• Biomarker
• Colorectal cancer
• Prognosis
• TCGA
• ZNF26

• Humans
• Colorectal Neoplasms/genetics
• Colorectal Neoplasms/pathology
• Prognosis
• Biomarkers, Tumor/genetics
• Gene Expression Regulation, Neoplastic
• Male
• Female
• Kaplan-Meier Estimate
• Transcriptome
• Middle Aged
• Gene Expression Profiling

• RNA processing
• cell nucleus
• chromatin
• gene expression
• myofiber
• ribonucleic acid (RNA) transcription
• satellite cell
• skeletal muscle atrophy

• Muscle, Skeletal/metabolism
• Cell Nucleus/metabolism
• Muscle Fibers, Skeletal/metabolism

• Humans
• Transcription Factors/genetics
• Nuclear Proteins/genetics
• Gene Expression Regulation
• Chromatin/genetics
• Leukemia, Myeloid, Acute/genetics
• Bromodomain Containing Proteins

• R35 GM133732 NIGMS NIH HHS
• HHS | NIH | National Institute of General Medical Sciences (NIGMS)

• 15(S)-HETE
• ALOX15
• PGE2
• glucocorticoids
• inflammation
• parturition

• 82271717, 81830042 and 82071677 National Natural Science Foundation of China
• 2022YFC2704602 National Key R & D Program of China
• SHSMU-ZLCX20210201 Innovative Research Team of High-level Local Universities in Shanghai

• DNA damage response
• HMGB1
• PAR
• PARP1
• histone H1
• nucleosome core particle

Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.

• Cellular Reprogramming/genetics
• Chromatin/genetics
• Epigenesis, Genetic
• Epigenomics
• Induced Pluripotent Stem Cells

• exercise
• mitochondrial biogenesis
• skeletal muscle
• subcellular
• transcription factors

• Cell Nucleus/metabolism
• Exercise/physiology
• Gene Expression Regulation
• Humans
• Mitochondria, Muscle/metabolism
• Mitochondrial Proteins/metabolism
• Movement
• Muscle, Skeletal/metabolism
• Transcription Factors/metabolism

• DP200103542 Australian Research Council

• Entropically favored
• Hydrogen bond disruption
• Hydrophobic interaction
• In-vitro nucleosome disassembly
• Mammalian cell cytotoxicity
• Nucleobase destacking

The dysregulation of transcriptional factors (TFs) leads to malignant growth and the development of colorectal cancer (CRC). Herein, we sought to identify the transcription factors relevant to the prognosis of colorectal cancer patients. We found 526 differentially expressed TFs using the TCGA database of colorectal cancer patients (n = 544) for the differential analysis of TFs (n = 1,665) with 210 upregulated genes as well as 316 downregulated genes. Subsequently, GO analysis and KEGG pathway analysis were performed for these differential genes for investigating their pathways and function. At the same time, we established a genetic risk scoring model for predicting the overall survival (OS) by using the mRNA expression levels of these differentially regulated TFs, and defined the CRC into low and high-risk categories which showed significant survival differences. The genetic risk scoring model included four high-risk genes (HSF4, HEYL, SIX2, and ZNF26) and two low-risk genes (ETS2 and SALL1), and validated the OS in two GEO databases (p = 0.0023 for the GSE17536, p = 0.0193 for the GSE29623). To analyze the genetic and epigenetic changes of these six risk-related TFs, a unified bioinformatics analysis was conducted. Among them, ZNF26 is progressive in CRC and its high expression is linked with a poor diagnosis as well. Knockdown of ZNF26 inhibits the proliferative capacity of CRC cells. Moreover, the positive association between ZNF26 and cyclins (CDK2, CCNE2, CDK6, CHEK1) was also identified. Therefore, as a novel biomarker, ZNF26 may be a promising candidate in the diagnosis and prognostic evaluation of colorectal cancer.

• CRC
• GEO
• TCGA
• ZNF26
• prognosis
• transcription factors

Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.

• ATAC
• CUT&RUN
• ChIP
• Chromatin
• DNase
• MNase
• genomics
• nucleosome occupancy
• transcription factors

Nucleosomes restrict DNA accessibility throughout eukaryotic genomes, with repercussions for replication, transcription, and other DNA-templated processes. How this globally restrictive organization emerged during evolution remains poorly understood. Here, to better understand the challenges associated with establishing globally restrictive chromatin, we express histones in a naive system that has not evolved to deal with nucleosomal structures: Escherichia coli. We find that histone proteins from the archaeon Methanothermus fervidus assemble on the E. coli chromosome in vivo and protect DNA from micrococcal nuclease digestion, allowing us to map binding footprints genome-wide. We show that higher nucleosome occupancy at promoters is associated with lower transcript levels, consistent with local repressive effects. Surprisingly, however, this sudden enforced chromatinization has only mild repercussions for growth unless cells experience topological stress. Our results suggest that histones can become established as ubiquitous chromatin proteins without interfering critically with key DNA-templated processes.

