Spreading of silent chromatin: inaction at a distance

The thesis aims to identify and initiate functional characterization of the SWI/SNF and ISWI complexes in Tetrahymena thermophila. Through affinity purification of the conserved subunit Snf5 followed by mass spectrometry (AP-MS), I identified the first SWI/SNF complex in protists. One of the subunits I found is a small bromodomain containing protein named Ibd1. Through AP-MS of Ibd1 I found Ibd1 is versatile and interacts with several additional chromatin remodeling complexes. Bromodomains are known to have affinity for acetylated lysine residues within proteins such as histones. A peptide array experiment suggests that Ibd1 also has affinity for acetylated chromatin. Indirect immunofluorescence (IF) of Ibd1 hints at a role in transcription. My analysis of Tetrahymena Iswi1 shows expression during meiosis, vegetative growth and starvation. IF data shows its localization is consistent with Iswi1 function in mitosis/meiosis or maintenance of silent chromatin. AP-MS of ISW1 discovered several interacting proteins of unknown function.

Download Full-text

Drosophila UTX Is a Histone H3 Lys27 Demethylase That Colocalizes with the Elongating Form of RNA Polymerase II

Molecular and Cellular Biology ◽

10.1128/mcb.01504-07 ◽

2007 ◽

Vol 28 (3) ◽

pp. 1041-1046 ◽

Cited By ~ 79

Author(s):

Edwin R. Smith ◽

Min Gyu Lee ◽

Benjamin Winter ◽

Nathan M. Droz ◽

Joel C. Eissenberg ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Histone H3 ◽

Silent Chromatin ◽

H3k4 Methylation ◽

Active Chromatin ◽

Pol Ii ◽

H3k27 Methylation ◽

Histone H3 Methylation ◽

Heat Shock Induction

ABSTRACT Histone H3 methylation at Lys27 (H3K27 methylation) is a hallmark of silent chromatin, while H3K4 methylation is associated with active chromatin regions. Here we report that a Drosophila JmjC family member, dUTX, specifically demethylates di- and trimethylated but not monomethylated H3K27. dUTX localization on chromatin correlates with the elongating form of RNA polymerase II (Pol II), and dUTX can associate with Pol II. Furthermore, heat shock induction results in the recruitment of dUTX to the hsp70 gene, like that of several other Pol II elongation factors. Our data indicate that dUTX is intimately associated with actively transcribed genes and may provide a paradigm for how H3K27 demethylation is required for the activation of preinitiated Pol II on transcriptionally poised genes.

Download Full-text

Phosphorylation of repressive histone code readers by casein kinase 2 plays diverse roles in heterochromatin regulation

The Journal of Biochemistry ◽

10.1093/jb/mvz045 ◽

2019 ◽

Vol 166 (1) ◽

pp. 3-6 ◽

Cited By ~ 1

Author(s):

Yota Murakami

Keyword(s):

Histone Modifications ◽

Constitutive Heterochromatin ◽

Histone H3 ◽

Casein Kinase ◽

Casein Kinase 2 ◽

Histone Code ◽

Effector Proteins ◽

Regulatory Proteins ◽

Silent Chromatin ◽

Facultative Heterochromatin

Abstract Heterochromatin is a condensed and transcriptionally silent chromatin structure and that plays important roles in epigenetic regulation of the genome. Two types of heterochromatin exist: constitutive heterochromatin is primarily associated with trimethylation of histone H3 at lysine 9 (H3K9me3), and facultative heterochromatin with trimethylation of H3 at lysine 27 (H3K27me3). The methylated histones are bound by the chromodomain of histone code ‘reader’ proteins: HP1 family proteins for H3K9me3 and Polycomb family proteins for H3K27me3. Each repressive reader associates with various ‘effector’ proteins that provide the functional basis of heterochromatin. Heterochromatin regulation is primarily achieved by controlling histone modifications. However, recent studies have revealed that the repressive readers are phosphorylated, like other regulatory proteins, suggesting that phosphorylation also participates in heterochromatin regulation. Detailed studies have shown that phosphorylation of readers affects the binding specificities of chromodomains for methylated histone H3, as well as the binding of effector proteins. Thus, phosphorylation adds another layer to heterochromatin regulation. Interestingly, casein kinase 2, a strong and predominant kinase within the cell, is responsible for phosphorylation of repressive readers. In this commentary, I summarize the regulation of repressive readers by casein kinase 2-dependent phosphorylation and discuss the functional meaning of this modification.

Download Full-text

Formation of Boundaries of Transcriptionally Silent Chromatin by Nucleosome-Excluding Structures

Molecular and Cellular Biology ◽

10.1128/mcb.24.5.2118-2131.2004 ◽

2004 ◽

Vol 24 (5) ◽

pp. 2118-2131 ◽

Cited By ~ 61

Author(s):

Xin Bi ◽

Qun Yu ◽

Joseph J. Sandmeier ◽

Yanfei Zou

Keyword(s):

Chromatin Structure ◽

Barrier Function ◽

Eukaryotic Genome ◽

Silent Chromatin ◽

Active Chromatin ◽

Chromatin Domains ◽

Distinct Gene ◽

Lexa Protein ◽

Nucleosome Formation

ABSTRACT The eukaryotic genome is divided into chromosomal domains of distinct gene activities. Transcriptionally silent chromatin tends to encroach upon active chromatin. Barrier elements that can block the spread of silent chromatin have been documented, but the mechanisms of their function are not resolved. We show that the prokaryotic LexA protein can function as a barrier to the propagation of transcriptionally silent chromatin in yeast. The barrier function of LexA correlates with its ability to disrupt local chromatin structure. In accord with this, (CCGNN) n and poly(dA-dT), both of which do not favor nucleosome formation, can also act as efficient boundaries of silent chromatin. Moreover, we show that a Rap1p-binding barrier element also disrupts chromatin structure. These results demonstrate that nucleosome exclusion is one of the mechanisms for the establishment of boundaries of silent chromatin domains.

Download Full-text