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PubMed2026

dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.

MOTIVATION: Despite the growing use of HiChIP to investigate protein-directed chromatin architecture, a comprehensive and reproducible pipeline for analysing these datasets-from raw reads to multiscale 3D genome features-remains lacking. Existing tools often focus on isolated components, such as loop calling or matrix generation, but fall short in integrating structural annotation, functional enrichment, and spatial modeling within a unified framework. To address this gap, we developed dcHiChIP, a modular, scalable Nextflow-based workflow that streamlines the analysis of HiChIP data, enabling both routine processing and in-depth exploration of chromatin organization and regulatory interactions. RESULTS: dcHiChIP enables robust and reproducible analysis of HiChIP datasets across multiple scales of chromatin architecture. It accepts raw sequencing data as input and generates high-quality loop calls, domain annotations, and 3D genome models. It also performs functional annotation and motif enrichment analyses. Applied to benchmark CTCF HiChIP datasets, dcHiChIP identifies major chromatin architectural features such as TADs/CCDs, A/B compartments, and chromatin stripes, and offers efficient, end-to-end execution with support for batch processing and workflow resumability. AVAILABILITY: dcHiChIP is publicly available on GitHub at https://github.com/SFGLab/dcHiChIP, with documentation at https://sfglab.github.io/dcHiChIP/. The software version used in this study is archived at Zenodo: https://doi.org/10.5281/zenodo.22030542.

Chromatin↗
PubMed2002

Mastermind mediates chromatin-specific transcription and turnover of the Notch enhancer complex.

Signaling through the Notch pathway activates the proteolytic release of the Notch intracellular domain (ICD), a dedicated transcriptional coactivator of CSL enhancer-binding proteins. Here we show that chromatin-dependent transactivation by the recombinant Notch ICD-CBF1 enhancer complex in vitro requires an additional coactivator, Mastermind (MAM). MAM provides two activation domains necessary for Notch signaling in mammalian cells and in Xenopus embryos. We show that the central MAM activation domain (TAD1) recruits CBP/p300 to promote nucleosome acetylation at Notch enhancers and activate transcription in vitro. We also find that MAM expression induces phosphorylation and relocalization of endogenous CBP/p300 proteins to nuclear foci in vivo. Moreover, we show that coexpression with MAM and CBF1 strongly enhances phosphorylation and proteolytic turnover of the Notch ICD in vivo. Enhanced phosphorylation of the ICD and p300 requires a glutamine-rich region of MAM (TAD2) that is essential for Notch transcription in vivo. Thus MAM may function as a timer to couple transcription activation with disassembly of the Notch enhancer complex on chromatin.

Animals↗
PubMed2000

Functional selectivity of recombinant mammalian SWI/SNF subunits.

The SWI/SNF family of chromatin-remodeling complexes plays a key role in facilitating the binding of specific transcription factors to nucleosomal DNA in diverse organisms from yeast to man. Yet the process by which SWI/SNF and other chromatin-remodeling complexes activate specific subsets of genes is poorly understood. We show that mammalian SWI/SNF regulates transcription from chromatin-assembled genes in a factor-specific manner in vitro. The DNA-binding domains (DBDs) of several zinc finger proteins, including EKLF, interact directly with SWI/SNF to generate DNase I hypersensitivity within the chromatin-assembled beta-globin promoter. Interestingly, we find that two SWI/SNF subunits (BRG1 and BAF155) are necessary and sufficient for targeted chromatin remodeling and transcriptional activation by EKLF in vitro. Remodeling is achieved with only the BRG1-BAF155 minimal complex and the EKLF zinc finger DBD, whereas transcription requires, in addition, an activation domain. In contrast, the BRG1-BAF155 complex does not interact or function with two unrelated transcription factors, TFE3 and NF-kappaB. We conclude that specific domains of certain transcription factors differentially target SWI/SNF complexes to chromatin in a gene-selective manner and that individual SWI/SNF subunits play unique roles in transcription factor-directed nucleosome remodeling.

Adenosine Triphosphatases↗
PubMed1992

The transcribed template and the transcription loop in Balbiani rings.

The active Balbiani ring (BR) genes in the giant puffs in Chironomus salivary glands can be visualized in three dimensions within the cell nucleus. The chromatin template exhibits a dynamic structure: at the RNA polymerases the template is fully extended, while in between polymerases it can be packed into a nucleosome, a nucleosome filament, or even into a thick chromatin fiber, if the spacing between consecutive polymerases is large enough. Even in its extended state, the template harbours histone H1, and most likely also the core histones, indicating that the nucleosomes unfold and refold during transcription. Apart from the transcribed template, a transcription loop contains a thin, extended, apparently flexible and nucleosome-free fiber upstream of the gene, and a loosely coiled nucleosome filament downstream of the gene.