• E. coli
• Methanothermus fervidus
• chromatin
• chromosomes
• evolution
• evolutionary biology
• gene expression
• histones

Protein lysine methylation is a critical and dynamic post-translational modification that can regulate protein stability and function. This post-translational modification is regulated by lysine methyltransferases and lysine demethylases. Recent studies using mass-spectrometric techniques have revealed that in addition to histones, a great number of transcription factors are also methylated, often at multiple sites and to different degrees (mono-, di-, trimethyl lysine). The biomedical significance of transcription factor methylation in human diseases, including cancer, has been explored recently. Some studies have demonstrated that interfering with transcription factor lysine methylation both in vitro and in vivo can inhibit cancer cell proliferation, thereby reversing tumor progression. The inhibitors targeting lysine methyltransferases and lysine demethylases have been under development for the past two decades, and may be used as potential anticancer agents in the clinic. In this review, we focus on the current findings of transcription factor lysine methylation, and the effects on both transcriptional activity and target gene expression. We outlined the biological significance of transcription factor lysine methylation on tumor progression and highlighted its clinical value in cancer therapy.

• Acetylation
• Chromatin/metabolism
• Co-Repressor Proteins
• Histones/metabolism
• Humans
• Lysine Acetyltransferase 5/metabolism
• Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism
• Peroxisome Proliferator-Activated Receptors/metabolism
• Pregnane X Receptor/metabolism
• Receptors, Androgen/metabolism
• Receptors, Cytoplasmic and Nuclear/metabolism
• Receptors, Estrogen/metabolism
• Receptors, Glucocorticoid/metabolism
• Repressor Proteins/metabolism

FACT, in addition to its role in transcription, is likely implicated in both transcription-coupled nucleotide excision repair and DNA double strand break repair. Here, we present evidence that FACT could be directly involved in Base Excision Repair and elucidate the chromatin remodeling mechanisms of FACT during BER. We found that, upon oxidative stress, FACT is released from transcription related protein complexes to get associated with repair proteins and chromatin remodelers from the SWI/SNF family. We also showed the rapid recruitment of FACT to the site of damage, coincident with the glycosylase OGG1, upon the local generation of oxidized DNA. Interestingly, FACT facilitates uracil-DNA glycosylase in the removal of uracil from nucleosomal DNA thanks to an enhancement in the remodeling activity of RSC. This discloses a novel property of FACT wherein it has a co-remodeling activity and strongly enhances the remodeling capacity of the chromatin remodelers. Altogether, our data suggest that FACT may acts in concert with RSC to facilitate excision of DNA lesions during the initial step of BER.

In the nucleus, DNA is packaged into chromatin. The repeating unit of chromatin, the nucleosome, consists of a histone octamer around which DNA is wrapped into two superhelical turns. The nucleosome is a barrier for various nuclear processes which require access to DNA. To repair lesions on DNA, this barrier has to be overcome by either nucleosome remodeling or by histone eviction. Here we present evidence that FACT, a protein known to be involved in transcription, is also involved in BER, by boosting nucleosome remodeling. Upon in vivo oxidized DNA lesion induction, FACT exhibits a BER-like protein behavior, and it is recruited to the sites of DNA damages. In vitro experiments show that FACT boosts the remodeling activity of the chromatin remodeler RSC and is implicated in DNA repair. The presence of FACT greatly facilitates the removal of uracil from nucleosomal, but not from naked DNA, in a RSC-mediated reaction. Taken collectively, our in vitro and in vivo data reveal a role of FACT in BER by helping the remodeling of chromatin at the sites of lesions.

