scholarly journals Post-mitotic accumulation of histone variant H3.3 in new cortical neurons establishes neuronal transcriptome, identity, and connectivity

2021 ◽  
Author(s):  
Owen H Funk ◽  
Yaman Qalieh ◽  
Daniel Z Doyle ◽  
Mandy M Lam ◽  
Kenneth Y Kwan
Keyword(s):  
Cortical Neurons ◽  
Neural Progenitor Cells ◽  
De Novo ◽  
Histone H3 ◽  
Histone Variants ◽  
Total Histone ◽  
Critical Window ◽  
Histone H3 Variant ◽  
Transcriptomic Changes ◽  
Encoding Genes

Histone variants, which can be expressed outside of S-phase and deposited DNA synthesis-independently, provide replacement histones in terminally post-mitotic cells, including neurons. Histone variants can also serve active roles in gene regulation by modulating chromatin states or enabling nucleosome turnover at regulatory regions. Here, we find that newborn cortical excitatory neurons substantially accumulate the histone H3 variant H3.3 immediately post-mitosis. Co-deletion of H3.3-encoding genes H3f3a and H3f3b from new neurons abrogates this accumulation, and causes widespread disruptions in the developmental establishment of the neuronal transcriptome. These broad transcriptomic changes coincide with neuronal maturation phenotypes in acquisition of distinct neuronal identities and formation of axon tracts. Stage-dependent deletion of H3f3a and H3f3b from (1) cycling neural progenitor cells, (2) neurons immediately after terminal mitosis, or (3) several days later, reveals the first post-mitotic days as a critical window for de novo H3.3. After H3.3 accumulation within this developmental window, co-deletion of H3f3a and H3f3b from neurons causes progressive H3.3 depletion over several months without widespread transcriptional disruptions. Our study thus uncovers a key role for H3.3 in establishing neuronal transcriptome, identity, and connectivity immediately post-mitosis that is distinct from its role in maintaining total histone H3 levels over the neuronal lifespan.

scholarly journals Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jan Wisniewski ◽  
Bassam Hajj ◽  
Jiji Chen ◽  
Gaku Mizuguchi ◽  
Hua Xiao ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Elevated Temperatures ◽  
De Novo ◽  
Histone H3 ◽  
S Phase ◽  
Nuclear Accumulation ◽  
Histone H3 Variant ◽  
Functionally Impaired ◽  
Cell Cycle Dynamics ◽  
Cell Lethality

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.

scholarly journals Induction of spontaneous human neocentromere formation and long-term maturation

2021 ◽  
Vol 220 (3) ◽  
Author(s):  
Marina Murillo-Pineda ◽  
Luis P. Valente ◽  
Marie Dumont ◽  
João F. Mata ◽  
Daniele Fachinetti ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
De Novo ◽  
Histone H3 ◽  
Engineering System ◽  
Chromosome Engineering ◽  
Histone H3 Variant ◽  
Chromosomal Passenger ◽  
Long Read ◽  
Functional Kinetochore

Human centromeres form primarily on α-satellite DNA but sporadically arise de novo at naive ectopic loci, creating neocentromeres. Centromere inheritance is driven primarily by chromatin containing the histone H3 variant CENP-A. Here, we report a chromosome engineering system for neocentromere formation in human cells and characterize the first experimentally induced human neocentromere at a naive locus. The spontaneously formed neocentromere spans a gene-poor 100-kb domain enriched in histone H3 lysine 9 trimethylated (H3K9me3). Long-read sequencing revealed this neocentromere was formed by purely epigenetic means and assembly of a functional kinetochore correlated with CENP-A seeding, eviction of H3K9me3 and local accumulation of mitotic cohesin and RNA polymerase II. At formation, the young neocentromere showed markedly reduced chromosomal passenger complex (CPC) occupancy and poor sister chromatin cohesion. However, long-term tracking revealed increased CPC assembly and low-level transcription providing evidence for centromere maturation over time.

scholarly journals snRNA and Heterochromatin Formation Are Involved in DNA Excision during Macronuclear Development in Stichotrichous Ciliates

