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In this study, changes in chromatin organization in promoters of hypoxia-inducible genes were investigated during hypoxia-reoxygenation conditions. (elsevierpure.com)
Remodeling enzymes set up the canonical nucleosome organization of genes. (tu-dresden.de)
Genome-wide studies in Saccharomyces cerevisiae , for example, have revealed that promoters of most actively transcribed genes are depleted of nucleosomes and that histone density is inversely proportional to the transcription rate within coding regions, suggesting that nucleosomes are dynamically disassembled and reassembled at each passage of the polymerase ( 16 ). (asm.org)
Nucleosome occupancy (white corresponding to large occupancy values) for the 2000 shortest S. Cerevisiae genes ordered by increasing length from top to bottom and aligned on the promoter (null distance). (ens-lyon.fr)
Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. (abcam.com)
Regulation of developmental genes by CREs commonly imply physical enhancer-promoter (E-P) interactions that are established by looping mechanisms. (cabd.es)
CreA/CRE1 binds to the promoters of the respective target genes via the consensus motif 5'-SYGGRG-3', whose function in vivo has been shown both in Aspergillus nidulans and Trichoderma reesei [ 9 - 12 ]. (biomedcentral.com)
We propose that the transient expression of CTCFL in spermatogonia and preleptotene spermatocytes serves to occupy a subset of promoters and maintain the expression of male germ cell genes. (unican.es)
OPN genes have relatively higher nucleosome occupancy near the TSS regions. (ncku.edu.tw)
DPN genes are more nucleosome-free close to the TSS regions. (ncku.edu.tw)
These dCas9-activator fusions targeted to the promoter region of endogenous genes can then modulate gene expression 7 - 11 . (cdc.gov)

Indeed, in the absence of PRDM9, meiotic DSBs occur at transcription regulatory regions, such as promoters and enhancers (Brick et al. (springer.com)
Promoters, enhancers and physical interactions between regions of DNA are important in ways that are only now becoming apparent, directing phases of development, and often perturbed in cancers. (birmingham.ac.uk)
PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. (nih.gov)
Gene regulation occurs largely at the transcriptional level through cis-regulatory elements (CREs), including promoters and enhancers, where transcription factors (TFs) bind and stimulate transcription. (cabd.es)
Binding of sequence-specific transcription factors and associated chromatin-modifying enzymes can induce post-translational modification of histone tails and can facilitate nucleosome removal [ 3 - 5 ], which can turn functional sequences such as promoters and enhancers into active, nucleosome-depleted sites [ 2 ]. (biomedcentral.com)
Enhancers have nucleosome-free regions and histone signals like many other open regions. (biostars.org)

In mammalian cells, active and silent rDNA promoters are characterized by specific histone modifications, DNA methylation, and positioning of the promoter-bound nucleosome (reviewed in reference 22 ). (asm.org)
Chromatin accessibility is modulated by several key epigenetic factors: histone post-translational modifications (PTMs), DNA methylation, nucleosome position/occupancy, transcription factors and chromatin architectural proteins (CAPs). (nih.gov)
This important manuscript reveals signatures of co-evolution of two nucleosome remodeling factors, Lsh/HELLS and CDCA7, which are involved in the regulation of eukaryotic DNA methylation. (elifesciences.org)
Could the emergence or loss of a specific nucleosome regulator affect the evolution of DNA methylation as an epigenetic mechanism? (elifesciences.org)
To date, however, epigenetic studies in the human brain are mostly limited to the exploration of DNA methylation and posttranslational modifications of the nucleosome core histones. (nih.gov)
The GAPDH gene is actively transcribed in all cell types and its promoter is highly enriched for histone modifications associated with active transcription, such as histone H3 Lys4 tri-methylation and general histone acetylation. (cellsignal.com)
This gene promoter shows very low levels of histone modifications associated with heterochromatin, such as histone H3 Lys9 or Lys27 tri-methylation. (cellsignal.com)
Mosaic BRCA1 promoter methylation contribution in hereditary breast/ovarian cancer pedigrees. (cdc.gov)

The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool. (wikipedia.org)
Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. (wikipedia.org)
Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins. (wikipedia.org)
The nucleosome core particle is composed of DNA and histone proteins. (wikipedia.org)
Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. (genengnews.com)
In our cells, DNA is wrapped around histone proteins into a series of bundles called nucleosomes, which are packed side by side into chromatin. (fredhutch.org)
These LRC are the signature of the DNA-histone proteins interactions within the nucleosomes, the basic units for DNA compaction in eukaryotic cell nuclei, that constitute a regulatory factor for accessibility to genetic material. (ens-lyon.fr)

