The Arabidopsis DREAM complex antagonizes WDR5A to modulate histone H3K4me2/3 deposition for a subset of genome repression

In vivo genetics of anaesthetic action

Rtt106 is a histone chaperone that has been suggested to play a role in heterochromatin-mediated silencing in Saccharomyces cerevisiae. It interacts physically and functionally with the chromatin assembly factor-1 (CAF-1), which is associated with replication-coupled nucleosomal deposition. In this work, we have taken several approaches to study Rtt106 in greater detail and have identified a previously unknown function of Rtt106. We found genetic interactions between rtt106Delta and mutations in genes encoding transcription elongation factors, including Spt6, TFIIS, and members of the PAF and yeast DSIF complexes. In addition, chromatin immunoprecipitation analysis indicates that Rtt106 is associated with transcribed regions of active genes. Furthermore, our results show that Rtt106 is required for the repression of transcription from a cryptic promoter within a coding region. This observation strongly suggests that Rtt106 is involved in the regulation of chromatin structure of transcribed regions. Finally, we provide evidence that Rtt106 plays a role in regulating the levels of histone H3 transcription-coupled deposition over transcribed regions. Taken together, our results indicate a direct link for Rtt106 with transcription elongation and the chromatin dynamics associated with RNA polymerase II passage.

Quantitative Genetic Interactions Reveal Biological Modularity

Transcription regulation by histone modifications is a major contributing factor to the structural and functional diversity in biology. These modifications are encrypted as histone codes or histone languages and function to establish and maintain heritable epigenetic codes that define the identity and the fate of the cell. Despite recent advances revealing numerous histone modifications associated with transcription regulation, how such modifications dictate the process of transcription is not fully understood. Here we describe spatial and temporal analyses of the histone modifications that are introduced during estrogen receptor α (ERα)-activated transcription. We demonstrated that aborting RNA polymerase II caused a disruption of the histone modifications that are associated with transcription elongation but had a minimal effect on modifications deposited during transcription initiation. We also found that the histone H3S10 phosphorylation mark is catalyzed by mitogen- and stress-activated protein kinase 1 (MSK1) and is recognized by a 14-3-3ζ/14-3-3ε heterodimer through its interaction with H3K4 trimethyltransferase SMYD3 and the p52 subunit of TFIIH. We showed that H3S10 phosphorylation is a prerequisite for H3K4 trimethylation. In addition, we demonstrated that SET8/PR-Set7/KMT5A is required for ERα-regulated transcription and its catalyzed H4K20 monomethylation is implicated in both transcription initiation and elongation. Our experiments provide a relatively comprehensive analysis of histone modifications associated with ERα-regulated transcription and define the biological meaning of several key components of the histone code that governs ERα-regulated transcription.

EKLF/Klf1 Regulates Erythroid Transcription By Its Pioneering Activity and Subsequent Control of RNA Pol II Pause-Release

E2F1 transcription factor mediates a link between fat and islets to promote β cell proliferation in response to acute insulin resistance.

