Chromatin Research Articles

Identifying topologically associating domains using differential kernels.

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix [Formula: see text], where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in [Formula: see text] within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states.

Comparison of the Amyloid Plaque Proteome in Down Syndrome, Early-Onset Alzheimer's Disease and Late-Onset Alzheimer's Disease.

Down syndrome (DS) is strongly associated with Alzheimer's disease (AD), attributable to APP overexpression. DS exhibits Amyloid-β (Aβ) and Tau pathology similar to early-onset AD (EOAD) and late-onset AD (LOAD). The study aimed to evaluate the Aβ plaque proteome of DS, EOAD and LOAD. Using unbiased localized proteomics, we analyzed amyloid plaques and adjacent plaque-devoid tissue ('non-plaque') from post-mortem paraffin-embedded tissues in four cohorts (n = 20/group): DS (59.8 ± 4.99 y/o), EOAD (63 ± 4.07 y/o), LOAD (82.1 ± 6.37 y/o) and controls (66.4 ± 13.04). We assessed functional associations using Gene Ontology (GO) enrichment and protein interaction networks. We identified differentially abundant Aβ plaque proteins vs. non-plaques (FDR < 5%, fold-change > 1.5) in DS (n = 132), EOAD (n = 192) and in LOAD (n = 128); there were 43 plaque-associated proteins shared between all groups. Positive correlations (p < 0.0001) were observed between plaque-associated proteins in DS and EOAD (R2 = 0.77), DS and LOAD (R2 = 0.73), and EOAD vs. LOAD (R2 = 0.67). Top Biological process (BP) GO terms (p < 0.0001) included lysosomal transport for DS, immune system regulation for EOAD, and lysosome organization for LOAD. Protein networks revealed a plaque enriched signature across all cohorts involving APP metabolism, immune response, and lysosomal functions. In DS, EOAD and LOAD non-plaque vs. control tissue, we identified 263, 269, and 301 differentially abundant proteins, including 65 altered non-plaque proteins across all cohorts. Differentially abundant non-plaque proteins in DS showed a significant (p < 0.0001) but weaker positive correlation with EOAD (R2 = 0.59) and LOAD (R2 = 0.33) compared to the stronger correlation between EOAD and LOAD (R2 = 0.79). The top BP GO term for all groups was chromatin remodeling (DS p = 0.0013, EOAD p = 5.79×10- 9, and LOAD p = 1.69×10- 10). Additional GO terms for DS included extracellular matrix (p = 0.0068), while EOAD and LOAD were associated with protein-DNA complexes and gene expression regulation (p < 0.0001). We found strong similarities among the Aβ plaque proteomes in individuals with DS, EOAD and LOAD, and a robust association between the plaque proteomes and lysosomal and immune-related pathways. Further, non-plaque proteomes highlighted altered pathways related to chromatin structure and extracellular matrix (ECM), the latter particularly associated with DS. We identified novel Aβ plaque proteins, which may serve as biomarkers or therapeutic targets.

Pharmacotherapeutic Considerations on Telomere Biology: The Positive Effect of Pharmacologically Active Substances on Telomere Length.

Telomeres are part of chromatin structures containing repeated DNA sequences, which function as protective caps at the ends of chromosomes and prevent DNA degradation and recombination, thus ensuring the integrity of the genome. While telomere length (TL) can be genetically inherited, TL shortening has been associated with ageing and multiple xenobiotics and bioactive substances. TL has been characterised as a reliable biomarker for the predisposition to developing chronic pathologies and their progression. This narrative review aims to provide arguments in favour of including TL measurements in a complex prognostic and diagnostic panel of chronic pathologies and the importance of assessing the effect of different pharmacologically active molecules on the biology of telomeres. Medicines used in the management of cardiovascular diseases, diabetes, schizophrenia, hormone replacement therapy at menopause, danazol, melatonin, and probiotics have been studied for their positive protective effects against TL shortening. All these classes of drugs are analysed in the present review, with a particular focus on the molecular mechanisms involved.

A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes

BackgroundAlthough genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.MethodsWe used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180 bp oligonucleotide reporters (“oligos”) in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve > 20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.ResultsWe identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total = 84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.ConclusionUsing MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.

DNA Damage and Chromatin Rearrangement Work Together to Promote Neurodegeneration.

