Higher-order Chromatin Structure Research Articles

Chromatin and epigenetic features of long-range gene regulation

The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. Developments in chromosome conformation capture technologies have revealed that interactions between regions of chromatin are pervasive and highly cell-type specific. The movement of enhancers and promoters in and out of higher-order chromatin structures within the nucleus are associated with changes in expression and histone modifications. However, the factors responsible for mediating these changes and determining enhancer:promoter specificity are still not completely known. In this review, we summarize what is known about the patterns of epigenetic and chromatin features characteristic of elements involved in long-range interactions. In addition, we review the insights into both local and global patterns of chromatin interactions that have been revealed by the latest experimental and computational methods.

Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency

Epigenetic mechanisms underlying somatic reprogramming have been extensively studied, but little isknown about the nuclear architecture of pluripotent stem cells (PSCs). Using circular chromosomeconformation capture with high-throughput sequencing (4C-seq) and fluorescence insitu hybridization (FISH), we identified chromosomal regions that colocalize frequently with the Oct4 locus in PSCs. These PSC-specific long-range interactions are established prior to transcriptional activation of endogenous Oct4 during reprogramming to induced PSCs and are facilitated by Klf4-mediated recruitment of cohesin. Depletion of Klf4 leads to unloading of cohesin at the Oct4 enhancer and disrupts long-range interactions prior to loss of Oct4 transcription and subsequent PSC differentiation, suggesting a causative role for Klf4 in facilitating long-range interactions independent of its transcriptional activity. Taken together, our results delineate the basic nuclear organization at the Oct4 locus in PSCs and suggest a functional role for Klf4-mediated higher-order chromatin structure in maintaining and inducing pluripotency.

Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines

In addition to alternative splicing, alternative polyadenylation has also been identified as a critical and prevalent regulatory mechanism in human gene expression. However, the mechanism of alternative polyadenylation selection and the involved factors is still largely unknown. We use the ENCODE data to scan DNA functional elements, including chromatin accessibility and histone modification, around transcript cleavage sites. Our results demonstrate that polyadenylation sites tend to be less sensitive to DNase I. However, these polyadenylation sites have preference in nucleosome-depleted regions, indicating the involvement of chromatin higher-order structure rather than nucleosomes in the resultant lower chromatin accessibility. More interestingly, for genes using two polyadenylation sites, the distal sites show even lower chromatin accessibility compared with the proximal sites or the unique sites of genes using only one polyadenylation site. We also observe that the histone modification mark, histone H3 lysine 36 tri-methylation (H3K36Me3), exhibits different patterns around the cleavage sites of genes using multiple polyadenylation sites from those of genes using a single polyadenylation site. Surprisingly, the H3K36Me3 levels are comparable among the alternative polyadenylation sites themselves. In summary, polyadenylation and alternative polyadenylation are closely related to functional elements on the DNA level. liang.chen@usc.edu.

Regulation of Human Cytomegalovirus Transcription in Latency: Beyond the Major Immediate-Early Promoter

Lytic infection of differentiated cell types with human cytomegalovirus (HCMV) results in the temporal expression of between 170–200 open reading frames (ORFs). A number of studies have demonstrated the temporal regulation of these ORFs and that this is orchestrated by both viral and cellular mechanisms associated with the co-ordinated recruitment of transcription complexes and, more recently, higher order chromatin structure. Importantly, HCMV, like all herpes viruses, establishes a lifelong latent infection of the host—one major site of latency being the undifferentiated haematopoietic progenitor cells resident in the bone marrow. Crucially, the establishment of latency is concomitant with the recruitment of cellular enzymes that promote extensive methylation of histones bound to the major immediate early promoter. As such, the repressive chromatin structure formed at the major immediate early promoter (MIEP) elicits inhibition of IE gene expression and is a major factor involved in maintenance of HCMV latency. However, it is becoming increasingly clear that a distinct subset of viral genes is also expressed during latency. In this review, we will discuss the mechanisms that control the expression of these latency-associated transcripts and illustrate that regulation of these latency-associated promoters is also subject to chromatin mediated regulation and that the instructive observations previously reported regarding the negative regulation of the MIEP during latency are paralleled in the regulation of latent gene expression.