2005 ◽  
Vol 4 (11) ◽  
pp. 1934-1941 ◽  
Author(s):  
Stefan A. Juranek ◽  
Sina Rupprecht ◽  
Jan Postberg ◽  
Hans J. Lipps
Keyword(s):  
Dna Sequences ◽  
Chromatin Immunoprecipitation ◽  
De Novo ◽  
Histone H3 ◽  
Heterochromatin Formation ◽  
Macronuclear Development ◽  
Dna Elimination ◽  
Histone H3 Variant ◽  
Specific Sequences

ABSTRACT Several models for specific excision of micronucleus-specific DNA sequences during macronuclear development in ciliates exist. While the template-guided recombination model suggests recombination events resulting in specific DNA excision and reordering of macronucleus-destined sequences (MDS) guided by a template, there is evidence that an RNA interference-related mechanism is involved in DNA elimination in holotrichous ciliates. We describe that in the stichotrichous ciliate Stylonychia, snRNAs homologous to micronucleus-specific sequences are synthesized during macronuclear differentiation. Western and in situ analyses demonstrate that histone H3 becomes methylated at K9 de novo during macronuclear differentiation, and chromatin immunoprecipitation revealed that micronucleus-specific sequences are associated with methylated H3. To link both observations, expression of a PIWI homolog, member of the RNA-induced silencing complex, was silenced. In these cells, the methylated micronucleus-specific histone H3 variant “X” is still present in macronuclear anlagen and no K9 methylation of histone H3 is observed. We suggest that snRNA recruits chromatin-modifying enzymes to sequences to be excised. Based on our and earlier observations, we believe that this mechanism is not sufficient for specific excision of sequences and reordering of MDS in the developing macronucleus and propose a model for internal eliminated sequence excision and MDS reordering in stichotrichous ciliates.

scholarly journals ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection

2021 ◽  
Vol 17 (4) ◽  
pp. e1009567
Author(s):  
Joseph M. Cabral ◽  
Camille H. Cushman ◽  
Catherine N. Sodroski ◽  
David M. Knipe
Keyword(s):  
Viral Replication ◽  
De Novo ◽  
Human Fibroblasts ◽  
Histone H3 ◽  
Gc Content ◽  
Lytic Infection ◽  
Nuclear Entry ◽  
Viral Dna ◽  
Total Histone ◽  
Viral Genomes

Histones are rapidly loaded on the HSV genome upon entry into the nucleus of human fibroblasts, but the effects of histone loading on viral replication have not been fully defined. We showed recently that ATRX is dispensable for de novo deposition of H3 to HSV genomes after nuclear entry but restricted infection through maintenance of viral heterochromatin. To further investigate the roles that ATRX and other histone H3 chaperones play in restriction of HSV, we infected human fibroblasts that were systematically depleted of nuclear H3 chaperones. We found that the ATRX/DAXX complex is unique among nuclear H3 chaperones in its capacity to restrict ICP0-null HSV infection. Only depletion of ATRX significantly alleviated restriction of viral replication. Interestingly, no individual nuclear H3 chaperone was required for deposition of H3 onto input viral genomes, suggesting that during lytic infection, H3 deposition may occur through multiple pathways. ChIP-seq for total histone H3 in control and ATRX-KO cells infected with ICP0-null HSV showed that HSV DNA is loaded with high levels of histones across the entire viral genome. Despite high levels of H3, ATAC-seq analysis revealed that HSV DNA is highly accessible, especially in regions of high GC content, and is not organized largely into ordered nucleosomes during lytic infection. ATRX reduced accessibility of viral DNA to the activity of a TN5 transposase and enhanced accumulation of viral DNA fragment sizes associated with nucleosome-like structures. Together, these findings support a model in which ATRX restricts viral infection by altering the structure of histone H3-loaded viral chromatin that reduces viral DNA accessibility for transcription. High GC rich regions of the HSV genome, especially the S component inverted repeats of the HSV-1 genome, show increased accessibility, which may lead to increased ability to transcribe the IE genes encoded in these regions during initiation of infection.

scholarly journals Trans-generational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line