Neurodegenerative diseases have a complex origin and are composed of genetic and environmental factors. Both DNA damage and chromatin rearrangement are important processes that occur under pathological conditions and in neurons functioning properly. While numerous studies have demonstrated the inseparable relationship between DNA damage and chromatin organization, understanding of this relationship, especially in neurodegenerative diseases, requires further study. Interestingly, recent studies revealed that known hallmark proteins involved in neurodegenerative diseases function in both DNA damage and chromatin reorganization, and this review discusses the current knowledge of this relationship. This review focused on hallmark proteins involved in various neurodegenerative diseases, such as the microtubule-associated protein tau, TAR DNA/RNA binding protein 43 (TDP-43), superoxide dismutase 1 (SOD1), fused in sarcoma (FUS), huntingtin (HTT), α-synuclein, and β-amyloid precursor protein (APP). Hence, DNA damage and chromatin rearrangement are associated with disease mechanisms in distinct neurodegenerative diseases. Targeting common modulators of DNA repair and chromatin reorganization may lead to promising therapies for treating neurodegeneration.

DNA Base Damage Repair Crosstalks with Chromatin Structures to Contract Expanded GAA Repeats in Friedreich's Ataxia.

Trinucleotide repeat (TNR) expansion is the cause of over 40 neurodegenerative diseases, including Huntington's disease and Friedreich's ataxia (FRDA). There are no effective treatments for these diseases due to the poor understanding of molecular mechanisms underlying somatic TNR expansion and contraction in neural systems. We and others have found that DNA base excision repair (BER) actively modulates TNR instability, shedding light on the development of effective treatments for the diseases by contracting expanded repeats through DNA repair. In this study, temozolomide (TMZ) was employed as a model DNA base damaging agent to reveal the mechanisms of the BER pathway in modulating GAA repeat instability at the frataxin (FXN) gene in FRDA neural cells and transgenic mouse mice. We found that TMZ induced large GAA repeat contraction in FRDA mouse brain tissue, neurons, and FRDA iPSC-differentiated neural cells, increasing frataxin protein levels in FRDA mouse brain and neural cells. Surprisingly, we found that TMZ could also inhibit H3K9 methyltransferases, leading to open chromatin and increasing ssDNA breaks and recruitment of the key BER enzyme, pol β, on the repeats in FRDA neural cells. We further demonstrated that the H3K9 methyltransferase inhibitor BIX01294 also induced the contraction of the expanded repeats and increased frataxin protein in FRDA neural cells by opening the chromatin and increasing the endogenous ssDNA breaks and recruitment of pol β on the repeats. Our study provides new mechanistic insight illustrating that inhibition of H3K9 methylation can crosstalk with BER to induce GAA repeat contraction in FRDA. Our results will open a new avenue for developing novel gene therapy by targeting histone methylation and the BER pathway for repeat expansion diseases.

NucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.

Micrococcal nuclease sequencing is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease and the requirement for high sequencing depth. Here, we present the nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. The nucMACC pipeline represents a systematic and genome-wide approach for detecting unstable ("fragile") nucleosomes. We have characterized the regulatory nucleosome landscape in Drosophila melanogaster, Saccharomyces cerevisiae, and mammals. Two functionally distinct sets of promoters were characterized, one associated with an unstable nucleosome and the other being nucleosome depleted. We show that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies.

An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution

In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.

TORC2 is required for the accumulation of γH2A in response to DNA damage

TOR protein kinases serve as the catalytic subunit of the TORC1 and TORC2 complexes, which regulate cellular growth, proliferation and survival. In the fission yeast, Schizosaccharomyces pombe, cells lacking TORC2 or its downstream kinase Gad8 (AKT or SGK1 in human cells) exhibit sensitivity to a wide range of stress conditions, including DNA damage stress. One of the first responses to DNA damage is the phosphorylation of C-terminal serine residues within histone H2AX in human cells (γH2AX), or histone H2A in yeast cells (γH2A). The kinases responsible for γH2A in S. pombe are the two DNA damage checkpoint kinases Rad3 and Tel1 (ATR and ATM, respectively, in human cells). Here we report that TORC2-Gad8 signaling is required for accumulation of γH2A in response to DNA damage and during quiescence. Using the TOR specific inhibitor, Torin1, we demonstrate that the effect of TORC2 on γH2A in response to DNA damage is immediate, rather than adaptive. The lack of γH2A is restored by deletion mutations of transcription and chromatin modification factors, including loss of components of Paf1C, SAGA, Mediator and the bromo-domain proteins Bdf1/Bdf2. Thus, we suggest that TORC2-Gad8 may affect the accumulation of γH2A by regulating chromatin structure and function.

SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells

BackgroundTransposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor binding sites for the CCCTC-binding factor (CTCF) and pivotal in orchestrating chromatin organization. However, the regulatory mechanisms controlling the activity of SINEs in the developing brain remains elusive.ResultsIn our study, we conduct a comprehensive genome-wide epigenetic analysis in mouse neural precursor cells using ATAC-seq, ChIP-seq, whole genome bisulfite sequencing, in situ Hi-C, and RNA-seq. Our findings reveal that the SET domain bifurcated histone lysine methyltransferase 1 (SETDB1)-mediated H3K9me3, in conjunction with DNA methylation, restricts chromatin accessibility on a selective subset of SINEs in neural precursor cells. Mechanistically, loss of Setdb1 increases CTCF access to these SINE elements and contributes to chromatin loop reorganization. Moreover, de novo loop formation contributes to differential gene expression, including the dysregulation of genes enriched in mitotic pathways. This leads to the disruptions of cell proliferation in the embryonic brain after genetic ablation of Setdb1 both in vitro and in vivo.ConclusionsIn summary, our study sheds light on the epigenetic regulation of SINEs in mouse neural precursor cells, suggesting their role in maintaining chromatin organization and cell proliferation during neurodevelopment.

O-307 Decrease of human sperm hypercondensed chromatin volume after slow freezing revealed by three-dimensional (3D) nuclear morphometry

Abstract Study question Are the 3D morphometry parameters of the human sperm nucleus affected by slow freezing? Summary answer The slow freezing-thawing cycle induces significant alterations on hypercondensed nucleus zone by reducing its volume and splits it into several small zones. What is known already Sperm cryopreservation is an essential technique for infertility care, but it seems to highly affect the genetic and epigenetic integrity of sperm nuclei with poorly identified mechanisms. Moreover, it is known that sperm nuclear alterations may be involved in pregnancy failures. Therefore, sperm nuclear biomarkers are an essential issue to assess the outcome of ART procedures when frozen sperm is used. Thereby, 3D visualization of chromatin is a good way to understand modifications in the organization and composition of sperm chromatin after a slow freezing procedure. Study design, size, duration Ten semen of patients were analyzed (Germetheque biobank) after informed consent. Standard semen parameters, DNA fragmentation, chromatin decondensation, sperm telomere length (STL) and 3D nuclear morphometry were performed before and after slow freezing. Morphometric measurements were performed from a digital representation of the sperm nucleus in 3 dimensions that allow us to measure the volume, flatness and elongation of each sperm nucleus and characterize hypercondensed zones, with live/dead spermatozoa distinction. Participants/materials, setting, methods After addition of cryoprotective medium v/v (Cryosperm®), sperm was frozen with a programmable freezer (NanoDigitcool®). Standards sperm parameters were measured in accordance with WHO guidelines 2021, DNA fragmentation by flow cytometry TUNEL assay, chromatin decondensation by epifluorescent microscopy with Chromomycin A3 and STL using qPCR. 3D nuclear representation was performed by a z-axis image acquisition series of DAPI/PI stained slides with optigrid epifluorescent microscopy. Analyses were carried out using the NucleusJ2.0 software with NODeJ plugin. Main results and the role of chance Freezing induces an alteration of sperm vitality (p &amp;lt; 0.0001) and progressive and total motility (p &amp;lt; 0.001 and p &amp;lt; 0.0001 respectively) and an increase in the percentage of sperm with DNA fragmentation (18.30% fresh vs 31.6% frozen, p &amp;lt; 0.05). We did not observe a modification of the median volume of the sperm nucleus before and after freezing (37.15 [IC = 36.5;38.14] and 37.10 [33.27;37.78] µm3 respectively), as the same for flatness and elongation (2.48 vs. 2.50 a.u. and 2.04 vs. 2.04 a.u. respectively). Nevertheless, five samples showed significant alterations of nucleus volume (p &amp;lt; 0.0001), due to diminution of flatness and more or less elongated. A significant decrease of the total volume of the hypercondensed chromatin zone was observed after freezing (0.94 [0.84;0.99] before vs. 0.61 [0.53;0.69] µm3 after freezing-thawing, p &amp;lt; 0.0001), with an effect size of -1.48 [-2.10; -0.86]. Decrease of total volume of hypercondensed region was measured homogeny in all the samples tested, particularly on live (1.00 vs. 0.68 µm3 respectively, p &amp;lt; 0.0001) compared with dead spermatozoa (0.72 vs. 0.57 µm3, p &amp;lt; 0.05). We showed also a significant increase of the number of hypercondensed zones in each nucleus (p &amp;lt; 0.001), reflecting a split into several parts of the hypercondensed chromatin. Limitations, reasons for caution A 3D-FISH analysis would allow to characterize the hypercondensed chromatin portion, probably as heterochromatin and which we suspect to be the nucleus ring. Moreover, a chromosomes specific marking would allow for the identification of whether whole chromosomes or specific parts of chromosomes (centromeres or telomeres) are affected by this decompaction. Wider implications of the findings This study is the first to make exacts measurements of human sperm nucleus because of a non-decondensing method. We demonstrate that slow freezing affects hypercondensed chromatin probably through a decondensation and modification of the nucleus-specific organization. This new assessment will allow a better proficiency of men fertility preservation techniques. Trial registration number NCT04715828