• Animals
• Chromatin/genetics
• Chromatin Assembly and Disassembly/genetics
• Chromosomal Proteins, Non-Histone/genetics
• DNA Damage/genetics
• DNA Repair/genetics
• DNA-Binding Proteins/biosynthesis
• DNA-Binding Proteins/genetics
• HeLa Cells
• High Mobility Group Proteins/biosynthesis
• High Mobility Group Proteins/genetics
• Histones/genetics
• Histones/metabolism
• Humans
• Nucleosomes/genetics
• Oxidative Stress/genetics
• Saccharomyces cerevisiae/genetics
• Saccharomyces cerevisiae Proteins/genetics
• Transcription Factors/genetics
• Transcription, Genetic
• Transcriptional Elongation Factors/biosynthesis
• Transcriptional Elongation Factors/genetics
• Uracil/metabolism
• Xenopus laevis

• Seventh Framework Programme EU, http://ec.europa.eu/research/index.cfm
• Association de Recherche sur le Cancer, http://www.fondation-arc.org/
• Agence Nationale de la Recherche
• Institut National du Cancer-INCA, http://www.e-cancer.fr/
• Institut National du Cabncer-INCA, http://www.e-cancer.fr/
• Fondation pour la Recherche Médicale
• La Ligue Nationale contre le Cancer (Fr), https://www.ligue-cancer.net/

High mobility group protein 1 (HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N’ and N’’) remain stable and exhibit a number of characteristics that are distinctly different from the canonical nucleosome. These findings complement previous studies that showed (1) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (2) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that a major facet of the mechanism of HMGB1 action involves a restructuring of aspects of the nucleosome that appear to relax structural constraints within the nucleosome. The findings are extended to reveal the differences between ER and the other steroid hormone receptors. A working proposal outlines mechanisms that highlight the multiple facets that HMGB1 may utilize in restructuring the nucleosome.

• Nucleosome dynamics
• Estrogen receptor
• High mobility group protein 1
• Conformational dynamics
• Energy landscape

• R15 GM054357 NIGMS NIH HHS

Nucleosomes play important roles in a cell beyond their basal functionality in chromatin compaction. Their placement affects all steps in transcriptional regulation, from transcription factor (TF) binding to messenger ribonucleic acid (mRNA) synthesis. Careful profiling of their locations and dynamics in response to stimuli is important to further our understanding of transcriptional regulation by the state of chromatin. We measured nucleosome occupancy in human hepatic cells before and after treatment with transforming growth factor beta 1 (TGFβ1), using massively parallel sequencing. With a newly developed method, SuMMIt, for precise positioning of nucleosomes we inferred dynamics of the nucleosomal landscape. Distinct nucleosome positioning has previously been described at transcription start site and flanking TF binding sites. We found that the average pattern is present at very few sites and, in case of TF binding, the double peak surrounding the sites is just an artifact of averaging over many loci. We systematically searched for depleted nucleosomes in stimulated cells compared to unstimulated cells and identified 24 318 loci. Depending on genomic annotation, 44–78% of them were over-represented in binding motifs for TFs. Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing.

• Chromosome subcompartments
• Computer simulation
• Crowding
• Nuclear bodies
• Nuclear structures

• Assisted-loading
• Chromatin structure
• Glucocorticoid receptor
• Glucocorticoids
• Nuclear receptor
• Transcription dynamics

• Animals
• Chromatin Assembly and Disassembly
• Circadian Clocks
• Genome, Human
• Glucocorticoids/physiology
• Humans
• Nucleic Acid Conformation
• Protein Binding
• Receptors, Glucocorticoid/physiology
• Response Elements
• Transcriptional Activation

• ZIA BC005450-29 Intramural NIH HHS

NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A–H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes.

In eukaryotes DNA is hierarchically packaged into chromatin by histones. The fundamental subunit of chromatin is the nucleosome. The packaging of DNA into nucleosomes not only restricts DNA accessibility for regulatory proteins but also provides opportunities to regulate DNA based processes. Accessibility of transcription factor NF-κB to their recognition sequences embedded in nucleosomes is highly controversial. On one hand in vivo studies have suggested that packaging of DNA into chromatin plays an important role in regulating the expression of NF-κB dependent genes, and on the other hand some in vitro studies reported that NF-κB can bind by itself to its recognition sequences embedded in the nucleosome. In this study, we show that NF-κB can specifically bind to its recognition sequences placed at the end of the nucleosome but not when placed inside the nucleosome core. We then demonstrate that disruption of nucleosome is necessary for the productive binding of NF-κB. Finally, we show that the presence of histone H1 does not affect the specific binding of NF-κB to its cognate sequence, when its binding region overlaps with the binding site of NF-κB. We propose that histone eviction is needed for NF-κB to bind specifically to its recognition sequence embedded in the nucleosome.