Animals↗
PubMed1999

Genomic sites of topoisomerase II activity determined by comparing DNA breakage enhanced by three distinct poisons.

To define the sites of topoisomerase II activity in two genomic regions of Drosophila melanogaster Kc cells, we have investigated in vivo DNA cleavage sites stimulated by three poisons with diverse sequence specificity, clerocidin, VM-26 and dh-EPI (an anthracycline analog). DNA cleavage was studied by PFGE (pulse-field gel electrophoresis), standard gel electrophoresis, and by genomic primer extension. Poisons stimulated specific intensity patterns of cleavage in the two genomic regions studied. At the centromeric satellite III DNA, fragments of about 270-310 and 385-430 kb could be detected specifically after treatment with clerocidin, suggesting a complex DNA loop organisation, which may correspond with a centromere-specific higher-order chromatin structure. Clerocidin-dependent DNA fragmentation was detectable by PFGE but not by standard agarose gel electrophoresis; while VM-26-dependent cleavage was detected with either method, dh-EPI was ineffective at this locus. Thus, clerocidin DNA cleavage sites were rarer than those of VM-26 at the satellite locus. In the histone H2A-H2B intergenic region, clerocidin and dh-EPI stimulated cleavage whereas VM-26 was only weakly effective. Some clerocidin cleavage sites did not undergo spontaneous reversion, indicating that this agent can stimulate irreversible cleavage in vivo. Direct genomic sequencing showed that many clerocidin and dh-EPI sites, although distinct, mapped to the transcription start and to the proximal promoter of the H2A gene, suggesting that the region is highly accessible to topoisomerase II. Thus, the enzyme may play a role in maintaining a highly accessible chromatin structure under normal cell growth conditions, possibly mediated by specialised protein complexes. This study demonstrates that the use of distinct poisons greatly improves the definition of genomic sites of topoisomerase II activity.

Animals↗
PubMed2003

Priming the nucleosome: a role for HMGB proteins?

The high-mobility-group B (HMGB) chromosomal proteins are characterized by the HMG box, a DNA-binding domain that both introduces a tight bend into DNA and binds preferentially to a variety of distorted DNA structures. The HMGB proteins seem to act primarily as architectural facilitators in the manipulation of nucleoprotein complexes; for example, in the assembly of complexes involved in recombination and transcription. Recent genetic and biochemical evidence suggests that these proteins can facilitate nucleosome remodelling. One mechanism by which HMGB proteins could prime the nucleosome for migration is to loosen the wrapped DNA and so enhance accessibility to chromatin-remodelling complexes and possibly also to transcription factors. By constraining a tight loop of untwisted DNA at the edge of a nucleosome, an HMGB protein could induce movements in the contacts between certain core histones that would result in an overall change in nucleosome structure.

HMGB Proteins↗
PubMed1989

Berenil-induced undercondensation in human heterochromatin.

The aromatic diamidine berenil specifically inhibits the condensation of a subset of constitutive heterochromatin in human lymphocyte cultures. In the normal male chromosome complement, only the quinacrine-brilliant Y heterochromatin exhibits distinct undercondensation. The optimal culture conditions for inhibiting heterochromatin condensation are achieved when berenil is added at a final concentration of 150 micrograms/ml 24 h before cell harvest. Various examples of the use of berenil in the analysis of chromosome rearrangements involving quinacrine-brilliant heterochromatin are presented. A variant, giant-satellited chromosome 22 was found to respond to berenil treatment, although its enlarged and quinacrine-bright short-arm region did not contain Y heterochromatin. Southern blot analysis and chromosome in situ hybridization suggested that most chromosome 22 variants do not stem from Y; acrocentric translocations. The experimentally undercondensed Y heterochromatin is characterized by moderate C-band labeling, bright quinacrine fluorescence, and specific silver staining. At the ultrastructural level, undercondensation is associated with loosely packed, mutliply folded chromatin fibers with a diameter of approximately 250 A and organized probably as loops.

Amidines↗
PubMed2005

Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage.

The differentiation potential of stem cells is determined by the ability of these cells to establish and maintain developmentally regulated gene expression programs that are specific to different lineages. Although transcriptionally potentiated epigenetic states of genes have been described for haematopoietic progenitors, the developmental stage at which the formation of lineage-specific gene expression domains is initiated remains unclear. In this study, we show that an intergenic cis-acting element in the mouse lambda5-VpreB1 locus is marked by histone H3 acetylation and histone H3 lysine 4 methylation at a discrete site in embryonic stem (ES) cells. The epigenetic modifications spread from this site toward the VpreB1 and lambda5 genes at later stages of B-cell development, and a large, active chromatin domain is established in pre-B cells when the genes are fully expressed. In early B-cell progenitors, the binding of haematopoietic factor PU.1 coincides with the expansion of the marked region, and the region becomes a center for the recruitment of general transcription factors and RNA polymerase II. In pre-B cells, E2A also binds to the locus, and general transcription factors are distributed across the active domain, including the gene promoters and the intergenic region. These results suggest that localized epigenetic marking is important for establishing the transcriptional competence of the lambda5 and VpreB1 genes as early as the pluripotent ES cell stage.

