MeCP2 and Major Satellite Forward RNA Cooperate for Pericentric Heterochromatin Organization

AbstractDNA methylation is essential for heterochromatin formation and repression of DNA repeat transcription, both of which are essential for genome integrity. Loss of DNA methylation is associated with disease, including cancer, but is also required for development. Alternative pathways to maintain heterochromatin are thus needed to limit DNA damage accumulation. Here, we find that DAXX, an H3.3 chaperone, protects pericentromeric heterochromatin and is essential for embryonic stem cells (ESCs) maintenance in the ground-state of pluripotency. Upon DNA demethylation-mediated damage, DAXX relocalizes to pericentromeric regions, and recruits PML and SETDB1, thereby promoting heterochromatin formation. In the absence of DAXX, the 3D-architecture and physical properties of pericentric heterochromatin are disrupted, resulting in derepression of major satellite DNA. Using epigenome editing tools, we demonstrate that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX and H3.3 unite DNA damage response and heterochromatin maintenance in ESCs.

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The PWWP Domain of Dnmt3a and Dnmt3b Is Required for Directing DNA Methylation to the Major Satellite Repeats at Pericentric Heterochromatin

Molecular and Cellular Biology ◽

10.1128/mcb.24.20.9048-9058.2004 ◽

2004 ◽

Vol 24 (20) ◽

pp. 9048-9058 ◽

Cited By ~ 171

Author(s):

Taiping Chen ◽

Naomi Tsujimoto ◽

En Li

Keyword(s):

Dna Methylation ◽

Fluorescent Protein ◽

Catalytic Domain ◽

Regulatory Region ◽

Pericentric Heterochromatin ◽

Pwwp Domain ◽

Major Satellite ◽

Satellite Repeats ◽

Associated Proteins ◽

Green Fluorescent

ABSTRACT Dnmt3a and Dnmt3b are responsible for the establishment of DNA methylation patterns during development. These proteins contain, in addition to a C-terminal catalytic domain, a unique N-terminal regulatory region that harbors conserved domains, including a PWWP domain. The PWWP domain, characterized by the presence of a highly conserved proline-tryptophan-tryptophan-proline motif, is a module of 100 to 150 amino acids found in many chromatin-associated proteins. However, the function of the PWWP domain remains largely unknown. In this study, we provide evidence that the PWWP domains of Dnmt3a and Dnmt3b are involved in functional specialization of these enzymes. We show that both endogenous and green fluorescent protein-tagged Dnmt3a and Dnmt3b are particularly concentrated in pericentric heterochromatin. Mutagenesis analysis indicates that their PWWP domains are required for their association with pericentric heterochromatin. Disruption of the PWWP domain abolishes the ability of Dnmt3a and Dnmt3b to methylate the major satellite repeats at pericentric heterochromatin. Furthermore, we demonstrate that the Dnmt3a PWWP domain has little DNA-binding ability, in contrast to the Dnmt3b PWWP domain, which binds DNA nonspecifically. Collectively, our results suggest that the PWWP domains of Dnmt3a and Dnmt3b are essential for targeting these enzymes to pericentric heterochromatin, probably via a mechanism other than protein-DNA interactions.

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Faculty Opinions recommendation of Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014618.194203 ◽

2003 ◽

Author(s):

Steven Henikoff

Keyword(s):

Dna Methylation ◽

Histone H3 ◽

Pericentric Heterochromatin ◽

Major Satellite ◽

Satellite Repeats

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DICER regulates the expression of major satellite repeat transcripts and meiotic chromosome segregation during spermatogenesis

Nucleic Acids Research ◽

10.1093/nar/gkaa460 ◽

2020 ◽

Author(s):

Ram Prakash Yadav ◽

Juho-Antti Mäkelä ◽

Hanna Hyssälä ◽

Sheyla Cisneros-Montalvo ◽

Noora Kotaja

Keyword(s):

Spatial Organization ◽

Meiotic Chromosome ◽

Physiological Role ◽

Pericentric Heterochromatin ◽

Dynamic Changes ◽

Satellite Repeat ◽

Major Satellite ◽

Transcript Processing ◽

Direct Targeting

Abstract Constitutive heterochromatin at the pericentric regions of chromosomes undergoes dynamic changes in its epigenetic and spatial organization during spermatogenesis. Accurate control of pericentric heterochromatin is required for meiotic cell divisions and production of fertile and epigenetically intact spermatozoa. In this study, we demonstrate that pericentric heterochromatin is expressed during mouse spermatogenesis to produce major satellite repeat (MSR) transcripts. We show that the endonuclease DICER localizes to the pericentric heterochromatin in the testis. Furthermore, DICER forms complexes with MSR transcripts, and their processing into small RNAs is compromised in Dicer1 knockout mice leading to an elevated level of MSR transcripts in meiotic cells. We also show that defective MSR forward transcript processing in Dicer1 cKO germ cells is accompanied with reduced recruitment of SUV39H2 and H3K9me3 to the pericentric heterochromatin and meiotic chromosome missegregation. Altogether, our results indicate that the physiological role of DICER in maintenance of male fertility extends to the regulation of pericentric heterochromatin through direct targeting of MSR transcripts.

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Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

eLife ◽

10.7554/elife.25317 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 31

Author(s):

Atsuko Shirai ◽

Takayuki Kawaguchi ◽

Hideaki Shimojo ◽

Daisuke Muramatsu ◽

Mayumi Ishida-Yonetani ◽

...