• Animals
• Binding Sites
• Chromatin/genetics
• Chromatin/ultrastructure
• DNA-Binding Proteins/genetics
• Dimerization
• Histones/genetics
• Histones/metabolism
• Mi-2 Nucleosome Remodeling and Deacetylase Complex
• NF-kappa B/genetics
• NF-kappa B/metabolism
• Nucleosomes/genetics
• Nucleosomes/metabolism
• Protein Binding
• Protein Biosynthesis
• Ultraviolet Rays
• Xenopus/genetics

Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.

Cellular transcription factors (TFs) are proteins that regulate gene expression, and thereby cellular activity and fate, by binding to specific DNA segments. The physicochemical determinants of protein-DNA binding specificity are not completely understood. Here, we report that the propensity of transient opening and re-closing of the double helix, resulting from thermal fluctuations, aka “DNA breathing” or “DNA bubbles,” can be associated with binding affinity in the case of Fis, a well-studied nucleoid-associated protein in Escherichia coli. We found that a particular breathing profile is characteristic of high-affinity Fis binding sites and that DNA fragments known to bind Fis in vivo are statistically enriched for this profile. Furthermore, we used simulations of DNA breathing dynamics to guide design of gel-shift experiments aimed at testing the idea that local breathing influences Fis binding. As a result, we show that via nucleotide modifications but without modifying nucleotides that directly contact Fis, we were able to transform a low-affinity Fis binding site into a high-affinity site and vice versa. The nucleotide modifications were designed only based on DNA breathing simulations. Our study suggests that strong Fis-DNA binding depends on DNA breathing - a novel physicochemical characteristic that could be used for prediction and rational design of TF binding sites.

• Binding Sites
• DNA/metabolism
• DNA-Binding Proteins/metabolism
• Escherichia coli Proteins/metabolism
• Models, Molecular
• Protein Binding

• R01 HL062458 NHLBI NIH HHS

High mobility group protein 1 (HMGB1) interacts with DNA and chromatin to influence the regulation of transcription, DNA repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, ATP-independent manner. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N′ and N″) remain stable and exhibit characteristics distinctly different from the canonical nucleosome. These findings complement previous studies that showed (i) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (ii) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that one aspect of the mechanism of HMGB1 action involves a restructuring of the nucleosome that appears to relax structural constraints within the nucleosome.

• chromatin remodeling
• dna methylation
• dnase i hypersensitivity
• enhancer
• histone modifications
• nuclear receptors
• nucleosome positioning
• promoter

• Animals
• Chromatin/physiology
• Chromatin/ultrastructure
• Gene Expression Regulation
• Humans
• Receptors, Cytoplasmic and Nuclear/physiology

• Z01 BC005450 Intramural NIH HHS

• Animals
• Chromatin/physiology
• Chromatin/ultrastructure
• Deoxyribonuclease I/chemistry
• Deoxyribonuclease I/metabolism
• Humans
• Transcriptional Activation

• BB/E023002/1 Biotechnology and Biological Sciences Research Council

• Animals
• Binding Sites
• CREB-Binding Protein/analysis
• Chromobox Protein Homolog 5
• Chromosomal Proteins, Non-Histone/analysis
• DNA/chemistry
• DNA/genetics
• DNA/metabolism
• E1A-Associated p300 Protein/analysis
• Hepatocytes/chemistry
• Mice
• Nucleosomes/chemistry
• Nucleosomes/metabolism
• Transcription Initiation Site

• P01 DK049210 NIDDK NIH HHS
• P30 DK019525 NIDDK NIH HHS
• P01-DK049210 NIDDK NIH HHS
• P30DK19525 NIDDK NIH HHS

• Base Pairing
• Chromosomes/chemistry
• DNA/chemistry
• Models, Molecular
• Polymers/chemistry

• Animals
• Cell Line
• Chromatin/classification
• Chromatin/metabolism
• DNA-Binding Proteins/analysis
• DNA-Binding Proteins/metabolism
• Drosophila Proteins/analysis
• Drosophila Proteins/metabolism
• Drosophila melanogaster/genetics
• Drosophila melanogaster/metabolism
• Euchromatin/metabolism
• Heterochromatin/metabolism
• Histones/metabolism
• Principal Component Analysis

• T32 GM082797 NIGMS NIH HHS
• R01 HG003008 NHGRI NIH HHS
• T32GM082797 NIGMS NIH HHS
• U54CA121852 NCI NIH HHS
• R01HG003008 NHGRI NIH HHS
• U54 CA121852 NCI NIH HHS
• T32 GM008798 NIGMS NIH HHS

• inflammation
• lung
• signal transduction
• smooth muscle
• transcription coactivators