Acetylation↗
PubMed2005

Novel function of neuronal PAS domain protein 1 in erythropoietin expression in neuronal cells.

The basic helix loop helix-PAS (bHLH-PAS) transcription factors have diverse roles in physiologic responses to the environment and in early development. One bHLH-PAS protein, neuronal PAS domain protein 1 (NPAS1), is reported to be expressed only in the central nervous system beginning at the late embryonic stage, but its function is unknown. Using an anti-NPAS1 antibody, we have shown that NPAS1 expression in cerebral cortex was observed first around embryonic Day 16.5 (E16.5) and was then dispersed throughout the region as cortical development progressed. From the similarity with hypoxia-inducible factor-1alpha (HIF-1alpha), we investigated whether NPAS1 regulates transcription of erythropoietin (EPO), which is the target of HIF-1alpha and is expressed in the brain during the early developmental stage. In the present study, we have shown that NPAS1 binds to the enhancer region of Epo in vivo. A luciferase reporter assay revealed a repressive effect of NPAS1 on hypoxia-responsive element-regulated gene expression. These results raise the possibility that NPAS1 plays a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level.

Animals↗
PubMed1997

Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins.

The human beta-globin gene cluster is regulated in part by a distal locus control region that is required for opening a chromatin domain in erythroid cells and enhancing expression of the beta-like globin genes at the correct developmental stages. One part of the locus control region, called hypersensitive site 2 (HS2), functions as a strong enhancer. Matches to the consensus binding sites for basic helix-loop-helix (bHLH) proteins (E boxes) are well conserved within the HS2 core. We show that mutations of the HS2 core that alter an invariant E box cause a 3.5-fold reduction in enhancement of expression of an epsilon-globin reporter gene in transiently transfected K562 cells, both before and after induction. Mutations of the HS2 core that alter a less-highly conserved E box cause a more modest reduction in enhancement. Footprint analysis shows binding of erythroid nuclear proteins in vitro to the invariant E box as well as an adjacent CAC/GTG box. Probes containing the E box regions form sequence-specific complexes with proteins from both K562 and MEL nuclear extracts; these are disrupted by the same mutations that decrease enhancement. Some of these latter complexes contain known bHLH proteins, as revealed by specific loss of individual complexes when treated with antibodies against TAL1 and USF. Interaction between the E boxes and the bHLH proteins, as well as other binding proteins, could account for the role of these sites in enhancement by HS2.

Base Sequence↗
PubMed2003

Twist2, a novel ADD1/SREBP1c interacting protein, represses the transcriptional activity of ADD1/SREBP1c.

Adipocyte determination and differentiation dependent factor 1 (ADD1)/sterol regulatory element binding protein isoform (SREBP1c) is a key transcription factor in fatty acid metabolism and insulin- dependent gene expression. Although its transcriptional and post-translational regulation has been extensively studied, its regulation by interacting proteins is not well understood. To identify cellular proteins that associate with ADD1/SREBP1c, we employed the yeast two-hybrid system with an adipocyte cDNA library. Using the N-terminal domain of ADD1/SREBP1c as bait, we identified Twist2 (also known as Dermo-1), a basic helix-loop-helix (bHLH) protein, as a novel ADD1/SREBP1c interacting protein. Over-expression of Twist2 strongly repressed the transcriptional activity of ADD1/SREBP1c, primarily by reducing its binding to target sequences. Inhibition of histone deacetylase (HDAC) activity with HDAC inhibitors relieved this repression. Our data suggest that physical interaction between Twist2 and ADD1/SREBP1c attenuates transcriptional activation by ADD1/SREBP1c by inhibiting its binding to DNA, and that this inhibition is at least partly dependent on chromatin modification by HDACs.

Acetylation↗
PubMed2004

Gene recruitment of the activated INO1 locus to the nuclear membrane.

