Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers

Abstract The Cyc8-Tup1 corepressor complex is targeted to promoters by pathway-specific DNA-binding repressors, thereby inhibiting the transcription of specific classes of genes. Genetic screens have identified mutations in a variety of Pol II holoenzyme components (Srb8, Srb9, Srb10, Srb11, Sin4, Rgr1, Rox3, and Hrs1) and in the N-terminal tails of histones H3 and H4 that weaken repression by Cyc8-Tup1. Here, we analyze the effect of individual and multiple mutations in many of these components on transcriptional repression of natural promoters that are regulated by Cyc8-Tup1. In all cases tested, individual mutations have a very modest effect on SUC2 RNA levels and no detectable effect on levels of ANB1, MFA2, and RNR2. Furthermore, multiple mutations within the Srb components, between Srbs and Sin4, and between Srbs and histone tails affect Cyc8-Tup1 repression to the same modest extent as the individual mutations. These results argue that the weak effects of the various mutations on repression by Cyc8-Tup1 are not due to redundancy among components of the Pol II machinery, and they argue against a simple redundancy between the holoenzyme and chromatin pathways. In addition, phenotypic analysis indicates that, although Srbs8–11 are indistinguishable with respect to Cyc8-Tup1 repression, the individual Srbs are functionally distinct in other respects. Genetic interactions among srb mutations imply that a balance between the activities of Srb8 + Srb10 and Srb11 is important for normal cell growth.

Download Full-text

Unlike its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival

Cells ◽

10.3390/cells10010192 ◽

2021 ◽

Vol 10 (1) ◽

pp. 192

Author(s):

Siska Van Belle ◽

Sara El Ashkar ◽

Kateřina Čermáková ◽

Filip Matthijssens ◽

Steven Goossens ◽

...

Keyword(s):

Growth Factor ◽

Cell Survival ◽

Cell Lines ◽

Protein Interactions ◽

Leukemic Cell ◽

Related Protein ◽

Histone Tails ◽

Knockout Mouse Model ◽

Leukemic Cell Lines

HDGF-related protein 2 (HRP-2) is a member of the Hepatoma-Derived Growth Factor-related protein family that harbors the structured PWWP and Integrase Binding Domain, known to associate with methylated histone tails or cellular and viral proteins, respectively. Interestingly, HRP-2 is a paralog of Lens Epithelium Derived Growth Factor p75 (LEDGF/p75), which is essential for MLL-rearranged (MLL-r) leukemia but dispensable for hematopoiesis. Sequel to these findings, we investigated the role of HRP-2 in hematopoiesis and MLL-r leukemia. Protein interactions were investigated by co-immunoprecipitation and validated using recombinant proteins in NMR. A systemic knockout mouse model was used to study normal hematopoiesis and MLL-ENL transformation upon the different HRP-2 genotypes. The role of HRP-2 in MLL-r and other leukemic, human cell lines was evaluated by lentiviral-mediated miRNA targeting HRP-2. We demonstrate that MLL and HRP-2 interact through a conserved interface, although this interaction proved less dependent on menin than the MLL-LEDGF/p75 interaction. The systemic HRP-2 knockout mice only revealed an increase in neutrophils in the peripheral blood, whereas the depletion of HRP-2 in leukemic cell lines and transformed primary murine cells resulted in reduced colony formation independently of MLL-rearrangements. In contrast, primary murine HRP-2 knockout cells were efficiently transformed by the MLL-ENL fusion, indicating that HRP-2, unlike LEDGF/p75, is dispensable for the transformation of MLL-ENL leukemogenesis but important for leukemic cell survival.

Download Full-text

Persistent Interactions of Core Histone Tails with Nucleosomal DNA following Acetylation and Transcription Factor Binding

Molecular and Cellular Biology ◽

10.1128/mcb.18.11.6293 ◽

1998 ◽

Vol 18 (11) ◽

pp. 6293-6304 ◽

Cited By ~ 96

Author(s):

Vesco Mutskov ◽

Delphine Gerber ◽

Dimitri Angelov ◽

Juan Ausio ◽

Jerry Workman ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Molecular Biology ◽

Binding Sites ◽

Cross Linking ◽

Uv Laser ◽

Histone Tail ◽

Histone Tails ◽

Nucleosomal Dna ◽

Core Histones

ABSTRACT In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

Download Full-text

Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability

Molecular and Cellular Biology ◽

10.1128/mcb.02229-06 ◽

2007 ◽

Vol 27 (11) ◽

pp. 4037-4048 ◽

Cited By ~ 89

Author(s):

Helder Ferreira ◽

Joanna Somers ◽

Ryan Webster ◽

Andrew Flaus ◽

Tom Owen-Hughes

Keyword(s):

Dynamic Properties ◽

Histone H3 ◽

Fine Tuning ◽

Histone Tails ◽

Histone Proteins ◽

Regulatory Factors ◽

Nucleosome Dynamics ◽

Nucleosome Sliding ◽

Eukaryotic Genomes ◽

Dna Wrapping

ABSTRACT Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 αN helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.

