3D-FISH analysis of embryonic nuclei in mouse highlights several abrupt changes of nuclear organization during preimplantation development

Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis

Following fertilization, gametes undergo epigenetic reprogramming in order to revert to a totipotent state. How embryonic cells subsequently acquire their fate and the role of chromatin dynamics in this process are unknown. Genetic and experimental embryology approaches have identified some of the players and morphological changes that are involved in early mammalian development, but the exact events underlying cell fate allocation in single embryonic cells have remained elusive. Experimental and technological advances have recently provided novel insights into chromatin dynamics and nuclear architecture in single cells; these insights have reshaped our understanding of the mechanisms underlying cell fate allocation and plasticity in early mammalian development.

Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, MethylRO

In mammals, DNA is methylated at CpG sites, which play pivotal roles in gene silencing and chromatin organization. Furthermore, DNA methylation undergoes dynamic changes during development, differentiation, and in pathological processes. The conventional methods represent snapshots; therefore, the dynamics of this marker within living organisms remains unclear. To track this dynamics, we made a knockin mouse that expresses a red fluorescent protein (RFP)-fused methyl-CpG-binding domain (MBD) protein from the ROSA26 locus ubiquitously; we named it MethylRO (methylation probe in ROSA26 locus). Using this mouse, we performed RFP-mediated methylated DNA immunoprecipitation sequencing (MeDIP-seq), whole-body section analysis, and live-cell imaging. We discovered that mobility and pattern of heterochromatin as well as DNA methylation signal intensity inside the nuclei can be markers for cellular differentiation status. Thus, the MethylRO mouse represents a powerful bioresource and technique for DNA methylation dynamics studies in developmental biology, stem cell biology, as well as in disease states.

•

Changes in DNA methylation are tracked in living mice

•

Heterochromatin structure changes dynamically during development and differentiation

•

Heterochromatin of preimplantation embryonic cells is highly dynamic than ESCs

•

Heterochromatin pattern in nucleus can be a marker for cell differentiation states

The maternal nucleolus plays a key role in centromere satellite maintenance during the oocyte to embryo transition

The oocyte (maternal) nucleolus is essential for early embryonic development and embryos originating from enucleolated oocytes arrest at the 2-cell stage. The reason for this is unclear. Surprisingly, RNA polymerase I activity in nucleolus-less mouse embryos, as manifested by pre-rRNA synthesis, and pre-rRNA processing are not affected, indicating an unusual role of the nucleolus. We report here that the maternal nucleolus is indispensable for the regulation of major and minor satellite repeats soon after fertilisation. During the first embryonic cell cycle, absence of the nucleolus causes a significant reduction in major and minor satellite DNA by 12% and 18%, respectively. The expression of satellite transcripts is also affected, being reduced by more than half. Moreover, extensive chromosome bridging of the major and minor satellite sequences was observed during the first mitosis. Finally, we show that the absence of the maternal nucleolus alters S-phase dynamics and causes abnormal deposition of the H3.3 histone chaperone DAXX in pronuclei of nucleolus-less zygotes.

Perinucleolar relocalization and nucleolin as crucial events in the transcriptional activation of key genes in mantle cell lymphoma

In mantle cell lymphoma (MCL), one allele of the cyclin D1 (Ccnd1) gene is translocated from its normal localization on chromosome 11 to chromosome 14. This is considered as the crucial event in the transformation process of a normal naive B-cell; however, the actual molecular mechanism leading to Ccnd1 activation remains to be deciphered. Using a combination of three-dimensional and immuno-fluorescence in situ hybridization experiments, the radial position of the 2 Ccnd1 alleles was investigated in MCL-derived cell lines and malignant cells from affected patients. The translocated Ccnd1 allele was observed significantly more distant from the nuclear membrane than its nontranslocated counterpart, with a very high proportion of IgH-Ccnd1 chromosomal segments localized next to a nucleolus. These perinucleolar areas were found to contain active RNA polymerase II (PolII) clusters. Nucleoli are rich in nucleolin, a potent transcription factor that we found to bind sites within the Ccnd1 gene specifically in MCL cells and to activate Ccnd1 transcription. We propose that the Ccnd1 transcriptional activation in MCL cells relates to the repositioning of the rearranged IgH-Ccnd1-carrying chromosomal segment in a nuclear territory with abundant nucleolin and active PolII molecules. Similar transforming events could occur in Burkitt and other B-cell lymphomas.