P-066 A multi-bioassay approach to identify male gamete fertilization dysfunction

Abstract Study question Can a multi-bioassay approach identify a specific male gamete dysfunction often overlooked by a standard semen analysis? Summary answer In cases of persistent fertilization failure, additional testing may assist in pinpointing underlying factors contributing to compromised sperm embryo developmental competence and tailor treatment. What is known already Conventional semen analysis, while informative, ineffectively captures the complete spectrum of male gamete dysfunction. Despite adequate sperm concentration and motility, some couples may still experience fertilization failure with Intracytoplasmic Sperm Injection (ICSI). This highlights the complexity of male infertility, that extends beyond standard parameters. In addressing sperm-related fertilization challenges, various assisted oocyte activation (AOA) methods have been proposed to trigger intracellular Ca2+ release, leading to calcium spikes and meiosis initiation. Study design, size, duration In the past 10 months, we identified couples (n = 50) with a history of poor ICSI fertilization, exhibiting suboptimal head morphology. Screening for acrosomal dysfunction involved assessing the presence of PLCxand related gene mutations. We measured the degree of chromatin compaction by histone-to-protamine ratio and evaluated sperm chromatin fragmentation (SCF). To correct for eventual acrosomal dysfunction, couples were counseled to undergo subsequent ICSI cycles with AOA. Clinical outcome was compared between historical and treatment cycles. Participants/materials, setting, methods Fifty men with a history of poor ICSI fertilization were included. A standard semen analysis was conducted according to WHO guidelines. The presence of PLCx was measured through immunofluorescent staining (normal threshold, ≥ 30%), corroborated by gene mutation detection though DNA-seq. Sperm histone-to-protamine ratio was evaluated by Aniline Blue (normal threshold, &amp;lt;15% histone retention). SCF was assessed utilizing the TUNEL assay (normal threshold, ≤15%). AOA was performed using ionomycin or recombinant PLCx protein. Main results and the role of chance Fifty men experienced a poor clinical outcome following ICSI with a fertilization of 7.4% (48/647), embryo implantation of 6.6% (1/15), clinical pregnancy of 6.6% (1/15), and pregnancy loss rate of 100% (1/1). Their semen analysis, interestingly, revealed the following semen parameters: 3.0±1 mL volume, 50.0±20 x106/mL concentration, 41.4±21% motility, and 1.9±1% normal morphology. Nonetheless, PLCx content was diminished, with values ranging from 2-27%. Genomic assessment confirmed mutations in PLCx, DPY19L2, SPATA16 and PICK1 genes, all implicated in sperm nuclear remodeling and acrosome formation. An elevated histone content at 29.7% was positively correlated with an increased SCF at 18.0% (R2=0.6, P&amp;lt;0.001). In subsequent cycles employing AOA, the normal fertilization increased to 42.3% (305/721), the embryo implantation reached 13.0% (9/69), the clinical pregnancy rose to 21.1% (8/38), and the delivery rate was 21.1% (8/38), without any pregnancy loss. (P&amp;lt;0.001). Limitations, reasons for caution While this study affirms the effectiveness of a multifaceted assessment in pinpointing specific sperm dysfunctions and customizing treatment, it is still a retrospective observation requiring independent validation in a larger population. Wider implications of the findings Semen analysis alone fails to address specific aspects of male gamete dysfunction. Incorporating additional bioassays to assess chromatin structure, integrity, and acrosomal function offers valuable insights for fertility management in tailoring personalized treatments. This comprehensive approach enhances the understanding of male reproductive health, maximizing the potential for successful clinical outcome. Trial registration number not applicable