HDAC Up-Regulation in Early Colon Field Carcinogenesis Is Involved in Cell Tumorigenicity through Regulation of Chromatin Structure

Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC) family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC). However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs) interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA) targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS) to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.

Human glutathione S‐transferase A ( GSTA ) family genes are regulated by steroidogenic factor 1 (SF‐1) and are involved in steroidogenesis

Steroidogenic factor 1 (SF-1) is a master regulator for steroidogenesis. In this study, we identified novel SF-1 target genes using a genome-wide promoter tiling array and a DNA microarray. SF-1 was found to regulate human glutathione S-transferase A (GSTA) family genes (hGSTA1-hGSTA4), a superfamily of detoxification enzymes clustered on chromosome 6p12. All hGSTA genes were up-regulated by transduction of SF-1 into human mesenchymal stem cells, while knockdown of endogenous SF-1 in H295R cells down-regulated all hGSTA genes. Chromatin immunoprecipitation assays, however, revealed that SF-1 bound directly to the promoters of hGSTA3 and weakly of hGSTA4. Chromosome conformation capture assays revealed that the coordinated expression of the genes was based on changes in higher-order chromatin structure triggered by SF-1, which enables the formation of long-range interactions, at least between hGSTA1 and hGSTA3 gene promoters. In steroidogenesis, dehydrogenation of the 3-hydroxy group and subsequent Δ(5)-Δ(4) isomerization are thought to be enzymatic properties of 3β-hydroxysteroid dehydrogenase (3β-HSD). Here, we demonstrated that, in steroidogenic cells, the hGSTA1 and hGSTA3 gene products catalyze Δ(5)-Δ(4) isomerization in a coordinated fashion with 3β-HSD II to produce progesterone or Δ(4)-androstenedione from their Δ(5)-precursors. Thus, hGSTA1 and hGSTA3 gene products are new members of steroidogenesis working as Δ(5)-Δ(4) isomerases.

PU.1 Level-Directed Chromatin Structure Remodeling at the Irf8 Gene Drives Dendritic Cell Commitment

Dendritic cells (DCs) are essential regulators of immune responses; however, transcriptional mechanisms that establish DC lineage commitment are poorly defined. Here, we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the interferon regulatory factor 8 (Irf8) gene to initiate DC fate choice. An Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental-stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation.

A satellite explosion in the genome of holocentric nematodes.

Centromere sequences in the genome are associated with the formation of kinetochores, where spindle microtubules grow in mitosis. Centromere sequences usually have long tandem repeats (satellites). In holocentric nematodes it is not clear how kinetochores are formed during mitosis; they are distributed throughout the chromosomes. For this reason it appeared of interest to study the satellites in nematodes in order to determine if they offer any clue on how kinetochores are assembled in these species. We have studied the satellites in the genome of six nematode species. We found that the presence of satellites depends on whether the nematode chromosomes are holocentric or monocentric. It turns out that holocentric nematodes are unique because they have a large number of satellites scattered throughout their genome. Their number, length and composition are different in each species: they apparently have very little evolutionary conservation. In contrast, no scattered satellites are found in the monocentric nematode Trichinella spiralis. It appears that the absence/presence of scattered satellites in the genome distinguishes monocentric from holocentric nematodes. We conclude that the presence of satellites is related to the holocentric nature of the chromosomes of most nematodes. Satellites may stabilize a higher order structure of chromatin and facilitate the formation of kinetochores. We also present a new program, SATFIND, which is suited to find satellite sequences.

Abstract 2975: Rad21, as a high order chromatin architecture molecule, regulates global gene transcription.

