Chromatin Regulation Research Articles

Epigenomic, transcriptomic and proteomic characterizations of reference samples.

A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced a large amount of different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structural variations (SVs). However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of the epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform. Protein expression of the transcripts overlapping CGIs were much higher than the protein expression of the non-CGI transcripts in both cell lines. We further demonstrated the evidence that certain SNVs were incorporated into mutated peptides. We observed that open chromatin regions had low methylation which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expression. The CG-poor regions had higher repressive epigenetic regulations (higher DNA methylation) and less open chromatin, resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.

Lipoprotein metabolism mediates hematopoietic stem cell responses under acute anemic conditions

Hematopoietic stem cells (HSCs) react to various stress conditions. However, it is unclear whether and how HSCs respond to severe anemia. Here, we demonstrate that upon induction of acute anemia, HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia, lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs, transcription levels of lipid metabolism-related genes, such as very low-density lipoprotein receptor (Vldlr), are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential, whereas HSCs in Apoe knockout mice do not respond to anemia induction. VldlrhighHSCs show higher erythroid potential, which is enhanced after acute anemia induction. VldlrhighHSCs are epigenetically distinct because of their low chromatin accessibility, and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays an important role in HSC regulation under severe anemic conditions.

Genome-Wide Mapping of Main Histone Modifications and Coordination Regulation of Metabolic Genes under Salt Stress in Pea (Pisum sativum L)

Abstract Pea occupy a key position in modern biogenetics, playing a multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2 and the transcriptome in pea under normal condition, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across approximately 82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

Abstract C078: Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignant and stromal cell subtypes

Abstract Pancreatic ductal adenocarcinoma (PDAC) disease progression involves complex cell state transitions in both malignant and non-malignant populations within the tumor microenvironment. To uncover PDAC cell states and epigenetic features associated with clinical outcome, we profiled 40 tumor samples (33 primary tumors and 7 metastases) from 39 patients with single cell ATAC-seq, along with 10 sample-matched single cell RNA-seq profiles. Through topic modeling of high dimensional chromatin data, we uncovered distinct cis-regulatory networks underlying the classical and basal-like molecular subtypes of PDAC, which showed differential activity in basal-classical hybrid cells. Furthermore, delineation of epigenetic alterations by basal, classical, and hybrid subtypes revealed a core set of chromatin regions opened in all PDAC subtypes relative to ductal and acinar cells. These universally open regions showed striking overlap with gastrointestinal enhancers, highlighting a common endoderm lineage infidelity process across pancreatic tumors. Within the stromal compartment, we identified novel regulators of myofibroblastic cancer-associated fibroblasts (myCAFs) and inflammatory CAFs (iCAFs) from enhancer networks active in each CAF subtype. Importantly, our data uncover a highly prognostic gene program active in only one of two distinct myCAF chromatin states found in our data, highlighting a putative tumor-promoting myCAF subpopulation. Our work provides a high-resolution description of epigenetic cell state heterogeneity in PDAC, revealing novel regulators and gene programs associated with PDAC subtypes and clinical outcome. Citation Format: Kevin MacPherson-Hawthorne, Jason M. Link, Patrick Worth, Brett Sheppard, Andrew Fields, Colin Daniel, Andrew Nishida, Carl Pelz, Trent Waugh, Ethan Agritelle, John Muschler, Andrew Adey, Rosalie Sears. Chromatin accessibility profiling of human pancreatic tumors reveals epigenetic features of malignant and stromal cell subtypes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C078.

Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts.

The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.

PRC1 Protein Subcomplexes Architecture: Focus on the Interplay between Distinct PCGF Subunits in Protein Interaction Networks.

The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb repressor complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed their specialized roles in distinct aspects of epigenetic regulation, our understanding of the variation in the protein interaction networks of distinct PCGF subunits in different PRC1 complexes is incomplete. We carried out an affinity purification mass spectrometry (AP-MS) screening of three PCGF subunits, PCGF1 (NSPC1), PCGF2 (MEL18), and PCGF4 (BMI1), to define their interactome and potential cellular function in pluripotent human embryonal carcinoma cell "NT2". The bioinformatic analysis revealed that these interacting proteins cover a range of functional pathways, often involved in cell biology and chromatin regulation. We also found evidence of mutual regulation (at mRNA and protein level) between three distinct PCGF subunits. Furthermore, we confirmed that the disruption of these subunits results in reduced cell proliferation ability. We reveal an interplay between the compositional diversity of the distinct PCGF containing PRC1 complex and the potential role of PCGF proteins within the wider cellular network.