2020 ◽  
Author(s):  
Reinier F. Prosée ◽  
Joanna M. Wenda ◽  
Caroline Gabus ◽  
Kamila Delaney ◽  
Francoise Schwager ◽  
...  
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Protein A ◽  
Histone H3 ◽  
Centromeric Chromatin ◽  
C Elegans ◽  
Centromere Function ◽  
Centromere Protein A ◽  
Histone H3 Variant ◽  
Meiosis I

AbstractCentromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematode Caenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is established de novo on chromatin during diplotene of meiosis I. Here we show that the N-terminal tail of CENP-A is required for the de novo establishment of centromeres, but dispensable for centromere maintenance during embryogenesis. Worms homozygous for a CENP-A tail deletion maintain a functional centromere during development, but give rise to inviable offspring because they fail to re-establish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2, and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct in C. elegans.

scholarly journals Quantitative single-molecule microscopy reveals that CENP-A Cnp1 deposition occurs during G2 in fission yeast

Open Biology ◽  
2012 ◽  
Vol 2 (7) ◽  
pp. 120078 ◽  
Author(s):  
David Lando ◽  
Ulrike Endesfelder ◽  
Harald Berger ◽  
Lakxmi Subramanian ◽  
Paul D. Dunne ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Single Molecule ◽  
Cell Biology ◽  
Histone H3 ◽  
Histone Variants ◽  
Epigenetic Mechanism ◽  
Eukaryotic Cells ◽  
Stochastic Variation ◽  
Histone H3 Variant

The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and ‘counts’ individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-A Cnp1 with single-molecule sensitivity in fission yeast ( Schizosaccharomyces pombe ). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-A Cnp1 levels at fission yeast ( S. pombe ) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-A Cnp1 is deposited solely during the G2 phase of the cell cycle.

scholarly journals The ratio between centromeric proteins CENP-A and CENP-C maintains homeostasis of human centromeres

2019 ◽  
Author(s):  
Daniël P. Melters ◽  
Tatini Rakshit ◽  
Minh Bui ◽  
Sergei A. Grigoryev ◽  
David Sturgill ◽  
...  
Keyword(s):  
Mitotic Spindle ◽  
De Novo ◽  
Histone H3 ◽  
Chromosomal Locus ◽  
Centromeric Chromatin ◽  
Dna Accessibility ◽  
Nucleosome Dynamics ◽  
Histone H3 Variant ◽  
Correct Ratio

AbstractThe centromere is the chromosomal locus that seeds the kinetochore, allowing for a physical connection between the chromosome and the mitotic spindle. At the heart of the centromere is the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle the constitutive centromere associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome dynamics in vivo is unknown. Here, we purify kinetochore associated native centromeric chromatin and analyze its biochemical features using a combinatorial approach. We report that kinetochore bound chromatin has strongly reduced DNA accessibility and a distinct stabilized nucleosomal configuration. Disrupting the balance between CENP-A and CENP-C result in reduced centromeric occupancy of RNA polymerase 2 and impaired de novo CENP-A loading on the centromeric chromatin fiber, correlating with significant mitotic defects. CENP-A mutants that restore the ratio rescue the mitotic defects. These data support a model in which CENP-C bound centromeric nucleosomes behave as a barrier to the transcriptional machinery and suggest that maintaining the correct ratio between CENP-A and CENP-C levels is critical for centromere homeostasis.

scholarly journals Hap2-Ino80 facilitated transcription promotes de novo establishment of CENP-A chromatin

2019 ◽  
Author(s):  
Puneet P. Singh ◽  
Manu Shukla ◽  
Sharon A. White ◽  
Pin Tong ◽  
Tatsiana Auchynnikava ◽  
...  
Keyword(s):  
Fission Yeast ◽  
De Novo ◽  
Histone H3 ◽  
Chromatin Assembly ◽  
Centromere Function ◽  
Kinetochore Assembly ◽  
Auxiliary Subunit ◽  
Evolutionarily Conserved ◽  
Histone H3 Variant ◽  
Chromatin Integrity