Abstract Rad21 is a subunit of cohesin complex, which is well known to be involved in sister chromatid cohesion at mitotic phase. In recent studies, Rad21 has been also known to be associated with long-range chromosome interaction to dynamically regulate gene transcription. However, Very little is known about Rad21-mediated high order chromatin structure and global changes in gene transcription in human cancer. In this study, we silenced Rad21 gene using Lenti-virus knockdown system and performed transcriptome analysis to verify the changes in gene transcription by knockdown of Rad21. Among genes showing significant transcription changes by the reduction of Rad21, we chose several target genes decreasing its transcription and checked the transcriptional change with passaging over a 60 day period. Interestingly, the change in transcription level of some genes appeared by the earliest passage time point, whereas those of other genes arose during the course of long-term passage. Consistent with gene transcription changes, results from a ChIP assay demonstrated that Rad21-knockdown cells showed low level of Rad21 occupancy and active histone marks (H3K4me3 and Pol2) on the target genes, indicating that dynamic histone modifications also contribute to regulation of the target genes. To figure out whether the reduction of Rad21 binding directly affects the chromatin loops, we applied Chromosome Conformation Capture (3C) -qPCR in Rad21-knockdown cells. The results demonstrated that the decreased Rad21 expression cause overal reduction of locus interaction on the target genes, indicating that Rad21 binding was directly required for long-range interactions at the target gene regions and gene transcription regulation. Taken together, the results of our study demonstrated that long-range chromosome interaction mediated by Rad21 can dynamically regulate global gene transcription in human cancer cells, indicating that it may be important for cancer development. Citation Format: Jiyeon Yun, Sang-Hyun Song, Jee-Youn Kang, Hwang-Phill Kim, Sae-Won Han, Do-Youn Oh, Seock-Ah Im, Yung-Jue Bang, Tae-You Kim. Rad21, as a high order chromatin architecture molecule, regulates global gene transcription. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2975. doi:10.1158/1538-7445.AM2013-2975 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Large-scale organization of ribosomal DNA chromatin is regulated by Tip5

The DNase I accessibility and chromatin organization of genes within the nucleus do correlate to their transcriptional activity. Here, we show that both serum starvation and overexpression of Tip5, a key regulator of ribosomal RNA gene (rDNA) repression, dictate DNase I accessibility, facilitate the association of rDNA with the nuclear matrix and thus regulate large-scale rDNA chromatin organization. Tip5 contains four AT-hooks and a TAM (Tip5/ARBP/MBD) domain, which were proposed to bind matrix-attachment regions (MARs) of the genome. Remarkably, the TAM domain of Tip5 functions as nucleolar localization and nuclear matrix targeting module, whereas AT-hooks do not mediate association with the nuclear matrix, but they are required for nucleolar targeting. These findings suggest a dual role for Tip5’s AT-hooks and TAM domain, targeting the nucleolus and anchoring to the nuclear matrix, and suggest a function for Tip5 in the regulation of higher-order rDNA chromatin structure.

Targeted disruption of the nucleosomal binding protein HMGN5 results in altered glutathione metabolism and mild hepatic dysfunction

High mobility group nucleosome‐binding protein 5 (HMGN5) is a chromatin architectural protein that regulates gene expression by decompacting higher‐order chromatin structure; however, the physiological role of this protein is unknown. To examine the function of HMGN5 in vivo, we generated mice lacking the chromatin binding domain of the protein. Compared to wild type littermates, male Hmgn5−/Y mice had elevated serum albumin (p=0.03), fasting non‐HDL cholesterol (p=0.03), fasting triglycierides (p=0.05), and alanine transaminase (p=0.08), suggesting a mild hepatic dysfunction. An UPLC‐QTOF‐MS‐based metabolomic study in Hmgn5−/Y mice identified a 41% increase in hepatic glutathione (p=0.02) and significantly (p<0.05) decreased urinary concentrations of compounds related to the glutathione precursor glycine, such as betaine (−62%), phenylacetylglycine (−50%), and creatine (−42%). Microarray analysis and validation by real‐time PCR revealed that the expression of two genes affecting glutathione function, Gpx6 and Hk1, was significantly (p<0.05) decreased in Hmgn5−/Y mouse liver tissue. In sum, these data suggest that functional loss of the chromatin remodeling protein HMGN5 leads to transcriptional changes that alter glutathione metabolism resulting in mild hepatic dysfunction.Grant Funding Source: NIH/NCI/CCR Intramural Program

Global analysis of SUMO chain function reveals multiple roles in chromatin regulation

Like ubiquitin, the small ubiquitin-related modifier (SUMO) proteins can form oligomeric "chains," but the biological functions of these superstructures are not well understood. Here, we created mutant yeast strains unable to synthesize SUMO chains (smt3(allR)) and subjected them to high-content microscopic screening, synthetic genetic array (SGA) analysis, and high-density transcript profiling to perform the first global analysis of SUMO chain function. This comprehensive assessment identified 144 proteins with altered localization or intensity in smt3(allR) cells, 149 synthetic genetic interactions, and 225 mRNA transcripts (primarily consisting of stress- and nutrient-response genes) that displayed a >1.5-fold increase in expression levels. This information-rich resource strongly implicates SUMO chains in the regulation of chromatin. Indeed, using several different approaches, we demonstrate that SUMO chains are required for the maintenance of normal higher-order chromatin structure and transcriptional repression of environmental stress response genes in budding yeast.