In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. (wikipedia.org)
Eukaryotic DNA stored as chromatin whose basic repeating unit is the nucleosome, plays an integral role in gene regulation. (nih.gov)
Nucleosomes form the fundamental repeating units of eukaryotic chromatin [1] , which is used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it (in mammalian cells approximately 2 m of linear DNA have to be packed into a nucleus of roughly 10 µm diameter). (wikidoc.org)

TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. (biorxiv.org)
The male germ cell gene regulator CTCFL is functionally different from CTCFand binds CTCF-like consensus sites in a nucleosome composition-dependent manner. (unican.es)
CTCFL binds promoters with loosely assembled nucleosomes, whereas CTCF favors consensus sites surrounded by phased nucleosomes. (unican.es)

Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. (wikipedia.org)
The nucleosome core particle consists of approximately 146 base pairs (bp) of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer, consisting of 2 copies each of the core histones H2A, H2B, H3, and H4. (wikipedia.org)
Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. (wikipedia.org)
The structures of over 20 different nucleosome core particles have been solved to date, including those containing histone variants and histones from different species. (wikipedia.org)
The structure of the nucleosome core particle is remarkably conserved, and even a change of over 100 residues between frog and yeast histones results in electron density maps with an overall root mean square deviation of only 1.6Å. (wikipedia.org)

The nomenclature of different promoter-associated RNA polymerase II (Pol II) species is explicitly defined in an effort to provide consistency in future literature. (nature.com)
Recent years have witnessed a sea change in our understanding of transcription regulation: whereas traditional models focused solely on the events that brought RNA polymerase II (Pol II) to a gene promoter to initiate RNA synthesis, emerging evidence points to the pausing of Pol II during early elongation as a widespread regulatory mechanism in higher eukaryotes. (nature.com)
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. (open.ac.uk)

The nucleosome contains over 120 direct protein-DNA interactions and several hundred water mediated ones [13] . (wikidoc.org)
1990 . Alternative DNA-protein interactions in variable-length internucleosomal regions associated with Drosophila Adh distal promoter expression. (rochester.edu)

Transcriptionally active chromatin regions are characterized by the dynamic disruption and re-assembly of promoter proximal nucleosomes. (umassmed.edu)
For example, chromosomal "loopings" are pivotal for the orderly process of gene expression, by enabling distal regulatory enhancer or silencer elements to directly interact with proximal promoter and transcription start sites, potentially bypassing hundreds of kilobases of interspersed sequence on the linear genome. (nih.gov)
Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. (open.ac.uk)

Previously, we (and others) showed that nucleosome locations within promoters play critical roles in chromatin accessibility, thus controlling gene activity. (nih.gov)
Pioneer TFs can bind chromatin in a closed configuration and promote chromatin accessibility through the displacement of nucleosomes. (cabd.es)

The evaluation was done on four classes of biological sequences - CpG-poor promoters, all promoters, exons and nucleosome positioning sequences. (umd.edu)
In the case of nucleosome positioning sequences, optimal accuracy was achieved at a gap length of 4. (umd.edu)
Chromatin footprinting has shown that stage- and tissue-specific transcription initiation from the Adh distal promoter involves a coordinated assembly of a multiprotein complex interacting with specific cis -acting sequences at the distal promoter, at the enhancer of distal promoter (AAE), and at a single nucleosome precisely positioned between these 2 regulatory regions. (rochester.edu)

The role of the nucleosome as a regulator of transcription was demonstrated by Lorch et al. (wikipedia.org)
Our results establish that ORC, in addition to its canonical role as the MCM loader, has a second crucial function as a master regulator of nucleosome organization at the replication origin, a crucial prerequisite for efficient chromosome replication. (nature.com)
Fig. 1: ORC is a master regulator of nucleosome organization at origins of replication. (nature.com)

Within 1 h after the hypoxia exposure was ended (reoxygenation), HIF complexes were dissociated from the promoter regions. (elsevierpure.com)
Figure 1: Defining the terms used to describe promoter-associated Pol II complexes. (nature.com)
Correspondingly, the locations of nucleosomes in the genome are precisely controlled by so called nucleosome remodeling complexes. (tu-dresden.de)
reports suggested that targeting of H2A.Z to bivalent promoters may depend on PRC1/2 complexes and vice versa ( Creyghton et al. (researchgate.net)

Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1. (nature.com)

Furthermore in the plot of classification accuracy versus the gap, a periodicity of 10-11 bps was observed which might indicate structural preferences in the nucleosome positioning sequence. (umd.edu)
When further modeling DNA as a semifexible polymer explicitly taking into account the structural disorder induced by the sequence, we have provided some evidence that the observed LRC favor the spontaneous formation as well as the cooperative positioning of nucleosomes along the chromosomes including the nucleosome free regions experimentally observed at gene promoters (see figure below). (ens-lyon.fr)
bottom) Predictions based on a physical modeling of sequence-dependent nucleosome energy profile. (ens-lyon.fr)
Note that the organization of the nucleosomal assembly results from the confinement of nucleosomes between sequence induced high energy barriers corresponding to the nucleosome free regions observed at the promoters and gene ends. (ens-lyon.fr)