• Blotting, Western
• CREB-Binding Protein/genetics
• CREB-Binding Protein/metabolism
• Cell Survival/drug effects
• Cell Survival/genetics
• Cells, Cultured
• Chemokine CXCL10/genetics
• Chemokine CXCL10/metabolism
• Chromatin Immunoprecipitation
• Humans
• Interferon-gamma/pharmacology
• Myocytes, Smooth Muscle/drug effects
• Myocytes, Smooth Muscle/metabolism
• NF-kappa B/genetics
• NF-kappa B/metabolism
• Phosphorylation/drug effects
• Protein Binding/drug effects
• Protein Binding/genetics
• RNA Polymerase II/metabolism
• Reverse Transcriptase Polymerase Chain Reaction
• STAT1 Transcription Factor/genetics
• STAT1 Transcription Factor/metabolism
• Tumor Necrosis Factor-alpha/pharmacology

• BB/E52708X/1 Biotechnology and Biological Sciences Research Council

• nucleosome
• nucleosome positioning
• dna bending
• dna sequence patterns
• dna kinks

• Arginine/metabolism
• Base Sequence
• DNA/chemistry
• DNA/genetics
• DNA/metabolism
• Histones/chemistry
• Histones/metabolism
• Models, Molecular
• Molecular Sequence Data
• Nucleic Acid Conformation
• Nucleosomes/chemistry
• Nucleosomes/genetics
• Nucleosomes/metabolism
• Pliability
• Protein Binding
• Thermodynamics

• Z01 BC010844 Intramural NIH HHS

• Animals
• Cell Lineage
• Chromatin/metabolism
• Chromatin/ultrastructure
• Embryo Implantation
• Embryo, Mammalian/cytology
• Female
• Germ Layers/cytology
• Germ Layers/metabolism
• Germ Layers/ultrastructure
• Mice
• Mice, Inbred C57BL
• Nuclear Envelope/metabolism
• Nuclear Envelope/ultrastructure
• Pluripotent Stem Cells/cytology
• Pluripotent Stem Cells/metabolism

• FRN14311 Canadian Institutes of Health Research
• MOP77803 Canadian Institutes of Health Research

• Binding Sites
• Enhancer Elements, Genetic
• Hepatocyte Nuclear Factor 3-alpha/genetics
• Homeodomain Proteins/genetics
• Humans
• Male
• Models, Genetic
• Molecular Sequence Data
• Nucleosomes/physiology
• Octamer Transcription Factor-1/genetics
• Prostatic Neoplasms/genetics
• Receptors, Androgen/genetics
• Transcription Factors/genetics

• P50 CA090381 NCI NIH HHS
• R01 HG004069 NHGRI NIH HHS
• 1R01 HG004069-02 NHGRI NIH HHS
• 2P50 CA090381-06 NCI NIH HHS

Transcription from the mouse mammary tumor virus (MMTV) promoter can be induced by progestins. The progesterone receptor (PR) binds to a cluster of five hormone responsive elements (HREs) and activates the promoter by synergistic interactions with the ubiquitous transcription factor, nuclear factor 1 (NF1). Progesterone treatment of cells in culture leads to activation of the Src/Ras/Erk/Msk1 cascade. Selective inhibition of Erk, or its target kinase Msk1, interferes with chromatin remodeling and blocks MMTV activation. A complex of activated PR, Erk and Msk1 is recruited to promoter after 5 min of hormone treatment and phosphorylates histone H3 at serine 10. This modification promotes the displacement of HP1γ and subsequent chromatin remodeling. Progestin treatment leads to the recruitment of the BAF complex, which selectively displaces histones H2A and H2B from the nucleosome containing the HREs. The acetyltransferase PCAF is also required for induction of progesterone target genes and acetylates histone H3 at K14, an epigenetic mark, which interacts with Brg1 and Brm, anchoring the BAF complex to chromatin. In nucleosomes assembled on either MMTV or mouse rDNA promoter sequences, SWI/SNF displaces histones H2A and H2B from MMTV, but not from the rDNA nucleosome. Thus, the outcome of nucleosome remodeling by purified SWI/SNF depends on DNA sequence. The resultant H3/H4 tetramer particle is then the substrate for subsequent events in induction. Thus, initial activation of the MMTV promoter requires activation of several kinases and PCAF leading to phosphoacetylation of H3, and recruitment of BAF with subsequent removal of H2A/H2B.

Distinct developmental fates in Drosophila melanogaster are specified by quantitative differences in transcription factor occupancy on a common set of bound regions.

We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional.

Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors.

It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.