Keyword(s):

Nucleic Acid ◽

Nucleic Acids ◽

Binding Affinity ◽

Histone H3 ◽

Pericentric Heterochromatin ◽

Nucleic Acid Binding ◽

Major Satellite ◽

Satellite Rnas ◽

Heterochromatin Assembly

SUV39H is the major histone H3 lysine 9 (H3K9)-specific methyltransferase that targets pericentric regions and is crucial for assembling silent heterochromatin. SUV39H recognizes trimethylated H3K9 (H3K9me3) via its chromodomain (CD), and enriched H3K9me3 allows SUV39H to target specific chromosomal regions. However, the detailed targeting mechanisms, especially for naïve chromatin without preexisting H3K9me3, are poorly understood. Here we show that Suv39h1’s CD (Suv39h1-CD) binds nucleic acids, and this binding is important for its function in heterochromatin assembly. Suv39h1-CD had higher binding affinity for RNA than DNA, and its ability to bind nucleic acids was independent of its H3K9me3 recognition. Suv39h1 bound major satellite RNAs in vivo, and knockdown of major satellite RNAs lowered Suv39h1 retention on pericentromere. Suv39h1 mutational studies indicated that both the nucleic acid–binding and H3K9me–binding activities of Suv39h1-CD were crucial for its pericentric heterochromatin assembly. These results suggest that chromatin-bound RNAs contribute to creating SUV39H’s target specificity.

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Suv39h-Mediated Histone H3 Lysine 9 Methylation Directs DNA Methylation to Major Satellite Repeats at Pericentric Heterochromatin

Current Biology ◽

10.1016/s0960-9822(03)00432-9 ◽

2003 ◽

Vol 13 (14) ◽

pp. 1192-1200 ◽

Cited By ~ 802

Author(s):

Bernhard Lehnertz ◽

Yoshihide Ueda ◽

Alwin A.H.A. Derijck ◽

Ulrich Braunschweig ◽

Laura Perez-Burgos ◽

...

Keyword(s):

Dna Methylation ◽

Histone H3 ◽

Pericentric Heterochromatin ◽

Major Satellite ◽

Satellite Repeats

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BRCA1 foci in normal S-phase nuclei are linked to interphase centromeres and replication of pericentric heterochromatin

The Journal of Cell Biology ◽

10.1083/jcb.200602055 ◽

2006 ◽

Vol 175 (5) ◽

pp. 693-701 ◽

Cited By ~ 31

Author(s):

Gayle J. Pageau ◽

Jeanne B. Lawrence

Keyword(s):

Pericentric Heterochromatin ◽

S Phase ◽

Nuclear Antigen ◽

Brdu Incorporation ◽

Embryonic Cells ◽

Major Satellite ◽

Inactive X Chromosome ◽

Xist Rna ◽

Brdu Labeling ◽

Proliferating Cell

Breast cancer–associated protein 1 (BRCA1) forms foci at sites of induced DNA damage, but any significance of these normal S-phase foci is unknown. BRCA1 distribution does not simply mirror or overlap that of replicating DNA; however, BRCA1 foci frequently abut sites of BrdU incorporation, mostly at mid-to-late S phase. Although BRCA1 does not overlap XIST RNA across the inactive X chromosome, BRCA1 foci position overwhelmingly in heterochromatic regions, particularly the nucleolar periphery where many centromeres reside. In humans and mice, including early embryonic cells, BRCA1 commonly associates with interphase centromere–kinetochore complexes, including pericentric heterochromatin. Proliferating cell nuclear antigen or BrdU labeling demonstrates that BRCA1 localizes adjacent to, or “paints,” major satellite blocks as chromocenters replicate, where topoisomerase is also enriched. BRCA1 loss is often associated with proliferative defects, including postmitotic bridges enriched with satellite DNA. These findings implicate BRCA1 in replication-linked maintenance of centric/pericentric heterochromatin and suggest a novel means whereby BRCA1 loss may contribute to genomic instability and cancer.

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Np95 Is Implicated in Pericentromeric Heterochromatin Replication and in Major Satellite Silencing

Molecular Biology of the Cell ◽

10.1091/mbc.e06-09-0874 ◽

2007 ◽

Vol 18 (3) ◽

pp. 1098-1106 ◽

Cited By ~ 61

Author(s):

Roberto Papait ◽

Christian Pistore ◽

Diego Negri ◽

Daniela Pecoraro ◽

Lisa Cantarini ◽

...

Keyword(s):

Transcriptional Repression ◽

Genome Stability ◽

Pericentric Heterochromatin ◽

Histone H4 ◽

Strong Reduction ◽

Major Satellite ◽

Heterochromatin Formation ◽

A Cell ◽

Target Promoters ◽

Segregation Of Chromosomes

Heterochromatin plays an important role in transcriptional repression, for the correct segregation of chromosomes and in the maintenance of genome stability. Pericentric heterochromatin (PH) replication and formation have been proposed to occur in the pericentric heterochromatin duplication body (pHDB). A central question is how the underacetylated state of heterochromatic histone H4 tail is established and controlled, because it is a key event during PH replication and is essential to maintain the compacted and silenced state of these regions. Np95 is a cell cycle regulated and is a nuclear histone-binding protein that also recruits HDAC-1 to target promoters. It is essential for S phase and for embryonic formation and is implicated in chromosome stability. Here we show that Np95 is part of the pHDB, and its functional ablation causes a strong reduction in PH replication. Depletion of Np95 also causes a hyperacetylation of lysines 8, 12, and 16 of heterochromatin histone H4 and an increase of pericentromeric major satellite transcription, whose RNAs are key players for heterochromatin formation. We propose that Np95 is a new relevant protein involved in heterochromatin replication and formation.

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