Acute myeloid leukemias are a highly heterogeneous group of diseases associated with corruption of myeloid cell differentiation, accumulation of immature blasts, and emergence of a transformed leukemia initiating cell (LIC) capable of sustaining leukemic expansion. Genetic and phenotypic properties of LICs are highly variable among AML patients as a consequence of variable cytogenetics, stem/progenitor cell of origin and stage of disease progression. The orphan nuclear receptors NR4A1 and NR4A3 are potent AML tumor suppressors whose deletion in mice leads to rapid AML development. They are also silenced in cytogenetically diverse human LICs, and their anti-leukemic effect is associated with acute transcriptional repression of c-MYC and reprogramming of a core MYC oncogenic gene signature that is common to LICs of distinct cytogenetic backgrounds. c-MYC transcription is controlled at the step of transcriptional elongation, and high levels of c-MYC expression are maintained in many cancers, including AML, by establishment of cancer cell-selective super enhancers that are marked by high levels of the BET bromodomain protein, BRD4, a key regulator of c-MYC transcription elongation together with BRD4 associated components of the Mediator coactivator complex. BRD4 promotes transcription elongation of c-MYC by recruiting the positive transcription elongation factor, P-TEFb, a catalytic component of the super elongation complex (SEC) which phosphorylates RNA PolII at serine 2 to enable release of promoter paused RNA PolII. Here we investigated the transcriptional mechanisms of NR4A1-dependent c-MYC repression. Interrogation of genome-wide NR4A1 binding in Kasumi-1 AML-ETO positive human AML cells revealed NR4A1 occupancy within the 5’ proximal regions of the c-MYC gene and at a downstream enhancer region previously identified as a c-MYC super enhancer in the RN2 mouse model of MLL-AF9/NrasG12D driven AML. Consistent with its classification as a super enhancer, we found strong enrichment of BRD4 and the MED1 component of the Mediator complex at the c-MYC enhancer in Kasumi-1 AML cells in the absence of NR4A1. Interrogation of the effects of acute rescue of NR4A1 expression on the enhancer status of this region and transcriptional elongation of c-MYC revealed that NR4A1 represses c-MYC transcription elongation by interacting directly with the enhancer locus to inhibit recruitment of Mediator complex and BRD4, leading to loss of P-TEFb recruitment to both the enhancer and c-MYC gene and a loss of elongation competent RNA PolII. Together, these data indicate the NR4A1 negatively regulates transcriptional elongation at the c-MYC locus by interfering with factors required for super enhancer maintenance and AML selective overexpression of c-MYC. Since AML cells which rely on c-MYC overexpression are extremely sensitive to BRD4 inhibition, our results predict that strategies directed toward NR4A activation in AML cells may provide an alternative means of targeting c-MYC driven AMLs. Citation Format: Ryan P. Duren, Orla M. Conneely. Transcriptional mechanisms of NR4A orphan nuclear receptor tumor suppression in AML. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-83. doi:10.1158/1538-7445.AM2014-LB-83

Initially, the E2F transcription factor was discovered as a factor able to bind the adenovirus E2 promoter and activate viral genes. Afterwards it was shown that E2F also binds to promoters of nonviral genes such as C-MYC and DHFR, which were already known at that time to be important for cell growth and DNA metabolism, respectively. These findings provided the first clues that the E2F transcription factor might be an important regulator of the cell cycle. Since this initial discovery in 1987, several additional E2F family members have been identified, and more than 100 targets genes have been shown to be directly regulated by E2Fs, the majority of these are important for controlling the cell cycle. The progression of a cell through the cell cycle is accompanied with the increased expression of a specific set of genes during one phase of the cell cycle and the decrease of the same set of genes during a later phase of the cell cycle. This roller coaster ride, or oscillation, of gene expression is essential for the proper progression through the cell cycle to allow accurate DNA replication and cell division. The E2F transcription factors have been shown to be critical for the temporal expression of the oscillating cell cycle genes. This review will focus on how the oscillation of E2Fs and their targets is regulated by transcriptional, post-transcriptional and post-translational mechanism in mammals, yeast, flies, and worms. Furthermore, we will discuss the functional impact of E2Fs on the cell cycle progression and outline the consequences when E2F expression is disturbed.

Important progress in the understanding of elongation control by RNA polymerase II (RNAPII) has come from the recent identification of the positive transcription elongation factor b (P-TEFb) and the demonstration that this factor is a protein kinase that phosphorylates the carboxyl-terminal domain (CTD) of the RNAPII largest subunit. The P-TEFb complex isolated from mammalian cells contains a catalytic subunit (CDK9), a cyclin subunit (cyclin T1 or cyclin T2), and additional, yet unidentified, polypeptides of unknown function. To identify additional factors involved in P-TEFb function we performed a yeast two-hybrid screen using CDK9 as bait and found that cyclin K interacts with CDK9 in vivo. Biochemical analyses indicate that cyclin K functions as a regulatory subunit of CDK9. The CDK9-cyclin K complex phosphorylated the CTD of RNAPII and functionally substituted for P-TEFb comprised of CDK9 and cyclin T in in vitro transcription reactions.

A Cellular Memory of Developmental History Generates Phenotypic Diversity in C. elegans

The Double Bromodomain Proteins Brd2 and Brd3 Couple Histone Acetylation to Transcription

MSL Complex Is Attracted to Genes Marked by H3K36 Trimethylation Using a Sequence-Independent Mechanism

H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling.

Inherited Blood Cancer Predisposition through Altered Transcription Elongation

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function