The spatial arrangement of chromatin within the nucleus can affect reactions that occur on the DNA and is likely to be regulated. Here we show that activation of INO1 occurs at the nuclear membrane and requires the integral membrane protein Scs2. Scs2 antagonizes the action of the transcriptional repressor Opi1 under conditions that induce the unfolded protein response (UPR) and, in turn, activate INO1. Whereas repressed INO1 localizes throughout the nucleoplasm, the gene is recruited to the nuclear periphery upon transcriptional activation. Recruitment requires the transcriptional activator Hac1, which is produced upon induction of the UPR, and is constitutive in a strain lacking Opi1. Artificial recruitment of INO1 to the nuclear membrane permits activation in the absence of Scs2, indicating that the intranuclear localization of a gene can profoundly influence its mechanism of activation. Gene recruitment to the nuclear periphery, therefore, is a dynamic process and appears to play an important regulatory role.

Basic Helix-Loop-Helix Proteins↗
PubMed2004

Generic features of tertiary chromatin structure as detected in natural chromosomes.

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different approximately 400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or "beads", referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters.

Base Sequence↗
PubMed1988

[Electron microscopy research on the chromatin structure of dispersed lampbrush chromosomes in the hen].

The lampbrush chromosomes from the late previtellogenic and early vitellogenic oocytes of adult hens were spread according to Miller's technique and examined in electron microscope. The nucleosomes in the threads of the non-transcribed chromatin are uniformly distributed, the spaces between the nucleosomes correspond by their length to the linker DNA. Nucleosomes are absent in the transcriptional units with high intensity transcription. In transcriptional units with moderate and weak transcription the nucleosomes are identified in the axial chromatin fibril between RNA-polymerase granules, the space between them varying. The compactization ratio of DNA (the number of DNA mkm in a 1 mkm chromatin fiber) in non-transcribed fibrils is equal to 2.1, in transcriptional units with moderate and weak activity it is 1.7, and in transcriptional units with intensive transcription it is close to 1. The DNA compaction ratio in lateral loops of lampbrushes is determined by the intensity of transcription. It is supposed that in the native state the inactive chromatin with uniform spacing of nucleosomes has a supernucleosomal structure, while the DNA compaction ratio in the transcribed sequences corresponds to that on Miller's spreads.

Animals↗
PubMed2003

Histone acetyltransferase-dependent chromatin remodeling and the vascular clock.

Rhythmic gene expression is central to the circadian control of physiology in mammals. Transcriptional activation of Per and Cry genes by heterodimeric bHLH-PAS proteins is a key event in the feedback loop that drives rhythmicity; however, the mechanism is not clearly understood. Here we show the transcriptional coactivators and histone acetyltransferases, p300/CBP, PCAF, and ACTR associate with the bHLH-PAS proteins, CLOCK and NPAS2, to regulate positively clock gene expression. Furthermore, Cry2 mediated repression of NPAS2:BMAL1 is overcome by overexpression of p300 in transactivation assays. Accordingly, p300 exhibits a circadian time-dependent association with NPAS2 in the vasculature, which precedes peak expression of target genes. In addition, a rhythm in core histone H3 acetylation on the mPer1 promoter in vivo correlates with the cyclical expression of their mRNAs. Temporal coactivator recruitment and HAT-dependent chromatin remodeling on the promoter of clock controlled genes in the vasculature permits the mammalian clock to orchestrate circadian gene expression.

Acetyltransferases↗
PubMed1983

Stereoscopic scanning electron microscopy of the chromosomes in Vicia faba (broad beans).

Metaphase chromosomes of Vicia faba (broad beans) were observed in situ with a scanning electron microscope by cryofracturing the cell. The chromosome is composed of tortuous fibers 500 A in diameter. They may be seen distributed randomly, but sometimes they are seen running parallel in the chromosome. The parallel fibers spiral around the main body of the chromosome, whereas they run longitudinally in the secondary constriction. If a chromosome is composed of a single strand (unineme hypothesis for the chromosome), the parallel fiber arrangement may imply that a single fiber is looping back and forth in the chromosome.

Chromatin↗
PubMed2001

Function and regulation of the transcription factors of the Myc/Max/Mad network.

The members of the Myc/Max/Mad network function as transcriptional regulators. Substantial evidence has been accumulated over the last years that support the model that Myc/Max/Mad proteins affect different aspects of cell behavior, including proliferation, differentiation, and apoptosis, by modulating distinct target genes. The unbalanced expression of these genes, e.g. in response to deregulated Myc expression, is most likely an important aspect of Myc's ability to stimulate tumor formation. Myc and Mad proteins affect target gene expression by recruiting chromatin remodeling activities. In particular Myc interacts with a SWI/SNF-like complex that may contain ATPase activity. In addition Myc binds to TRRAP complexes that possess histone acetyl transferase activity. Mad proteins, that antagonize Myc function, recruit an mSin3 repressor complex with histone deacetylase activity. Thus the antagonism of Myc and Mad proteins is explained at the molecular level by the recruitment of opposing chromatin remodeling activities.

Animals↗