P-057 Do the reduction of sexual abstinence influence sperm DNA fragmentation? Exploring the relationship between the two parameters

Abstract Study question Is the reduction of sexual abstinence (SA) really beneficial on sperm DNA fragmentation? Summary answer Despite recent studies support short SA’s positive impact on sperm parameters, apparently a reduced SA has not a clear impact on sperm DNA fragmentation. What is known already Sperm DNA fragmentation (sDF) has been linked to male infertility, affecting the success of fertility treatments. It’s strictly associated with failure and/or no longer time to conceive, impaired embryo development or higher miscarriege rates. The exact mechanism for age-dependent patterns of sperm decline is still not fully understood. Several factors, such as the increase in free radicals in conjuction with the rising in SA, have been discussed in literature. Recent studies support short SA’s positive impact on sperm parameters, despite controversial results; hence, we decided to analyze the trend in our facility: Humanitas Fertility Center. Study design, size, duration The present retrospective analysis, performed between 2021 and 2023, aims to investigate whether or not a reduced SA is beneficial on sperm DNA fragmentation in patients undergoing IVF. In our study 828 patients (from 21 to 59 years old) underwent both sperm analysis and sDF evaluation through Sperm Chromatin Structure Assay (SCSA). A DNA fragmentation index (DFI) lower than 30% indicates a sperm population with a good chromatin integrity, according to current knowledge. Participants/materials, setting, methods Patients were split in 4 groups, based on their age (≤38 and &amp;gt;38 years) and days of SA (0-3 and 4-7 days). Group 1 (n = 111/828): ≤38 years, ≤3 days; Group 2 (n = 359/828): ≤38 years, &amp;gt;3 days; Group 3 (n = 83/828): &amp;gt;38 years, ≤3 days; Group 4 (n = 275/828): &amp;gt;38 years, &amp;gt;3 days. Statistics was performed to analyze the variance among DFI values belonging to the four groups analyzed. Main results and the role of chance The results are expressed as mean(±SD). In Group 1, DFI %: 22,5(±14,7); in Group 2, DFI %: 21,5(±14,3); in Group 3, DFI %: 22,3(±14,9); in Group 4, DFI %: 26(±16,3). Surprisingly we observed the same behavior between most of the groups analyzed, except for the one belonging to the older patients. As a matter of fact, we found no statistical difference by comparing the DFI values belonging to samples of the same age stratification (≤38 or &amp;gt; 38 years), indeed Group 1 vs. Group 2: P=0,546; Group 3 vs. Group 4: P=0,1152. Different results were observed by comparing groups with the same SA days (≤3 or &amp;gt; 3), but belonging to a different age stratification, as it follows: Group 1 vs. Group 3: P=0,6384; Group 2 vs. Group 4: P=0,0001. This leads us to think that only the mixture of advanced paternal age (&amp;gt;38 years) and the increase of SA defines a worsening of DFI, according to our patients’ stratification. Limitations, reasons for caution There’s no homogeneity in the number of patients recruited with ≤3 days of SA compared to those with &amp;gt;3 days, as expected. Men undergoing fertility treatments follow strict SA guidelines; moreover, there’s no consensus about to request a second semen sample in clinical practice, in order to eliminate SA. Wider implications of the findings Exploring the inclusion of a broader spectrum of patients with low SA, despite their age, or instructing them to undergo semen analysis with a 0-day SA, could yield interesting insights. This could lead to targeted interventions and treatments, offering further hope for individuals with sDF issues. Trial registration number Not applicable

DNA structural features and variability of complete MHC locus sequences.

The major histocompatibility (MHC) locus, also known as the Human Leukocyte Antigen (HLA) genes, is located on the short arm of chromosome 6, and contains three regions (Class I, Class II and Class III). This 5Mbp locus is one of the most variable regions of the human genome, yet it also encodes a set of highly conserved and important proteins related to immunological response. Genetic variations in this region are responsible for more diseases than in the entire rest of the human genome. However, information on local structural features of the DNA is largely ignored. With recent advances in long-read sequencing technology, it is now becoming possible to sequence the entire 5Mbp MHC locus, producing complete diploid haplotypes of the whole region. Here, we describe structural maps based on the complete sequences from six different homozygous HLA cell lines. We find long-range structural variability in the different sequences for DNA stacking energy, position preference and curvature, variation in repeats, as well as more local changes in regions forming open chromatin structures, likely to influence gene expression levels. These structural maps can be useful in visualizing large scale structural variation across HLA types, in particular when this can be complemented with epigenetic signals.