In some of the hypoxia-inducible promoters, nucleosome-free DNA regions (NFRs) were established in parallel with hypoxia-induced transcription. (elsevierpure.com)
In Saccharomyces cerevisiae , meiotic DSBs preferentially occur at nucleosome-depleted regions in gene promoters (Ohta et al. (springer.com)
rDNA coding regions are also depleted of nucleosomes, relative to the rDNA spacer. (asm.org)
Coding regions of active rDNA were initially thought to be devoid of nucleosomes, as suggested by electron microscopy and psoralen cross-linking experiments ( 4 ). (asm.org)
The authors hypothesized that the nucleosomes containing the DNA that Pol II would need to access - the promoter regions - were "fragile", and thus primed to be quickly knocked off at the end of quiescence. (fredhutch.org)
To test this, they performed a weak enzyme digestion to only disrupt the most fragile nucleosomes, and indeed found that this exposed many of the regions that were rapidly reactivated. (fredhutch.org)

Thus, reversible changes in nucleosome organization mediated by transcription factors are notable features of stress-inducible gene regulation. (elsevierpure.com)
However, how this nucleosome organization is established and whether this organization is required for replication remain unknown. (nature.com)

Nucleosomes control promoter accessibility. (ncku.edu.tw)

A nucleosome is the basic structural unit of DNA packaging in eukaryotes. (wikipedia.org)

Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. (nature.com)
These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. (genengnews.com)
However, in contrast to prevailing views they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. (nih.gov)

The nucleosome is the fundamental subunit of chromatin. (wikipedia.org)
Although the TATA-Binding Protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-Associated Factor (TAF) subunits recognize downstream promoter elements, act as co-activators, and interact with nucleosomes. (biorxiv.org)

Genome-wide nucleosome positioning maps are now available for many model organisms and human cells. (wikipedia.org)
Pausing is now recognized to be a pervasive feature of promoters in mammals and Drosophila melanogaster , and the evidence supporting this from genome-wide studies is presented. (nature.com)
The Mueller-Planitz lab studies the core components of chromatin - the nucleosomes and the machinery that places them in the genome. (tu-dresden.de)
Aging, for instance, disrupts the nucleosome landscape, destabilizing the genome, and mutations in nucleosomes are drivers of cancers. (tu-dresden.de)
Nucleosomes serve both as barriers that restrict access to the genome and as a medium to accumulate epigenetic marks. (tu-dresden.de)
They develop cutting-edge technology to visualize individual nucleosome patterns in single cells, to deduce systems-level properties of tens of thousands of nucleosomes in cells, and to dissect the mechanism of nucleosome remodeling genome-wide in vivo and in vitro. (tu-dresden.de)
Our data suggest that nucleosome composition specifies the genome-wide binding of CTCFL and CTCF. (unican.es)
Tiling a given promoter region with several sgRNAs can produce more robust transcriptional activation 9 - 11 , but this requirement presents enormous challenges for scalability, and in particular for establishing pooled, genome-wide GOF screens. (cdc.gov)

In the nucleus it behaves as a DNA chaperone, sustains nucleosome dynamics and chromosomal stability, and contributes to telomere maintenance [ 10 ]. (hindawi.com)

The functional importance of the nucleosome-organizing activity of the ORC was demonstrated by orc1 mutations that maintained classical MCM-loader activity but abrogated the array-generation activity of ORC. (nature.com)
This transcription-dependent TAF complex promotes subsequent activator-independent transcription, and promoter response to TAF mutations in vivo correlates with the level of downstream, rather than overall, Taf1 crosslinking. (biorxiv.org)
We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations. (biorxiv.org)

Not every open and non-promoter region is an enhancer. (biostars.org)
Adh is transcribed from 2 tandem promoters ~700 bp apart, each has distinct developmental- and tissue-specific patterns, and each is regulated by a distinct enhancer. (rochester.edu)

Some also even the spacing between nucleosomes, setting a characteristic nucleosome-to-nucleosome distance. (tu-dresden.de)

Lis, J. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation. (nature.com)
In addition, the density and positioning of nucleosomes have also been linked to transcriptional regulation. (asm.org)

Kornberg, R. D. & Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. (nature.com)

Epigenetic profiles of elevated cell free circulating H3.1 nucleosomes as potential biomarkers for non-Hodgkin lymphoma. (cdc.gov)

Here we show that transcription induces stable TAF binding to downstream promoter DNA, independent of upstream contacts, TBP, or other basal transcription factors. (biorxiv.org)

