MLL-rearranged acute myeloid leukemia

2020 ◽  
Author(s):  
Yan Zi Au ◽  
Muxin Gu ◽  
Etienne De Braekeleer ◽  
Jason Yu ◽  
Swee Hoe Ong ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Developmental Disorders ◽  
Target Genes ◽  
Adaptor Proteins ◽  
Gene Promoters ◽  
Genome Wide ◽  
Lysine Residues ◽  
Acetyl Group ◽  
Lysine Acetyltransferase ◽  
Acute Myeloid

AbstractHistone acetyltransferases (HATs) catalyze the transfer of an acetyl group from acetyl-CoA to lysine residues of histones and play a central role in transcriptional regulation in diverse biological processes. Dysregulation of HAT activity can lead to human diseases including developmental disorders and cancer. Through genome-wide CRISPR-Cas9 screens, we identified several HATs of the MYST family as fitness genes for acute myeloid leukaemia (AML). Here we investigate the essentiality of lysine acetyltransferase KAT7 in AMLs driven by the MLL-X gene fusions. We found that KAT7 loss leads to a rapid and complete loss of both H3K14ac and H4K12ac marks, in association with reduced proliferation, increased apoptosis and differentiation of AML cells. Acetyltransferase activity of KAT7 is essential for the proliferation of these cells. Mechanistically, our data propose that acetylated histones provide a platform for the recruitment of MLL-fusion-associated adaptor proteins such as BRD4 and AF4 to gene promoters. Upon KAT7 loss, these factors together with RNA polymerase II rapidly dissociate from several MLL-fusion target genes that are essential for AML cell proliferation, including MEIS1, PBX3 and SENP6. Our findings reveal that KAT7 is a plausible therapeutic target for this poor prognosis AML subtype.

scholarly journals Lysine acetyltransferase Tip60 acetylates the APP adaptor Fe65 to increase its transcriptional activity

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Sabine Probst ◽  
Florian Riese ◽  
Larissa Kägi ◽  
Maik Krüger ◽  
Natalie Russi ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Target Genes ◽  
Adaptor Protein ◽  
Proteolytic Processing ◽  
Class Iii ◽  
Lysine Deacetylase ◽  
Lysine Residues ◽  
Lysine Acetyltransferase ◽  
Complex Forms ◽  
Spot Formation

AbstractProteolytic processing of the amyloid precursor protein (APP) releases the APP intracellular domain (AICD) from the membrane. Bound to the APP adaptor protein Fe65 and the lysine acetyltransferase (KAT) Tip60, AICD translocates to the nucleus. Here, the complex forms spherical condensates at sites of endogenous target genes, termed AFT spots (AICD-Fe65-Tip60). We show that loss of Tip60 KAT activity prevents autoacetylation, reduces binding of Fe65 and abolishes Fe65-mediated stabilization of Tip60. Autoacetylation is a prerequisite for AFT spot formation, with KAT-deficient Tip60 retained together with Fe65 in speckles. We identify lysine residues 204 and 701 of Fe65 as acetylation targets of Tip60. We do not detect acetylation of AICD. Mutation of Fe65 K204 and K701 to glutamine, mimicking acetylation-induced charge neutralization, increases the transcriptional activity of Fe65 whereas Tip60 inhibition reduces it. The lysine deacetylase (KDAC) class III Sirt1 deacetylates Fe65 and pharmacological modulation of Sirt1 activity regulates Fe65 transcriptional activity. A second acetylation/deacetylation cycle, conducted by CBP and class I/II KDACs at different lysine residues, regulates stability of Fe65. This is the first report describing a role for acetylation in the regulation of Fe65 transcriptional activity, with Tip60 being the only KAT tested that supports AFT spot formation.

scholarly journals Postrecruitment Regulation of RNA Polymerase II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