Identifying Key Genes Involved in Axillary Lymph Node Metastasis in Breast Cancer Using Advanced RNA-Seq Analysis: A Methodological Approach with GLMQL and MAS.

Our study aims to address the methodological challenges frequently encountered in RNA-Seq data analysis within cancer studies. Specifically, it enhances the identification of key genes involved in axillary lymph node metastasis (ALNM) in breast cancer. We employ Generalized Linear Models with Quasi-Likelihood (GLMQLs) to manage the inherently discrete and overdispersed nature of RNA-Seq data, marking a significant improvement over conventional methods such as the t-test, which assumes a normal distribution and equal variances across samples. We utilize the Trimmed Mean of M-values (TMMs) method for normalization to address library-specific compositional differences effectively. Our study focuses on a distinct cohort of 104 untreated patients from the TCGA Breast Invasive Carcinoma (BRCA) dataset to maintain an untainted genetic profile, thereby providing more accurate insights into the genetic underpinnings of lymph node metastasis. This strategic selection paves the way for developing early intervention strategies and targeted therapies. Our analysis is exclusively dedicated to protein-coding genes, enriched by the Magnitude Altitude Scoring (MAS) system, which rigorously identifies key genes that could serve as predictors in developing an ALNM predictive model. Our novel approach has pinpointed several genes significantly linked to ALNM in breast cancer, offering vital insights into the molecular dynamics of cancer development and metastasis. These genes, including ERBB2, CCNA1, FOXC2, LEFTY2, VTN, ACKR3, and PTGS2, are involved in key processes like apoptosis, epithelial-mesenchymal transition, angiogenesis, response to hypoxia, and KRAS signaling pathways, which are crucial for tumor virulence and the spread of metastases. Moreover, the approach has also emphasized the importance of the small proline-rich protein family (SPRR), including SPRR2B, SPRR2E, and SPRR2D, recognized for their significant involvement in cancer-related pathways and their potential as therapeutic targets. Important transcripts such as H3C10, H1-2, PADI4, and others have been highlighted as critical in modulating the chromatin structure and gene expression, fundamental for the progression and spread of cancer.

P-070 The effect of surgical interventions in sperm DNA fragmentation: a systematic review and meta-analysis

Abstract Study question Do surgical interventions improve sperm DNA fragmentation? Summary answer Orchiectomy, bariatric surgery and varicocelectomy improve sperm DNA fragmentation. What is known already Sperm DNA fragmentation, which is known to be one of the functional alterations that harms men’s fertile potential, is caused by several factors, and one of the most important is oxidative stress, caused by accumulation of reactive oxygen species (ROS) beyond the physiological limits of the organism. Some examples of diseases that cause this increase in ROS are testicular tumors, obesity and varicocele. Once they all have surgical corrections, the aim of this study was to observe if orchiectomy, bariatric surgery and varicocelectomy had a positive impact in sperm DNA fragmentation. Study design, size, duration A systematic review was developed, including 33 articles: 1 about orchiectomy, 4 about bariatric surgery, and the remaining ones about varicocelectomy. After the review was finished, a meta-analysis was conducted with all the numeric information extracted from the articles. The study was registered on PROSPERO database and was performed based on PRISMA guideline. Participants/materials, setting, methods Data extraction was made by two reviewers independently, and all the information was tabulated in a systematic spreadsheet. 7 articles were excluded, because they did not meet the inclusion criteria: they either included analysis of adolescent spermatogenesis or did not include analysis of sperm DNA fragmentation, and 5 articles were excluded from statistical analysis due to the studies’ designs and lack of essential statistical data. The statistical analysis was conducted by dmetar, metafor e meta. Main results and the role of chance The studies were carried out with men whose seminal samples were analysed before and after surgical intervention. The type of intervention (orchiectomy, bariatric surgery or varicocelectomy) and the way sperm DNA fragmentation was analysed (Terminal deoxynucleotidyl transferase dUTP nick end labeling – TUNEL, Cometa Assay or The Sperm Chromatin Structure Assay – SCSA) were not moderators of the estimated effect. However, the effect estimated increased according to the duration of the follow-up. When duration of follow-up was short (up to six months), there was no effect of interventions on sperm DNA fragmentation. The effect was greater when the duration was average (between six and nine months) and long (more than nine months). There was a reduction in sperm DNA fragmentation with interventions (effect estimated [confidence range 95%] = -1.22 [-1.65; -0.78]; p &amp;lt; 0.001). Despite different techniques were used to analyse sperm DNA fragmentation, the present study showed an improvement in this functional alteration after surgical interventions. Limitations, reasons for caution The small number of participants included in each article analysed, the heterogeneity between the follow-up time and the lack of quality numeric information in literature are possible limitations of this study. Besides, the fact that varicocelectomy had a bigger weight in this study must be analysed critically. Wider implications of the findings Therefore, this study is considered an important source for consistent and reliable information about sperm DNA fragmentation and the effect of surgical interventions on it. It is necessary to expand the studies on this topic, mostly due to the lack of randomized clinical trials. Trial registration number not applicable