Bivalent chromatin accommodates survivin and BRG1/SWI complex to activate DNA damage response in CD4+ cells

BackgroundBivalent regions of chromatin (BvCR) are characterized by trimethylated lysine 4 (H3K4me3) and lysine 27 on histone H3 (H3K27me3) deposition which aid gene expression control during cell differentiation. The role of BvCR in post-transcriptional DNA damage response remains unidentified. Oncoprotein survivin binds chromatin and mediates IFNγ effects in CD4+ cells. In this study, we explored the role of BvCR in DNA damage response of autoimmune CD4+ cells in rheumatoid arthritis (RA).MethodsWe performed deep sequencing of the chromatin bound to survivin, H3K4me3, H3K27me3, and H3K27ac, in human CD4+ cells and identified BvCR, which possessed all three histone H3 modifications. Protein partners of survivin on chromatin were predicted by integration of motif enrichment analysis, computational machine-learning, and structural modeling, and validated experimentally by mass spectrometry and peptide binding array. Survivin-dependent change in BvCR and transcription of genes controlled by the BvCR was studied in CD4+ cells treated with survivin inhibitor, which revealed survivin-dependent biological processes. Finally, the survivin-dependent processes were mapped to the transcriptome of CD4+ cells in blood and in synovial tissue of RA patients and the effect of modern immunomodulating drugs on these processes was explored.ResultsWe identified that BvCR dominated by H3K4me3 (H3K4me3-BvCR) accommodated survivin within cis-regulatory elements of the genes controlling DNA damage. Inhibition of survivin or JAK-STAT signaling enhanced H3K4me3-BvCR dominance, which improved DNA damage recognition and arrested cell cycle progression in cultured CD4+ cells. Specifically, BvCR accommodating survivin aided sequence-specific anchoring of the BRG1/SWI chromatin-remodeling complex coordinating DNA damage response. Mapping survivin interactome to BRG1/SWI complex demonstrated interaction of survivin with the subunits anchoring the complex to chromatin. Co-expression of BRG1, survivin and IFNγ in CD4+ cells rendered complete deregulation of DNA damage response in RA. Such cells possessed strong ability of homing to RA joints. Immunomodulating drugs inhibited the anchoring subunits of BRG1/SWI complex, which affected arthritogenic profile of CD4+ cells.ConclusionsBvCR execute DNA damage control to maintain genome fidelity in IFN-activated CD4+ cells. Survivin anchors the BRG1/SWI complex to BvCR to repress DNA damage response. These results offer a platform for therapeutic interventions targeting survivin and BRG1/SWI complex in autoimmunity.

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.

Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, variants associated with blood cell phenotypes are enriched in regulatory regions active during hematopoiesis. To systematically explore the nature of these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible to simultaneously profile both chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of a range of master transcription factors (TFs). This approach allowed us to examine the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within the TF-sensitive accessible chromatin regions, while representing less than 0.3% of the genome, show a ~100-fold enrichment in heritability across certain blood cell phenotypes; this enrichment is strikingly higher than for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.

Extracting regulatory active chromatin footprint from cell-free DNA

Cell-free DNA (cfDNA) has emerged as a pivotal player in precision medicine, revolutionizing the diagnostic and therapeutic landscape. While its clinical applications have significantly increased in recent years, current cfDNA assays have limited ability to identify the active transcriptional programs that govern complex disease phenotypes and capture the heterogeneity of the disease. To address these limitations, we have developed a non-invasive platform to enrich and examine the active chromatin fragments (cfDNAac) in peripheral blood. The deconvolution of the cfDNAac signal from traditional nucleosomal chromatin fragments (cfDNAnuc) yields a catalog of features linking these circulating chromatin signals in blood to specific regulatory elements across the genome, including enhancers, promoters, and highly transcribed genes, mirroring the epigenetic data from the ENCODE project. Notably, these cfDNAac counts correlate strongly with RNA polymerase II activity and exhibit distinct expression patterns for known circadian genes. Additionally, cfDNAac signals across gene bodies and promoters show strong correlations with whole blood gene expression levels defined by GTEx. This study illustrates the utility of cfDNAac analysis for investigating epigenomics and gene expression, underscoring its potential for a wide range of clinical applications in precision medicine.