Two scenarios could potentially explain the co-occurrence of H3K4me3 and H3K27me3 observed by ChIP-seq on bivalent promoters. (researchgate.net)
Many promoters in embryonic stem (ES) cells harbor a distinctive histone modification signature that combines the activating histone H3 Lys 4 trimethylation (H3K4me3) mark an. (researchgate.net)
Bivalent promoters are defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) chromatin marks. (researchgate.net)

We found that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. (genengnews.com)
Active and silent rDNAs have distinct chromatin states at the promoter and within the transcribed region. (asm.org)
SimpleChIP ® Rat GAPDH Promoter Primers contain a mix of forward and reverse PCR primers that are specific to a region of the rat glyceraldehyde-3-phosphate dehydrogenase (GAPDH) promoter. (cellsignal.com)

Adjacent nucleosomes are joined by a stretch of free DNA termed linker DNA (which varies from 10 - 80 bp in length depending on species and tissue type).The whole structure generates a cylinder of diameter 11 nm and a height of 5.5 nm. (wikipedia.org)
Adjacent nucleosomes are joined by a stretch of free DNA termed "linker DNA" which varies from 10 - 80 bp in length depending on species and tissue type [10] ). (wikidoc.org)

Nucleosome positioning via excluding genomic energy barriers. (ens-lyon.fr)

Multiple lines of evidence support the idea that Pol II and nucleosomes compete for promoter binding and suggest that a crucial role of paused Pol II involves maintenance of accessible promoter chromatin architecture. (nature.com)
Nucleosomes are crucial to human health. (tu-dresden.de)

The overarching aim of the Mueller-Planitz lab is to elucidate the biogenesis of the nucleosome landscape and dissect its biological function under physiological and pathological conditions. (tu-dresden.de)

Nucleosome core particles are observed when chromatin in interphase is treated to cause the chromatin to unfold partially. (wikipedia.org)
The string is the DNA, while each bead in the nucleosome is a core particle. (wikipedia.org)
Because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into fragments of lengths equal to multiplicity of distance between nucleosomes (180, 360, 540 base pairs etc. (wikipedia.org)
The crystal structure of the nucleosome core particle consisting of H2A , H2B , H3 and H4 and DNA. (wikidoc.org)

Within 24 h of reoxygenation, the hypoxia-induced transcription returned to basal levels and the nucleosome structure was reassembled in the hypoxia-inducible NFRs. (elsevierpure.com)

Partial DNAse digestion of chromatin reveals its nucleosome structure. (wikipedia.org)

To fit it into a nucleus with a diameter of ~10 μm, DNA is wrapped around histone octamers, creating strings of nucleosomes that can be further organized into higher-order levels of compaction [ 1 ]. (biomedcentral.com)

Nucleosomes were first observed as particles in the electron microscope by Don and Ada Olins in 1974, and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by Roger Kornberg. (wikipedia.org)
Non-condensed nucleosomes without the linker histone resemble "beads on a string of DNA" under an electron microscope. (wikipedia.org)

Using chromatin immunoprecipitation, micrococcal nuclease digestion, and chromatin fractionation, we observed that there are fewer nucleosomes at the active BES and that these are irregularly spaced compared to silent BESs. (asm.org)

These 'spacing remodelers' thereby generate arrays of nucleosomes with a surprising regularity, and these arrays are conserved throughout eukaryotes. (tu-dresden.de)

Regulation of nucleosome density is therefore an important mechanism to enable the transcription machinery to access the DNA. (asm.org)

PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. (nih.gov)

DNA must be compacted into nucleosomes to fit within the cell nucleus. (wikipedia.org)

In contrast, in the case of ''true'' bivalency, virtually all cells in the population carry both marks simultaneously at the promoter in question, leading to low, if any, expression for that gene in all cells. (researchgate.net)

For this, they focused on RSC, a chromatin remodeling complex that is known to be able to remove fragile nucleosomes. (fredhutch.org)

Anatomy11

Organisms9

Chemicals and Drugs56

Analytical, Diagnostic and Therapeutic Techniques and Equipment15

Phenomena and Processes59

Information Science3

Genes11

Enhancers6

Methylation8

Proteins7

Eukaryotic3

Binds3

Histones5

Polymerase3

Interactions2

Proximal3

Chromatin accessibility2

Sequences3

Regulator3

Complexes4

Budding yeast1

Sequence4

Regions6

Organization2

Accessibility1

Structural1

Initiation3

Subunit2

Genome8

Dynamics1

Mutations3

Enhancer2

Characteristic1

Transcriptional regulation2

Fundamental1

Epigenetic1

Downstream1

H3K4me33

Region3

Adjacent2

Barriers1

Crucial2

Biological1

Core4

Basal1

Reveals1

Compaction1

Electron2

Digestion1

Arrays1

Mechanism1

Sufficient1

Nucleus1

Expression1

Complex1