O-038 Impact of maternal aging on the DNA repair landscape in mouse oocytes

Abstract Study question How does maternal aging impact DNA damage accumulation and DNA repair capacity in mammalian oocytes? Summary answer Age-related changes in DNA repair compartments and chromatin organisation drive DNA damage accumulation in aged oocytes, ultimately contributing to the decline in DNA repair capacity. What is known already Oocyte loss occurs progressively from birth and accelerates as women approach their mid-30s, posing a significant challenge to female reproductive health. Recent studies have highlighted the role of the DNA repair response in driving ovarian ageing and oocyte loss. Aged oocytes accumulate elevated levels of DNA damage. Unless repaired, persistent DNA damage activates DNA repair checkpoints, causing the elimination of defective oocytes. Although we know DNA double-strand breaks (DSBs) in oocytes increase with maternal age, surprisingly, little is known about why this damage is not repaired efficiently. Study design, size, duration Oocytes were isolated from ovaries of 8 weeks or 68-86-week-old CD1 mice, which correspond to reproductively young and old females respectively. Over 600 and 1000 oocytes from aged any young females were used to analyse DNA damage levels, DNA repair effciency, DNA repair compartments and for other live assays. Participants/materials, setting, methods DNA damage was induced in CD1 oocytes from young and aged mice using neocarzinostatin. Levels of DNA damage and DNA repair proteins were quantified using immunofluoresnce confocal/STED microscopy. High-resolution light sheet microscopy was used to perform live imaging of dynamics of DNA damage foci and chromosome segregation during meiosis. Main results and the role of chance Our work demonstrates that aged oocytes have a lower DNA repair capacity and reduced mobility of DNA damage sites compared to young oocytes. We further show that incomplete DNA repair results in defective chromosome integrity and partitioning, thereby compromising oocyte quality. To investigate the causes of the age-related decline in DNA repair, we systematically studied the localization and abundance of several DNA repair proteins in oocytes from young and aged mice. We found that DNA repair proteins localized in spatially distinct DNA repair compartments in oocyte nuclei, that form during the late stages of oocyte growth, accompanied by changes in the activity of DNA repair pathways. Several DNA repair proteins, their corresponding compartments, and their response to DNA damage were altered in aged oocytes. Lastly, we demonstrate that age-related cohesin loss increases DNA damage levels and reduces DNA repair capacity. We hypothesize that cohesin dissociation with maternal ageing may make chromosomes prone to accumulate DNA damage without proper DNA repair. Thus, age-related changes in DNA repair compartments and chromatin organisation drive DNA damage accumulation in aged oocytes, ultimately contributing to the decline in reproductive potential. Limitations, reasons for caution Neocarzinostatin, a radiomimetic drug used to induce DNA DSBs in mouse oocytes in vitro, may not fully represent sources of DNA damage during aging. The CD1 mouse model and ages were selected to recapitulate equivalent advanced maternal age in women. Further investigation is needed to confirm these findings in humans. Wider implications of the findings Overall, we propose that altered DNA repair machinery and cohesin loss contribute to persistent DNA damage and reduced DNA repair capacity in aged oocytes, which can cause chromosome defects and fragmentation, and eventually trigger oocyte death, thereby accelerating the loss of female fertility. Trial registration number Not Applicable