LAP2alpha facilitates myogenic gene expression by preventing nucleoplasmic lamin A/C from spreading to active chromatin regions.

A-type lamins form a filamentous meshwork beneath the nuclear membrane that anchors large heterochromatic genomic regions at the nuclear periphery. A-type lamins also exist as a dynamic, non-filamentous pool in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). Both proteins associate with largely overlapping euchromatic genomic regions in the nucleoplasm, but the functional significance of this interaction is poorly understood. Here, we report that LAP2α relocates towards regions containing myogenic genes in the early stages of muscle differentiation, possibly facilitating efficient gene regulation, while lamins A and C mostly associate with genomic regions away from these genes. Strikingly, upon depletion of LAP2α, A-type lamins spread across active chromatin and accumulate at regions of active H3K27ac and H3K4me3 histone marks in the vicinity of myogenic genes whose expression is impaired in the absence of LAP2α. Reorganization of A-type lamins on chromatin is accompanied by depletion of the active chromatin mark H3K27ac and a significantly impaired myogenic differentiation. Thus, the interplay of LAP2α and A-type lamins is crucial for proper positioning of intranuclear lamin A/C on chromatin to allow efficient myogenic differentiation.

Epitranscriptomics and epigenetics: two sides of the same coin?

Gene expression is an intricate biological process that bridges gap between the genotype and the phenotype. Canonical and hereditable epigenetic mechanisms, such as histone and DNA modifications, regulate the release of genetic information encoded in DNA without altering the underlying sequence. Many other non-canonical players, such as chromatin regulators and noncoding RNAs, are also involved in regulating gene expression. Recently, RNA modifications (epitranscriptomics) have been shown to hold enormous potential in shaping cellular transcriptomes. However, their co-transcriptional nature and uncertain heritability mean that they fall outside the current definition of epigenetics, sparking an ongoing debate in the field. Here we will discuss the relationship between canonical and non-canonical epigenetic mechanisms that govern gene expression and offer our perspective on whether (or not) epitranscriptomic modifications can be classified as epigenetic mechanisms.

Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness.

Pluripotent stem cells are defined by their self-renewal capacity, which is the ability of the stem cells to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into any somatic cell lineage. However, understanding the mechanisms that control stem cell fitness versus the pluripotent cell identity is challenging. To investigate the interplay between these two aspects of pluripotency, we performed four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSC self-renewal conditions, and the dissolution of the primed pluripotency identity during early differentiation. Comparative analyses led to the discovery of genes with distinct roles in pluripotency regulation, including mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control pluripotent identity during early differentiation. We further discovered a core set of factors that control both stem cell fitness and pluripotent identity, including a network of chromatin factors that safeguard pluripotency. Our unbiased and systematic screening and comparative analyses disentangle two interconnected aspects of pluripotency, provide rich datasets for exploring pluripotent cell identity versus cell fitness, and offer a valuable model for categorizing gene function in broad biological contexts.

Abstract P393: Isolevuglandins Regulate Chromatin Accessibility in Hypertensive Human Monocytes