Coordinate Regulation of the Gel-forming Mucin Genes at Chromosome 11p15.5*

Four of the genes that encode gel-forming mucins, which are major components of the mucus layer protecting many epithelial surfaces, are clustered at chromosome 11p15.5 and show both cell- and tissue-specific expression patterns. We aimed to determine whether the individual genes were coordinately regulated by mechanisms involving higher order chromatin structure. CCCTC-binding factor (CTCF) sites were predicted in silico and CTCF occupancy then evaluated by chromatin immunoprecipitation. CTCF was found at many sites across the gene cluster, and its binding was correlated with mucin gene expression. Next, siRNA-mediated depletion of CTCF was shown to increase MUC2 expression in A549 lung carcinoma cells and both MUC6 and MUC5AC expression in LS180 colon carcinoma cells. These changes correlated with loss of CTCF binding at multiple sites, although others retained occupancy. In cells actively expressing the mucins, the gene cluster was shown by chromosome conformation capture to form looped three-dimensional structures with direct interactions between the MUC2 promoter region, regions 30 kb 5' to it, close to the MUC6 promoter and others near the 3' end of MUC5AC, >170 kb away. Finally, to demonstrate the importance of CTCF binding to mucin gene expression, Calu-3 lung carcinoma cells were exposed to lipopolysaccharide (LPS). LPS increased the expression of MUC2 and MUC5AC and reduced MUC5B. CTCF occupancy was concurrently depleted at specific binding sites close to these genes. These data suggest that CTCF binding and cell type-specific long-range interactions across the 11p15.5 gene cluster are critical mechanisms for coordinating gel-forming mucin gene expression.

Function of HP1 proteins as a component in kinetochore formation and its relation with chromosome instability

HP1 Family of proteins are involved in the formation and maintenance of chromatin higher order structure. In mammals there are known three isotypes (HP1a, HP1b and HP1g). Recently, it has been proposed that HP1 may play an important roll in inner centromere establishment, generated by its interaction with HMis12 complex, (HMis12C) which is relevant in kinetochore formation and microtubule recognition which ensure correct chromosomal segregation. However, alterations in chromatin structure or loss in H3K9 methylation lead to a reduction of the protein presence and changes of HP1 proteins localization to heterochromatin followed by chromosome instability. It has not been studied if this is mediated by loss of recruitment of HMis12C to the kinetochore and which is it relation with chromosomal instability generation. Thus, the aim of this study is to determine if alteration of HP1 proteins is capable of reducing HMis12C recruitment to the kinetochore. We elaborated transfected of constructions of HP1-GFP for each isotype in HCT116 cells and performed time-lapse to observe localization along cell cycle by confocal microscopy; in addition, we treated cells with TSA 1uM to analyze changes in HP1 localization. We used ChIP assay in satellite alpha and satellite 2 to determine presence of H3H9me3, HP1 proteins, CENPA, and HMis12 in normal HCT116 and in HCT116 transfected cells with HP1-GFP and with Jmjd2b to observe the effect of the loss of H3K9me3 to HMis12C incorporation. We found that each isotype present a different localization at interphase, but HP1a and b are present at the centromere at this fase, also this localization is highly dynamic in mitosis where HP1b is removed and HP1a is enriched at the chromosomes centromere. Treatment with TSA increases chromosome instability and generates relocalization of HP1 proteins to pericentromeric chromatin where H3K9me3 remains and propagates. Jmjd2b over-expression reduces HP1 presence at chromatin and also reduces HMis12 in mitosis. These results support another function of HP1 as a kinetochore partner leading incorporation of HMis12 during cell division. This work was supported by CONACYT 83959 and PAPIITIN213311

PcG-Mediated Higher-Order Chromatin Structures Modulate Replication Programs at the Drosophila BX-C

Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time.

Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging

The functional potential of hematopoietic stem cells (HSCs) declines during aging, and in doing so, significantly contributes to hematopoietic pathophysiology in the elderly. To explore the relationship between age-associated HSC decline and the epigenome, we examined global DNA methylation of HSCs during ontogeny in combination with functional analysis. Although the DNA methylome is generally stable during aging, site-specific alterations of DNA methylation occur at genomic regions associated with hematopoietic lineage potential and selectively target genes expressed in downstream progenitor and effector cells. We found that age-associated HSC decline, replicative limits, and DNA methylation are largely dependent on the proliferative history of HSCs, yet appear to be telomere-length independent. Physiological aging and experimentally enforced proliferation of HSCs both led to DNA hypermethylation of genes regulated by Polycomb Repressive Complex 2. Our results provide evidence that epigenomic alterations of the DNA methylation landscape contribute to the functional decline of HSCs during aging.

Heterochromatinization associated with cell differentiation as a model to study DNA double strand break induction and repair in the context of higher-order chromatin structure

Cell differentiation is associated with extensive gene silencing, heterochromatinization and potentially decreasing need for repairing DNA double-strand breaks (DSBs). Differentiation stages of blood cells thus represent an excellent model to study DSB induction, repair and misrepair in the context of changing higher-order chromatin structure. We show that immature granulocytes form γH2AX and 53BP1 foci, contrary to the mature cells; however, these foci colocalize only rarely and DSB repair is inefficient. Moreover, specific chromatin structure of granulocytes probably influences DSB induction.

Function of chromatin structure and dynamics in DNA damage, repair and misrepair: γ-rays and protons in action

According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure—the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams.

Nucleosome Conformation and the Higher Order Structure of Chromatin: spFRET Experiments on (Di)Nucleosomes

Chromatin, the structure in which DNA is compacted in eukaryotic cells, plays a key role in DNA regulation by governing DNA accessibility. FRET experiments on single nucleosomes, the basic units in chromatin, have revealed a dynamic nucleosome where spontaneous unwrapping from the ends provides access to the nucleosomal DNA. We investigate how the dynamics of individual nucleosomes couples to chromatin higher order structure. Therefore, we study DNA dynamics in nucleosomes flanked by linker DNA or a second nucleosome.A combination of single-pair (sp) FRET, Alternating Laser Excitation and FCS on nucleosomes in gel with increasing linker DNA length reveals that the fraction of partially unwrapped nucleosomes increases when the exiting DNA tails come close to each other. Electrostatic repulsion between the entering and exiting DNA drives nucleosomes to a more open conformation.Nucleosome-nucleosome interactions further affect DNA unwrapping. A stacking interaction, mediated by histone tails, is expected to bring nucleosomes face to face in order to establish the structure of a folded chromatin fiber. Dinucleosomes with 20, 50 or 55 bp linker DNA adopt a conformation similar to mononucleosomes, as measured with gel electrophoresis and bulk FRET. However, spFRET experiments show that the fraction of partially unwrapped nucleosomes increases from 15% to 25% for dinucleosomes with 55 bp linker DNA as compared to 50 bp and to mononucleosomes. We propose that this additional unwrapping helps to reduce the energy penalty for bending the linker DNA in stacked nucleosomes.These spFRET experiments reveal subtle changes in nucleosome conformation that form the basis to higher order chromatin structure and function.

Saccharomyces cerevisiaeLinker Histone—Hho1p Maintains Chromatin Loop Organization during Ageing

Intricate, dynamic, and absolutely unavoidable ageing affects cells and organisms through their entire lifetime. Driven by diverse mechanisms all leading to compromised cellular functions and finally to death, this process is a challenge for researchers. The molecular mechanisms, the general rules that it follows, and the complex interplay at a molecular and cellular level are yet little understood. Here, we present our results showing a connection between the linker histones, the higher-order chromatin structures, and the process of chronological lifespan of yeast cells. By deleting the gene for the linker histone in Saccharomyces cerevisiae we have created a model for studying the role of chromatin structures mainly at its most elusive and so far barely understood higher-order levels of compaction in the processes of yeast chronological lifespan. The mutant cells demonstrated controversial features showing slower growth than the wild type combined with better survival during the whole process. The analysis of the global chromatin organization during different time points demonstrated certain loss of the upper levels of chromatin compaction in the cells without linker histone. The results underlay the importance of this histone for the maintenance of the chromatin loop structures during ageing.