2008 ◽  
Vol 29 (5) ◽  
pp. 1123-1133 ◽  
Author(s):  
Miltiadis Kininis ◽  
Gary D. Isaacs ◽  
Leighton J. Core ◽  
Nasun Hah ◽  
W. Lee Kraus
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
Elongation Factor ◽  
Estrogen Signaling ◽  
Gene Promoters ◽  
Pol Ii ◽  
Activator Proteins ◽  
Classical Models ◽  
Target Promoters

ABSTRACT Under classical models for signal-dependent transcription in eukaryotes, DNA-binding activator proteins regulate the recruitment of RNA polymerase II (Pol II) to a set of target promoters. However, recent studies, as well as our results herein, show that Pol II is widely distributed (i.e., “preloaded”) at the promoters of many genes prior to specific signaling events. How Pol II recruitment and Pol II preloading fit within a unified model of gene regulation is unclear. In addition, the mechanisms through which cellular signals activate preloaded Pol II across mammalian genomes remain largely unknown. We show here that the predominant genomic outcome of estrogen signaling is the postrecruitment regulation of Pol II activity at target gene promoters, likely through specific changes in Pol II phosphorylation rather than through recruitment of Pol II to the promoters. Furthermore, we show that negative elongation factor binds to estrogen target promoters in conjunction with preloaded Pol II and represses gene expression until the appropriate signal is received. Finally, our studies reveal that the estrogen-dependent activation of preloaded Pol II facilitates rapid gene regulatory responses which play important physiological roles in regulating estrogen signaling itself. Our results reveal a broad use of postrecruitment Pol II regulation by the estrogen signaling pathway, a mode of regulation that is likely to apply to a wide variety of signal-regulated pathways.

scholarly journals Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

2021 ◽  
Author(s):  
Uthra Gowthaman ◽  
Maxim Ivanov ◽  
Isabel Schwarz ◽  
Heta P. Patel ◽  
Niels A. Müller ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Histone Deacetylation ◽  
Gene Promoters ◽  
Genetic Screens ◽  
Fluorescence Measurements ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Initiation Frequency

ABSTRACTNucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript with an unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. We identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC in high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements. Nascent transcription profiling showed a genome-wide role of Hda1C in DNC repression. Live-cell imaging of transcription revealed that Hda1C reduced the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC regions, supporting DNC repression by histone deacetylation. Our data support the interpretation that DNC results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.

scholarly journals MicroRNA miR-181a correlates with morphological sub-class of acute myeloid leukaemia and the expression of its target genes in global genome-wide analysis

Leukemia ◽  
2007 ◽  
Vol 21 (5) ◽  
pp. 912-916 ◽  
Author(s):  
S Debernardi ◽  
S Skoulakis ◽  
G Molloy ◽  
T Chaplin ◽  
A Dixon-McIver ◽  
...  
Keyword(s):  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Target Genes ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Acute Myeloid

scholarly journals Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual through variant-to-gene mapping

2020 ◽  
Author(s):  
Diana L. Cousminer ◽  
Yadav Wagley ◽  
James A. Pippin ◽  
Ahmed Elhakeem ◽  
Gregory P. Way ◽  
...  
Keyword(s):  
Gene Mapping ◽  
Cell Fate ◽  
Target Genes ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Gene Promoters ◽  
Skeletal Health ◽  
Effector Genes ◽  
Genome Wide

Introductory paragraphBone accrual impacts lifelong skeletal health, but genetic discovery has been hampered by cross-sectional study designs and uncertainty about target effector genes. Here, we captured this dynamic phenotype by modeling longitudinal bone accrual across 11,000 bone scans followed by genome-wide association studies (GWAS). We revealed 40 loci (35 novel), half residing in topological associated domains harboring known bone genes. Variant-to-gene mapping identified contacts between GWAS loci and nearby gene promoters, and siRNA knockdown of gene expression clarified the putative effector gene at three specific loci in two osteoblast cell models. The resulting target genes highlight the cell fate decision between osteogenic and adipogenic lineages as important in normal bone accrual.

scholarly journals Ligand-induced native G-quadruplex stabilization impairs transcription initiation