Heterochromatin establishment at pericentromeres depends on nuclear position

Mammalian development begins with fertilization followed by genome-wide epigenetic reprogramming involving de novo formation of pericentromeric heterochromatin. Here, Jachowicz et al. dissect the spatiotemporal kinetics of the first acquisition of heterochromatic signatures. Physically tethering pericentromeric chromatin to the nuclear periphery results in defective silencing and impaired development. This study demonstrates that correct nuclear organization in the early embryo is essential for chromatin reprogramming and developmental progression.

Mammalian development begins with fertilization of an oocyte by the sperm followed by genome-wide epigenetic reprogramming. This involves de novo establishment of chromatin domains, including the formation of pericentric heterochromatin. We dissected the spatiotemporal kinetics of the first acquisition of heterochromatic signatures of pericentromeric chromatin and found that the heterochromatic marks follow a temporal order that depends on a specific nuclear localization. We addressed whether nuclear localization of pericentric chromatin is required for silencing by tethering it to the nuclear periphery and show that this results in defective silencing and impaired development. Our results indicate that reprogramming of pericentromeric heterochromatin is functionally linked to its nuclear localization.

Spatial quantitation of FISH signals in diploid versus aneuploid nuclei

Fluorescence in situ hybridization (FISH) is the most widely used molecular technique to visualize chromosomal abnormalities. Here, we describe a novel 3D modeling approach to allow precise shape estimation and localization of FISH signals in the nucleus of human embryonic stem cells (hES) undergoing progressive but defined aneuploidy. The hES cell line WA09 acquires an extra copy of chromosome 12 in culture with increasing passages. Both diploid and aneuploid nuclei were analyzed to quantitate the differences in the localization of centromeric FISH signals for chromosome 12 as it transitions from euploidy to aneuploidy. We employed superquadric modeling primitives coupled with principal component analysis to determine the 3D position of FISH signals within the nucleus. A novel aspect of our modeling approach is that it allows comparison of FISH signals across multiple cells by normalizing the position of the centromeric signals relative to a reference landmark in oriented nuclei. Using this model we present evidence of changes in the relative positioning of centromeres in trisomy-12 cells when compared with diploid cells from the same population. Our analysis also suggests a significant change in the spatial distribution of at least one of the FISH signals in the aneuploid chromosome complements implicating that an overall change in centromere position may occur in trisomy-12 due to the addition of an extra chromosome. These studies underscore the unique utility of our modeling algorithms in quantifying FISH signals in three dimensions.

Histone post-translational modifications in preimplantation mouse embryos and their role in nuclear architecture

In mammals, epigenetic modifications are globally rearranged after fertilization, when gametes fuse to form the embryo. While gametes carry special epigenetic signatures and a unique nuclear organization, they attain embryo-specific patterns after fertilization. This "reprogramming" is promoted by intimate contact between the parental inherited genomes and the oocyte cytoplasm over the first cell cycles of development. Although the mechanisms of this reprogramming remain poorly understood, it appears that the particular epigenetic landscape established after fertilization is essential for further development. This review looks at histone post-translational modifications, focusing on their functions in chromatin organization and their role in nuclear architecture during mouse embryonic development. Epigenetic changes linked to the use of assisted reproductive technologies are also considered.

Something silent this way forms: the functional organization of the repressive nuclear compartment

The repressive compartment of the nucleus is comprised primarily of telomeric and centromeric regions, the silent portion of ribosomal RNA genes, the majority of transposable element repeats, and facultatively repressed genes specific to different cell types. This compartment localizes into three main regions: the peripheral heterochromatin, perinucleolar heterochromatin, and pericentromeric heterochromatin. Both chromatin remodeling proteins and transcription of noncoding RNAs are involved in maintenance of repression in these compartments. Global reorganization of the repressive compartment occurs at each cell division, during early development, and during terminal differentiation. Differential action of chromatin remodeling complexes and boundary element looping activities are involved in mediating these organizational changes. We discuss the evidence that heterochromatin formation and compartmentalization may drive nuclear organization.