Background: Isolevuglandins (isoLGs) are products of lipid peroxidation that are formed in the presence of reactive oxygen species. IsoLGs are increased in circulating CD14 + monocytes in patients with hypertension and contribute to inflammatory activation. When adducted to histones, isoLGs prevent nucleosome assembly. Moreover, isoLGs induce disassembly of pre-formed nucleosomes. IsoLGs can be induced in cell culture with tert-butyl hydroperoxide (tBHP) and are efficiently scavenged by ethyl-2-hydroxybenzylamine (Et-2HOBA). We hypothesized that isoLGs regulate chromatin accessibility in hypertensive (HTN) monocytes. Methods: Human CD14 + monocytes were isolated from 3 normotensive (NT) and 5 HTN subjects. HTN monocytes were treated with vehicle. NT monocytes were treated with vehicle, tBHP, or co-treated with tBHP and Et-2HOBA. Cells were cultured for 24 hours and submitted for bulk ATAC sequencing to assess regions of open chromatin across the genome. Data were analyzed using Partek Flow software. Reads were aligned to the GRCh38 human genome. Differences in chromatin accessibility were determined by DESeq2 analysis and were considered significant at an adjusted P-value of 0.05 and fold change of 1.5. Reads were filtered to focus on accessible chromatin at transcription start sites (TSS). First, chromatin accessibility of HTN monocytes was compared to NT monocytes. Second, to determine chromatin regions with isoLG-regulated accessibility that are associated with hypertension, we compared control and tBHP+Et2HOBA treated cells to a combined HTN and tBHP treated group. Results: HTN monocytes exhibited increased chromatin accessibility at 131 TSS and decreased accessibility at 56 TSS compared to NT monocytes. Chromatin accessibility was increased at 205 TSS and decreased at 183 TSS in response to both hypertension and isoLGs. Gene set enrichment revealed a significant increase in chromatin accessibility in genes regulating chemokine signaling, RAS signaling, lysosomal activity, and focal adhesion. Conclusions: We determined that significant differences in chromatin accessibility are present in HTN monocytes compared to NT monocytes. IsoLGs regulate chromatin accessibility in HTN monocytes. Moreover, isoLGs regulate accessibility of the TSS of genes involved in inflammation and cell migration. These findings implicate isoLGs as novel post-translational histone modifications that regulate chromatin accessibility and contribute to inflammation in hypertension.

Abstract 60: Atlas of Distal Nephron Mineralocorticoid Receptor-Dependent Transcriptome Reveals Novel Aldosterone Actions

Aldosterone regulation of Na+ and K+ balance and blood pressure are mediated by the mineralocorticoid receptor (MR, Nr3c2). Although several aldosterone/MR-dependent genes have been identified, their regulation cannot fully explain how aldosterone activates electrogenic Na+- K+ exchange in the aldosterone-sensitive distal nephron (ASDN). Here, we apply RNA-Seq and comprehensive downstream analysis to define the complete inventory of MR-regulated genes. MRfl/fl/Pax8,rtTA/LC1 mice were used to knock out the Nr3c2 gene in an inducible and kidney-specific manner. RNA-Seq analysis was conducted in the micro-dissected connecting tubule and cortical collecting duct tubule segments, followed by multimodal bioinformatic analyses. Direct MR-dependent gene regulation was validated in vitro on immortalized collecting duct cells, ex vivo with isolated distal nephron segments and gene reporter assays. All known aldosterone-response genes, including Sgk1, Scnn1a, Ndrg2, Per3, Tsc22d3, Zbtb16, MLPH, and Atp1a1 were significantly decreased in MR KO mice. 1193 additional genes were down-regulated in the MR KO, and 526 of these have a Mineralocorticoid Responsive Element (MRE), revealing the MR-dependent transcriptome is much larger than previously imagined. MREs were found in most genes with closed chromatin regions, suggesting MR binding might pioneer transcription for most of its regulated genes. The architecture of some MR-regulated genes, highlighted by the co-regulation of 7 Kallikrein genes, points to a novel mechanism of MR-regulation involving epigenetic remodeling in topology-associated domains. Pathway enrichment analysis revealed that MR-regulated genes are highly enriched in mitochondria-associated metabolic processes, and direct MR regulation of Klf15 was identified as a key transcriptional driver. In summary, the inventory of MR-regulated genes in the ASDN is much larger than previously imagined, involving new mechanisms of gene regulation. In addition to pathways that directly up-regulate transport, the data suggest that aldosterone-MR may directly influence metabolism to make energy-consuming transport highly efficient.

Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures.