2021 ◽  
Author(s):  
Conghui Li ◽  
Honghong Wang ◽  
Zhinang Yin ◽  
Pingping Fang ◽  
Ruijing Xiao ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Transcription Initiation ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Drug Induced ◽  
Transcriptional Regulatory Elements ◽  
Genome Wide ◽  
Self Association

G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines, and G4s are distributed widely across the genome. G4 participates in multiple biological processes including gene transcription, and G4-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, genome-wide studies of the exact roles of G4s in transcriptional regulation are still lacking. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G4s with high resolution and specificity. We find that native G4 signals are cell type–specific and are associated with transcriptional regulatory elements carrying active epigenetic modifications. Drug-induced promoter-proximal RNA polymerase II pausing promotes nearby G4 formation. In contrast, G4 stabilization by G4-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, ligand-induced G4 stabilization modulates chromatin states and impedes transcription initiation via inhibition of general transcription factors loading to promoters. Together, our study reveals a reciprocal genome-wide regulation between native G4 dynamics and gene transcription, which will deepen our understanding of G4 biology toward therapeutically targeting G4s in human diseases.

scholarly journals Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation

2016 ◽  
Vol 36 (17) ◽  
pp. 2236-2245 ◽  
Author(s):  
Gerald O. Hunter ◽  
Melanie J. Fox ◽  
Whitney R. Smith-Kinnaman ◽  
Madelaine Gogol ◽  
Brian Fleharty ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
Histone H3 ◽  
Repeat Sequence ◽  
Global Changes ◽  
Total Histone ◽  
Terminal Domain ◽  
Genome Wide

In eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y1S2P3T4S5P6S7)nthat undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion ofRTR1causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show thatRTR1deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence ofRTR1. Additionally, the loss of Rtr1in vivoleads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes.

scholarly journals Genome-Wide Association of Mediator and RNA Polymerase II in Wild-Type and Mediator Mutant Yeast

2014 ◽  
Vol 35 (1) ◽  
pp. 331-342 ◽  
Author(s):  
Emily Paul ◽  
Z. Iris Zhu ◽  
David Landsman ◽  
Randall H. Morse
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activation ◽  
Open Reading Frames ◽  
Temperature Sensitive ◽  
Gene Promoters ◽  
Content Type ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that inSaccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised inmed17temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complexin vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.

scholarly journals Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

2015 ◽  
Vol 112 (7) ◽  
pp. E677-E686 ◽  
Author(s):  
Rodrigo Peña-Hernández ◽  
Maud Marques ◽  
Khalid Hilmi ◽  
Teijun Zhao ◽  
Amine Saad ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Cellular Response ◽  
Target Genes ◽  
Regulatory Protein ◽  
Metabolic Stress ◽  
Ctcf Binding ◽  
Gene Promoters ◽  
The Impact

CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation.

scholarly journals Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

2017 ◽  
Author(s):  
Ethan Ford ◽  
Matthew R. Grimmer ◽  
Sabine Stolzenburg ◽  
Ozren Bogdanovic ◽  
Alex de Mendoza ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fusion Protein ◽  
Rna Polymerase Ii ◽  
Zinc Finger ◽  
Gene Promoters ◽  
Natural Conditions ◽  
Promoter Regions ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

AbstractIt is widely assumed that the addition of DNA methylation at CpG rich gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression in natural conditions. The effect of induced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we induced the simultaneous methylation of thousands of promoters in the genome of human cells using an engineered zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is frequently insufficient to transcriptionally repress promoters. Furthermore, DNA methylation deposited at promoter regions associated with H3K4me3 is rapidly erased after removal of the zinc finger-DNMT3A fusion protein. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation, with implications for the emerging field of epigenome engineering.One Sentence SummaryGenome-wide epigenomic manipulation of thousands of human promoters reveals that induced promoter DNA methylation is unstable and frequently does not function as a primary instructive biochemical signal for gene silencing and chromatin reconfiguration.

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