P-045 Deciphering meiotic chromatin organization by SCP3

Abstract Study question What’s the pattern of genome-wide chromatin occupancy of SCP3 during meiotic prophase, and how its interaction with chromatin is regulated? Summary answer We document SCP3 enriched at active chromatin regions with largely inherited from leptotene to pachytene stage, which facilitated by transcription and condensate assembly in spermatocytes. What is known already Meiosis is a critical step during the process of gametogenesis to form haploid cells which finally develop into functional gametes. The synaptonemal complex (SC) is a meiosis-specific protein assembly which bridges homologous chromosomes to establish the architecture of meiotic chromosome. Genetic ablation of genes encoding SC components impedes meiosis and gametogenesis in mice and mutation of these genes is frequently found in infertile patients. SCP3 localization changes with chromosome morphology in autosomes and is involved in maintaining the association of sex chromosomes. Male mice with null mutation of SCP3 failed to form SCs, resulting in developmental arrest during meiotic prophase. Study design, size, duration This study included male mice at post-natal day 10 (P10), 4 weeks or adult (8 weeks or older) were maintained on C57BL/6J background. Spermatocytes were performed modified CUT&amp;Tag using antibodies. ChIP-seq data was analyzed together with WGBS and ATAC-seq data. Participants/materials, setting, methods Spermatocytes were obtained by a discontinuous BSA density gradient. Cell pellet was resuspended in culture medium (MEM with 10% FBS) at a concentration of 105 cells/ml and cultured at 37 °C in a 5% CO2 incubator. Spermatocytes were cultured with or without 1,6-hexanediol or α-amanitin. Spermatocytes with or without drug treatment were collected at indicated time points for further examination and then modified CUT&amp;Tag and co-IP using anti-SCP3 and anti-POL II antibodies. Main results and the role of chance Chromatin occupancy of SCP3 in leptotene and pachytene spermatocytes, SCP3-Core sites retained upon treatment of 1,6-hexanediol which dissolves SCP3 condensate, and SCP1 occupancy at meiotic chromatin in pachytene spermatocytes. When we determined inter-peak distances and width of peaks, we observe that: (1) SCP3 occupancy in leptotene stage had greater inter-peak distances and narrower peak width than SCP3 occupancy in pachytene stage, demonstrating gradual accumulated SCP3 at chromatin during meiotic progression; (2) SCP3-Core sites have broader peak width than SCP3-NonCore sites, in agreement with stability of SCP3 occupancy at SCP3-Core sites; (3) SCP1 occupancy had greater inter-peak distances and narrower peak width than SCP3 occupancy in pachytene stage, supporting that SCP1 peaks are a subset of SCP3 peaks and SCP1’s major function in connecting LE and CE respectively. Generally, at pachytene-stage meiosis, SCP3 mainly occupies chromatin regions including transcriptionally active sites, Deu and Alu elements, while SCP1 mainly co-localizes with SCP3 at a subset of regions with open chromatin and high cohesin enrichment to connect meiotic chromosome axes with CE. In this way, a local active chromatin environment is created at meiotic chromosome axes, facilitating homologous chromosome recombination. Limitations, reasons for caution Our test was not successful to examine SCP3 occupancy with as few as less than 1000 spermatocytes using our protocol. It is improvement of efficiency of tagmentation or development of more efficient antibodies against SCP3 will be helpful for clinical sample detection. Wider implications of the findings SCP3 occupancy was largely inherited from leptotene to pachytene stage, facilitated by transcription and condensate assembly, and enriched at specific SINE repeats. Further exploration using knockout mouse models of meiotic axial proteins and epigenetic modifiers will provide valuable information on meiotic chromatin architecture and crosstalk among meiotic chromatin events. Trial registration number N/A

Polyamines regulate cell fate by altering the activity of histone-modifying enzymes.

Polyamines are polycationic alkyl-amines abundant in proliferating stem and cancer cells. How these metabolites influence numerous cellular functions remains unclear. Here we show that polyamine levels decrease during differentiation and that inhibiting polyamine synthesis leads to a differentiated-like cell state. Polyamines concentrate in the nucleus and are further enriched in the nucleoli of cells in culture and in vivo . Loss of polyamines drives changes in chromatin accessibility that correlate with altered histone post-translational modifications. Polyamines interact electrostatically with DNA on the nucleosome core, stabilizing histone tails in conformations accessible to modifying enzymes. These data reveal a mechanism by which an abundant metabolite influences chromatin structure and function in a non-sequence specific manner, facilitating chromatin remodeling during reprogramming and limiting it during fate commitment.

Long non-coding RNAs involved in Drosophila development and regeneration.

The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.