We can now analyze 3D physical interactions of chromatin regions with chromatin conformation capture technologies, in addition to the 1D chromatin state annotations, but methods to integrate this information are lacking. We propose a method to integrate the chromatin state of interacting regions into a vector representation through the contact-weighted sum of chromatin states. Unsupervised clustering on integrated chromatin states and Micro-C contacts reveals common patterns of chromatin interaction signatures. This provides an integrated view of the complex dynamics of concurrent change occurring in chromatin state and in chromatin interaction, adding another layer of annotation beyond chromatin state or Hi-C contact separately.

Abstract P215: The reninness score: integrative analysis of multi-omic data to define renin cell identity.

Renin cell (RC) descendants regain the endocrine renin phenotype to overcome homeostatic threats, a process known as recruitment. The determinants that control the identity, fate, and recruitment of RCs are not well understood. We aim to 1) define the chromatin pattern that determines RC identity; and 2) develop a computational tool to score samples by similarity to that pattern. We compared open chromatin regions (ATAC-seq) between non-renin-expressing (n = 184) and renin-expressing samples (n = 19) from three different sources and stimulation states: 1) primary RCs in basal state (WT); 2) primary RCs chronically stimulated to produce renin (Recruited); and 3) constitutively renin-expressing tumoral cells. Differential analyses between the three types of RCs and the non-RCs revealed 1,525 unique open chromatin regions shared in at least two RC groups, including regions associated with RC-specific genes: Ren1 and Akr1b7. Increased accessibility regions in RC groups are cell type specific and enriched in renin-related GO terms ( e.g., cAMP and Notch signaling pathway). The bZip family ( e.g. , Atf3, p < 10 -2147 ) was the most enriched motifs in tumoral cells, and MEF2 family ( e.g. , MEF2a, p < 10 -91 ) in primary cells. We did not find a unique set of TFs specific to the Recruited group, indicating that renin recruitment may not be regulated by a recruitment-specific factor family, but could instead be driven by post-translational modification, differential co-factors, or epigenetic modifications. Next, we used a machine-learning approach to calculate a "reninness" score by training a genomic region model with renin and non-renin bulkATAC-seq data. We identified a cluster of regions (n = 112,992) around the trained renin label, which included 89% (21,820 of 24,612) of the regions with increased accessibility from the differential analyses. We calculated the reninness score based on the distance between the trained label and the predicted bulkATA sample embeddings using the trained model. Homogeneous WT RCs had the highest score, followed by renin-expressing tumoral and primary cells. Non-RCs had the lowest scores. We also adapted bulkATAC region-embedding models to pseudo-bulk ATAC- and scATAC-seq data. The observed reninness scores show that the model can also capture differences in renin recruitment potential. In conclusion, we identified the chromatin configurations defining the identity and recruitment of RCs and developed a computational score to quantify it.

Profiling of chromatin accessibility and regulatory elements toward understanding the mechanisms underlying growth regulation in the Pacific oyster (Crassostrea gigas)

Changes in phenotype are precisely controlled by transcriptional regulators, which depend on chromatin remodeling. Although artificial genetic breeding has significantly improved the growth performance of the Pacific oyster (Crassostrea gigas), the identification of gene regulatory elements and transcription factors related to growth is obscure. In this study, we performed a genome-wide characterization of chromatin accessibility using two strains of C. gigas that exhibit significant differences in growth. The results showed that accessible chromatin regions were mainly distributed in the noncoding regions of the genome, with a greater proportion of distal intergenic regions than that of promoters and introns. A total of 2044 differentially accessible regions and 2574 differentially expressed genes were identified through comparative analysis. Genes annotated from regions with differential chromatin accessibility were enriched in cell adhesion molecules, JAK-STAT, insulin resistance, HIF-1α, and platelet activation signaling pathways. Correlation analysis of ATAC-seq and RNA-seq data showed that differential gene expression was positively correlated with differential chromatin accessibility. Furthermore, motif screening and identification of accessible chromatin regions revealed a set of transcription factors, including LHX3, TCF7L2, and LEF1, that may play important roles in the growth of C. gigas. Integrated analysis with public Hi-C datasets allowed the identification of a differential peak located 47 kb upstream of angiopoietin-2, which may act as a potential enhancer that affects the growth of C. gigas. In summary, our work contributes to a better understanding of growth-related regulation in C. gigas and provides valuable information for deciphering the economic traits underlying growth, which is conducive to the development of the breeding industry of C. gigas in the future.

