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PubMed2027

Genomic Profiling of Chromatin State Using CUT&Tag.

Alterations in chromatin state, mediated through histone modifications and the incorporation of histone variants, are fundamental to establishing transcriptional networks and cell identity. Recent advances in low-input epigenome profiling methods, such as CUT&Tag and CUT&RUN, have enabled the study of chromatin states from very limited starting materials. In this chapter, we describe procedures for generating CUT&Tag libraries to profile histone modifications and histone variants in early-developing zebrafish embryos.

Animals↗
PubMed2025

Integrative analysis of gene expression and histone modifications for DES, DSP, GJA1 and SMOC2 in adipose tissue reveals potential relationship to cardiometabolic health.

BACKGROUND: Adipose tissue influences cardiometabolic health through its endocrine activity and its role in regulating inflammation, lipid metabolism, and cardiovascular function. The expression of cardiac-associated genes within adipose tissue may reflect or contribute to cardiometabolic risk, yet this relationship remains poorly understood. This study investigates the expression profiles of the cardiac function associated genes GJA1, DES, DSP and SMOC2 in human adipose tissue, and analyses their associations with cardiometabolic traits. Additionally, we explore epigenomic mechanisms that may underlie their differential gene expression. METHODS: Expression profiling and functional enrichment analyses were conducted to identify depot-specific cardiac gene expression patterns. Quantitative PCR validated gene expression in paired subcutaneous (SAT) and omental visceral adipose tissue (OVAT) samples from 78 individuals with obesity. Gene expression was further validated in three independent cohorts (N = 1,548 total). Associations with clinical traits were assessed using Spearman correlations and multivariate linear regression, adjusted for age, sex, and BMI. Integration with transcriptomic and proteomic datasets publicly available from the Adipose Tissue Knowledge Portal was performed to strengthen clinical relevance. Epigenomic profiling using genome-wide ChIP-seq for histone marks (H3K4me3, H3K4me1, H3K27ac, H3K27me3) was conducted in paired SAT and OVAT samples from five individuals. RESULTS: DES, DSP, GJA1, and SMOC2 were significantly upregulated in OVAT compared to SAT. DES, DSP, and SMOC2 showed consistent expression patterns across all cohorts, while GJA1 exhibited context-dependent regulation. Gene expression in SAT was negatively correlated with cardiometabolic traits, including blood pressure, insulin resistance, and liver function markers. These associations were confirmed by regression analysis and supported by publicly available multi-omics data. Epigenetic analyses revealed OVAT-specific enrichment of active histone marks and reduced repressive marks, supporting higher differential transcriptional activity in OVAT. CONCLUSIONS: Depot-specific gene expression of DES, DSP, and SMOC2 in adipose tissue is robustly linked to cardiometabolic traits and supported by distinct epigenetic landscapes in OVAT vs SAT, highlighting their potential as novel biomarkers for cardiometabolic health.

Humans↗
PubMed1989

A region in the coding sequence is required for high-level expression of murine histone H3 gene.

Replication-dependent histone genes are expressed at high rates in S phase to provide the histone proteins required for chromosomal replication. Two genes, an H2a and H3 gene, located on chromosome 3 in the mouse and cloned together in a single 3-kilobase (plasmid MM614) restriction fragment are highly expressed. By transfecting mouse histone gene constructs into Chinese hamster ovary cells, we have identified a 110-nucleotide region within the coding sequence of the H3.2-614 gene that is required for high-level expression. Deletion of this region reduces expression of the gene by 20-fold. Additionally, the histone-coding region activates the human alpha-globin promoter, which is normally not expressed well in Chinese hamster ovary cells. Similar results with deletion constructions involving the H2a-614 gene suggest that an intragenic region plays an important role in transcription of these genes.

Animals↗
PubMed2025

Histone modifications in the regulation of erythropoiesis.

INTRODUCTION: The pathogenesis of anemia and other erythroid dysphasia are mains poorly understood, primarily due to limited knowledge about the differentiation processes and regulatory mechanisms governing erythropoiesis. Erythropoiesis is a highly complex and precise biological process, that can be categorized into three distinct stages: early erythropoiesis, terminal erythroid differentiation, and reticulocyte maturation, and this complex process is tightly controlled by multiple regulatory factors. Emerging evidence highlights the crucial role of epigenetic modifications, particularly histone modifications, in regulating erythropoiesis. Methylation and acetylation are two common modification forms that affect genome accessibility by altering the state of chromatin, thereby regulating gene expression during erythropoiesis. DISCUSSION: This review systematically examines the roles of histone methylation and acetylation, along with their respective regulatory enzymes, in regulating the development and differentiation of hematopoietic stem/progenitor cells (HSPCs) and erythroid progenitors. Furthermore, we discuss the involvement of these histone modifications in erythroid-specific developmental processes, including hemoglobin switching, chromatin condensation, and enucleation.Conclusions This review summarizes the current understanding of the role of histone modifications in erythropoiesis based on existing research, as a foundation for further research the mechanisms of epigenetic regulatory in erythropoiesis.

Erythropoiesis↗
PubMed1987

Transcription of the histone loci on lampbrush chromosomes of the newt Notophthalmus viridescens.