SUMMARYCentromeres are maintained epigenetically by the presence of CENP-A, an evolutionarily-conserved histone H3 variant, which directs kinetochore assembly and hence, centromere function. To identify factors that promote assembly of CENP-A chromatin, we affinity selected solubilised fission yeast CENP-ACnp1 chromatin. All subunits of the Ino80 complex were enriched, including the auxiliary subunit Hap2. In addition to a role in maintenance of CENP-ACnp1 chromatin integrity at endogenous centromeres, Hap2 is required for de novo assembly of CENP-ACnp1 chromatin on naïve centromere DNA and promotes H3 turnover on centromere regions and other loci prone to CENP-ACnp1 deposition. Prior to CENP-ACnp1 chromatin assembly, Hap2 facilitates transcription from centromere DNA. These analyses suggest that Hap2-Ino80 destabilises H3 nucleosomes on centromere DNA through transcription-coupled histone H3 turnover, driving the replacement of resident H3 nucleosomes with CENP-ACnp1 nucleosomes. These inherent properties define centromere DNA by directing a program that mediates CENP-ACnp1 assembly on appropriate sequences.

scholarly journals Transgenerational inheritance of centromere identity requires the CENP-A N-terminal tail in the C. elegans maternal germ line

PLoS Biology ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. e3000968
Author(s):  
Reinier F. Prosée ◽  
Joanna M. Wenda ◽  
Isa Özdemir ◽  
Caroline Gabus ◽  
Kamila Delaney ◽  
...  
Keyword(s):  
De Novo ◽  
Germ Line ◽  
Protein A ◽  
Histone H3 ◽  
Transgenerational Inheritance ◽  
Centromeric Chromatin ◽  
C Elegans ◽  
Centromere Function ◽  
Centromere Protein A ◽  
Histone H3 Variant

Centromere protein A (CENP-A) is a histone H3 variant that defines centromeric chromatin and is essential for centromere function. In most eukaryotes, CENP-A-containing chromatin is epigenetically maintained, and centromere identity is inherited from one cell cycle to the next. In the germ line of the holocentric nematode Caenorhabditis elegans, this inheritance cycle is disrupted. CENP-A is removed at the mitosis-to-meiosis transition and is reestablished on chromatin during diplotene of meiosis I. Here, we show that the N-terminal tail of CENP-A is required for the de novo establishment of centromeres, but then its presence becomes dispensable for centromere maintenance during development. Worms homozygous for a CENP-A tail deletion maintain functional centromeres during development but give rise to inviable offspring because they fail to reestablish centromeres in the maternal germ line. We identify the N-terminal tail of CENP-A as a critical domain for the interaction with the conserved kinetochore protein KNL-2 and argue that this interaction plays an important role in setting centromere identity in the germ line. We conclude that centromere establishment and maintenance are functionally distinct in C. elegans.

scholarly journals Centromere transcription allows CENP-A to transit from chromatin association to stable incorporation

2018 ◽  
Vol 217 (6) ◽  
pp. 1957-1972 ◽  
Author(s):  
Georg O.M. Bobkov ◽  
Nick Gilbert ◽  
Patrick Heun
Keyword(s):  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Chromosome Segregation ◽  
De Novo ◽  
Histone H3 ◽  
Culture Cells ◽  
Tissue Culture Cells ◽  
Histone H3 Variant ◽  
Loading System ◽  
Stable Incorporation

Centromeres are essential for chromosome segregation and are specified epigenetically by the presence of the histone H3 variant CENP-A. In flies and humans, replenishment of the centromeric mark is uncoupled from DNA replication and requires the removal of H3 “placeholder” nucleosomes. Although transcription at centromeres has been previously linked to the loading of new CENP-A, the underlying molecular mechanism remains poorly understood. Here, we used Drosophila melanogaster tissue culture cells to show that centromeric presence of actively transcribing RNA polymerase II temporally coincides with de novo deposition of dCENP-A. Using a newly developed dCENP-A loading system that is independent of acute transcription, we found that short inhibition of transcription impaired dCENP-A incorporation into chromatin. Interestingly, initial targeting of dCENP-A to centromeres was unaffected, revealing two stability states of newly loaded dCENP-A: a salt-sensitive association with the centromere and a salt-resistant chromatin-incorporated form. This suggests that transcription-mediated chromatin remodeling is required for the transition of dCENP-A to fully incorporated nucleosomes at the centromere.

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