Identification of a specific APOE transcript and functional elements associated with Alzheimer’s disease

BackgroundThe APOE gene is the strongest genetic risk factor for late-onset Alzheimer’s Disease (LOAD). However, the gene regulatory mechanisms at this locus remain incompletely characterized.MethodsTo identify novel AD-linked functional elements within the APOE locus, we integrated SNP variants with multi-omics data from human postmortem brains including 2,179 RNA-seq samples from 3 brain regions and two ancestries (European and African), 667 DNA methylation samples, and ChIP-seq samples. Additionally, we plotted the expression trajectory of APOE transcripts in human brains during development.ResultsWe identified an AD-linked APOE transcript (jxn1.2.2) particularly observed in the dorsolateral prefrontal cortex (DLPFC). The APOE jxn1.2.2 transcript is associated with brain neuropathological features, cognitive impairment, and the presence of the APOE4 allele in DLPFC. We prioritized two independent functional SNPs (rs157580 and rs439401) significantly associated with jxn1.2.2 transcript abundance and DNA methylation levels. These SNPs are located within active chromatin regions and affect brain-related transcription factor-binding affinities. The two SNPs shared effects on the jxn1.2.2 transcript between European and African ethnic groups.ConclusionThe novel APOE functional elements provide potential therapeutic targets with mechanistic insight into the disease etiology.

Unraveling the three-dimensional (3D) genome architecture in Neurodevelopmental Disorders (NDDs).

The human genome, comprising millions of pairs of bases, serves as the blueprint of life, encoding instructions for cellular processes. However, genomes are not merely linear sequences; rather, the complex of DNA and histones, known as chromatin, exhibits complex organization across various levels, which profoundly influence gene expression and cellular function. Central to understanding genome organization is the emerging field of three-dimensional (3D) genome studies. Utilizing advanced techniques such as Hi-C, researchers have unveiled non-random dispositions of genomic elements, highlighting their importance in transcriptional regulation and disease mechanisms. Topologically Associating Domains (TADs), that demarcate regions of chromatin with preferential internal interactions, play crucial roles in gene regulation and are increasingly implicated in various diseases such as cancer and schizophrenia. However, their role in Neurodevelopmental Disorders (NDDs) remains poorly understood. Here, we focus on TADs and 3D conservation across the evolution and between cell types in NDDs. The investigation into genome organization and its impact on disease has led to significant breakthroughs in understanding NDDs etiology such ASD (Autism Spectrum Disorder). By elucidating the wide spectrum of ASD manifestations, researchers aim to uncover the underlying genetic and epigenetic factors contributing to its heterogeneity. Moreover, studies linking TAD disruption to NDDs underscore the importance of spatial genome organization in maintaining proper brain development and function. In summary, this review highlights the intricate interplay between genome organization, transcriptional control, and disease pathology, shedding light on fundamental biological processes and offering insights into the mechanisms underlying NDDs like ASD.

Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns

Germline pathogenic TP53 variants predispose individuals to a high lifetime risk of developing multiple cancers and are the hallmark feature of Li-Fraumeni syndrome (LFS). Our group has previously shown that LFS patients harbor shorter plasma cell-free DNA fragmentation; independent of cancer status. To understand the functional underpinning of cfDNA fragmentation in LFS, we conducted a fragmentomic analysis of 199 cfDNA samples from 82 TP53 mutation carriers and 30 healthy TP53-wildtype controls. We find that LFS individuals exhibit an increased prevalence of A/T nucleotides at fragment ends, dysregulated nucleosome positioning at p53 binding sites, and loci-specific changes in chromatin accessibility at development-associated transcription factor binding sites and at cancer-associated open chromatin regions. Machine learning classification resulted in robust differentiation between TP53 mutant versus wildtype cfDNA samples (AUC-ROC = 0.710–1.000) and intra-patient longitudinal analysis of ctDNA fragmentation signal enabled early cancer detection. These results suggest that cfDNA fragmentation may be a useful diagnostic tool in LFS patients and provides an important baseline for cancer early detection.