We have investigated transcription of the histone gene cluster on lampbrush chromosomes of the newt Notophthalmus viridescens. Clusters of the five histone genes are separated by long tracts of a DNA repeat called satellite 1. Previous in situ hybridization results demonstrated the presence of histone gene coding regions, intergene spacers, and flanking satellite repeats in giant transcription units on lampbrush chromosomes. These results suggested a model in which transcription initiates at histone gene promoters and continues through the rest of the gene cluster into satellite repeats. The readthrough transcription model predicts that spacer regions upstream of the first promoter in the gene cluster should be absent from nascent transcripts on chromosome loops. We have used such upstream spacer probes for in situ hybridization to lampbrush chromosomes. Contrary to our expectation, the results show that upstream spacer regions are transcribed, and indicate that transcription often initiates upstream of the first histone gene promoter. The relationship of giant transcription units in oocyte nuclei to cytoplasmic histone mRNA is discussed.

Animals↗
PubMedDate not supplied

Cell-cycle regulatory sequences in a hamster histone promoter and their interactions with cellular factors.

Knowledge of how genes are regulated during the cell cycle is essential for understanding the process of cell growth on a molecular level. Numerous studies have established that, as mammalian cells go through the cell cycle, histone mRNA levels change, the largest amount being produced in the S phase. Both transcriptional and post-transcriptional mechanisms are responsible for this regulation and it has recently been demonstrated that nucleotide sequences in both the 5' and 3' termini of the histone gene are involved. From deletion analysis of a hamster H3.2 fusion gene, we report here that the crucial control signals for both cell-cycle regulation and high level expression in vivo are contained in a 32-nucleotide (nt) region about 150 nt upstream of the TATA sequence and do not require any histone protein coding sequence. By comparison, the promoter of the herpes simplex virus (HSV) thymidine kinase gene is serum-stimulated but not cell-cycle regulated. The cell-cycle control exerted by the histone DNA regulatory element acts at the transcriptional level, as the rate of transcription is stimulated during the DNA synthetic phase of the cell cycle. Using DNA-protein mobility shift experiments, we demonstrate the existence of high affinity cellular factors interacting with the histone H3.2 promoter sequence. The concentration of the protein-DNA complexes shows cell-cycle variation, particularly during the transition from late G1 to the DNA synthesis phase. These data provide evidence for in vivo interactions between the cell-cycle transcriptional regulatory factors and the cis-acting DNA domain.

Animals↗
PubMed1983

DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins.

The complete DNA sequences of two loci encoding H3 and H4 histones in Saccharomyces cerevisiae have been determined. Each locus contains one H3 and one H4 gene. The genes at each locus are divergently transcribed and the coding sequences are separated by 646 base-pairs at one locus and 676 base-pairs at the other. The H3 genes code for identical histone H3 proteins and the H4 genes code for identical histone H4 proteins. The yeast proteins differ from histones H3 and H4 of calf by 15 and 8 amino acid substitutions, respectively, and these differences are largely confined to the carboxy-terminal halves of the proteins. The genes demonstrate a bias in synonymous codon usage similar to that noted for other yeast genes. This bias is confined to the coding sequences of the genes and is specific for the reading frame encoding the proteins. The coding sequence of each gene is flanked on both sides by DNA with an A + T content of 70 to 80%. Possible regulatory sequences are located relative to the 5' and 3'-termini of the histone H3 and H4 RNA transcripts.

Base Sequence↗
PubMed1985

Expression of histone and tubulin genes during spermatogenesis. Evidence of post-meiotic transcription.

The synchrony of spermatogenesis in the winter flounder has enabled us to examine the population of mRNAs expressed in each testis cell type, from spermatogonia to spermatids. Two of the most abundant sets of mRNAs in this tissue were those coding for histones and tubulins. The levels of histone mRNAs rose sharply at the onset of spermatogenesis, declined rapidly after the 1 degree spermatocyte stage, and were barely detectable in early spermatids. Histone genes were expressed again briefly in mid-spermatids, along with a spermatid-specific H3 mRNA-like transcript which was more than twice the length (1 100 nucleotides) of the H3 mRNA. Whereas the first and major round of histone mRNA synthesis appeared to be coupled to DNA replication, the second round of synthesis occurred after meiosis and coincided with the major reorganization of chromatin structure that takes place during the mid-spermatid stage of spermatogenesis. Levels of alpha- and beta-tubulin mRNAs increased 25-fold around the time of transition between spermatocytes and spermatids when sperm tail synthesis is initiated. These mRNAs appear to be utilized right away rather than stored, since the percentage of tubulin mRNA in the polysome fraction also increased at that juncture.

Animals↗
PubMed1976

Reiteration frequency of the gene for tissue-specific histone H5 in the chicken genome.

Chicken erythroid cells contain a tissue specific histone known as H5 in addition to the five major histone species found in other organisms. The mRNA coding for this histone has been isolated by indirect immunoprecipitation from immature, non-dividing reticulocytes in which this is the only histone synthesised. The mRNA has been modified by the enzymatic addition of a 3' polyadenylic acid tract, and transcribed into complementary DNA (cDNA) using the RNA-dependent DNA-polymerase from avian myeloblastosis virus. Studies on the hybridisation of this cDNA indicate that the gene coding for the H5 histone is reiterated 10 times in the chicken genome.

Alleles↗