Download Full-text

Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails

BMC Biochemistry ◽

10.1186/1471-2091-12-48 ◽

2011 ◽

Vol 12 (1) ◽

pp. 48 ◽

Cited By ~ 53

Author(s):

Ina Bock ◽

Srikanth Kudithipudi ◽

Raluca Tamas ◽

Goran Kungulovski ◽

Arunkumar Dhayalan ◽

...

Keyword(s):

Binding Specificity ◽

Peptide Arrays ◽

Histone Tails ◽

Reading Domains

Download Full-text

Asymmetric breathing motions of nucleosomal DNA and the role of histone tails

The Journal of Chemical Physics ◽

10.1063/1.4997573 ◽

2017 ◽

Vol 147 (6) ◽

pp. 065101 ◽

Cited By ~ 8

Author(s):

Kaushik Chakraborty ◽

Sharon M. Loverde

Keyword(s):

Histone Tails ◽

Nucleosomal Dna

Download Full-text

Is the effect of Decitabine limited to hypomethylation and DNMTs?

10.21203/rs.2.13184/v1 ◽

2019 ◽

Author(s):

Sina Dalvand ◽

Amin Namdari ◽

Ashraf Alemi ◽

Mohammad Hassan Meshkibaf ◽

Sam Setayesh ◽

...

Keyword(s):

Gene Expression ◽

Mrna Expression ◽

Histone Deacetylases ◽

Dna Methyltransferase ◽

Chromatin Condensation ◽

Dna Demethylation ◽

Histone Tails ◽

Normal Cells ◽

Before And After ◽

Cancerous Cells

Abstract Background: Histone modifications play a crucial role in chromatin structure. Among enzymes, which regulate these processes, histone deacetylases (HDACs) can remove acetyl groups from histone tails, thus increasing their interaction with DNA and leading to chromatin condensation. 5-Aza-2′-deoxycytidine (AZad) or Decitabine is a potent hypomethylating agent that incorporates into DNA and traps DNA methyltransferase in the form of a covalent protein–DNA adduct. Azad, not only change the gene expression through demethylation of the gene's promoter, but it also can change gene expression independently from DNA demethylation. So, the present study was to distinguish whether AZad in addition to inhibitory effects on DNA methyltransferase, can change HDAC3 and HDAC7 mRNA expression in NALM-6, HL-60 cancer cell lines. Methods: HL-60, NALM-6 and normal cells were cultured, and the treatment dose of the AZad was obtained (1µM) by the MTT test. Finally, HDAC3 and HDAC7 mRNA expression were measured by Real Time PCR in HL-60 and NALM-6 cancerous cells before and after treatment. In addition, HDAC3 and HDAC7 mRNA expression in un-treated HL-60 and NALM-6 cancerous cells were compared to the normal cells. Results: Our result revealed that expression of HDAC3 and HDAC7, in HL-60 and NALM-6 cells increases as compared to normal cells. After treatment of HL-60 and NALM-6 cells with AZad, HDAC3 and HDAC7 mRNA expression were decreased significantly. Conclusions: Our data showed, the effects of AZad are not limited to direct hypomethylation of DNMTs but it can indirectly affect other epigenetic factors, such as HDACs activity, through converging pathways. Keywords: HDAC3 ; HDAC7 ; HL-60; NALM-6 ; Decitabine ; AZad

Download Full-text

Sum1p, the Origin Recognition Complex, and the Spreading of a Promoter-Specific Repressor in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.25.14.5920-5932.2005 ◽

2005 ◽

Vol 25 (14) ◽

pp. 5920-5932 ◽

Cited By ~ 22

Author(s):

Patrick J. Lynch ◽

Hunter B. Fraser ◽

Elena Sevastopoulos ◽

Jasper Rine ◽

Laura N. Rusche

Keyword(s):

Saccharomyces Cerevisiae ◽

Origin Recognition Complex ◽

Single Amino Acid ◽

Wild Type ◽

Genomic Context ◽

Functional Connection ◽

Histone Tails ◽

Repressive Chromatin ◽

Single Amino Acid Change ◽

Origin Recognition

ABSTRACT In Saccharomyces cerevisiae, Sum1p is a promoter-specific repressor. A single amino acid change generates the mutant Sum1-1p, which causes regional silencing at new loci where wild-type Sum1p does not act. Thus, Sum1-1p is a model for understanding how the spreading of repressive chromatin is regulated. When wild-type Sum1p was targeted to a locus where mutant Sum1-1p spreads, wild-type Sum1p did not spread as efficiently as mutant Sum1-1p did, despite being in the same genomic context. Thus, the SUM1-1 mutation altered the ability of the protein to spread. The spreading of Sum1-1p required both an enzymatically active deacetylase, Hst1p, and the N-terminal tail of histone H4, consistent with the spreading of Sum1-1p involving sequential modification of and binding to histone tails, as observed for other silencing proteins. Furthermore, deletion of the N-terminal tail of H4 caused Sum1-1p to return to loci where wild-type Sum1p acts, consistent with the SUM1-1 mutation increasing the affinity of the protein for H4 tails. These results imply that the spreading of repressive chromatin proteins is regulated by their affinities for histone tails. Finally, this study uncovered a functional connection between wild-type Sum1p and the origin recognition complex, and this relationship also contributes to mutant Sum1-1p localization.

Download Full-text