Asymmetric binding of histone H1 stabilizes MMTV nucleosomes and the interaction of progesterone receptor with the exposed HRE

Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation

Steroid receptors were classically described for regulating transcription by binding to target gene promoters. However, genome-wide studies reveal that steroid receptors-binding sites are mainly located at intragenic regions. To determine the role of these sites, we examined the effect of progestins on the transcription of the bcl-x gene, where only intragenic progesterone receptor-binding sites (PRbs) were identified. We found that in response to hormone treatment, the PR is recruited to these sites along with two histone acetyltransferases CREB-binding protein (CBP) and GCN5, leading to an increase in histone H3 and H4 acetylation and to the binding of the SWI/SNF complex. Concomitant, a more relaxed chromatin was detected along bcl-x gene mainly in the regions surrounding the intragenic PRbs. PR also mediated the recruitment of the positive elongation factor pTEFb, favoring RNA polymerase II (Pol II) elongation activity. Together these events promoted the re-distribution of the active Pol II toward the 3′-end of the gene and a decrease in the ratio between proximal and distal transcription. These results suggest a novel mechanism by which PR regulates gene expression by facilitating the proper passage of the polymerase along hormone-dependent genes.

Minireview: role of kinases and chromatin remodeling in progesterone signaling to chromatin

Steroid hormones regulate gene expression by interaction of their receptors with hormone-responsive elements on DNA or with other transcription factors, but they can also activate cytoplasmic signaling cascades. Rapid activation of Erk by progestins via an interaction of the progesterone receptor (PR) with the estrogen receptor is critical for transcriptional activation of the mouse mammary tumor virus (MMTV) promoter and other progesterone target genes. Erk activation leads to the phosphorylation of PR, activation of mitogen- and stress-activated protein kinase 1, and the recruitment of a complex of the three activated proteins and of P300/CBP-associated factor (PCAF) to a single nucleosome, resulting in the phosphoacetylation of histone H3 and the displacement of heterochromatin protein 1γ. Hormone-dependent gene expression requires ATP-dependent chromatin remodeling complexes. Two switch/sucrose nonfermentable-like complexes, Brahma-related gene 1-associated factor (BAF) and polybromo-BAF are present in breast cancer cells, but only BAF is recruited to the MMTV promoter and cooperates with PCAF during activation of hormone-responsive promoters. PCAF acetylates histone H3 at K14, an epigenetic mark recognized by BAF subunits, thus anchoring the complex to chromatin. BAF catalyzes localized displacement of histones H2A and H2B, facilitating access of nuclear factor 1 and additional PR complexes to the hidden hormone-responsive elements on the MMTV promoter. The linker histone H1 is a structural component of chromatin generally regarded as a general repressor of transcription. However, it contributes to a better regulation of the MMTV promoter by favoring a more homogeneous nucleosome positioning, thus reducing basal transcription and actually enhancing hormone induced transcription. During transcriptional activation, H1 is phosphorylated and displaced from the promoter. The kinase cyclin-dependent kinase 2 is activated after progesterone treatment and could catalyze progesterone-induced phosphorylation of histone H1 by chromatin remodeling complexes. The initial steps of gene induction by progestins involve changes in the chromatin organization of target promoters that require the activation of several kinase signaling pathways initiated by membrane anchored PR. Because these pathways also respond to other external signals, they serve to integrate the hormonal response in the global context of the cellular environment.

Nuclear factor 1 synergizes with progesterone receptor on the mouse mammary tumor virus promoter wrapped around a histone H3/H4 tetramer by facilitating access to the central hormone-responsive elements

Steroid hormones induce transcription of their responsive genes by complex mechanisms including synergism between the hormone receptors and other transcription factors. On the mouse mammary tumor virus (MMTV) promoter progesterone induction is mediated by the reciprocal synergism between progesterone receptor (PR) and the ubiquitous transcription factor nuclear factor 1 (NF1). PR binding mediates ATP-dependent displacement of histone H2A and H2B, enabling NF1 access to its target site. In minichromosomes assembled in vitro NF1 binding facilitates access of PR to the hormone-responsive elements (HREs) by precluding reforming of the histone octamer, but the function of NF1 in living cells remains unclear. Here we show that depleting NF1 by small interfering RNAs or mutating the NF1-binding site significantly compromises transcription of the MMTV promoter. The central HREs 2 and 3 are not needed for ATP-dependent H2A/H2B displacement or NF1 binding but are critical for full PR binding and MMTV transactivation. We found that NF1 binding to the MMTV promoter on a H3/H4 histone tetramer particle exposes the central HREs and facilitates their binding by PR, suggesting a possible mechanism for the reciprocal synergism between PR and NF1.

Erk signaling and chromatin remodeling in MMTV promoter activation by progestins

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.

Depletion of human histone H1 variants uncovers specific roles in gene expression and cell growth

At least six histone H1 variants exist in somatic mammalian cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be actively involved in the regulation of gene expression. However, it is not well known whether the different variants have distinct roles or if they regulate specific promoters. We have explored this by inducible shRNA-mediated knock-down of each of the H1 variants in a human breast cancer cell line. Rapid inhibition of each H1 variant was not compensated for by changes of expression of other variants. Microarray experiments have shown a different subset of genes to be altered in each H1 knock-down. Interestingly, H1.2 depletion caused specific effects such as a cell cycle G1-phase arrest, the repressed expression of a number of cell cycle genes, and decreased global nucleosome spacing. On its side, H1.4 depletion caused cell death in T47D cells, providing the first evidence of the essential role of an H1 variant for survival in a human cell type. Thus, specific phenotypes are observed in breast cancer cells depleted of individual histone H1 variants, supporting the theory that distinct roles exist for the linker histone variants.

Eukaryotic DNA is packaged into chromatin through its association with histone proteins. The linker histone H1 sits at the base of the nucleosome near the DNA entry and exit sites to stabilize two full turns of DNA. In particular, histone H1 participates in nucleosome spacing and formation of the higher-order chromatin structure. In addition, H1 seems to be actively involved in the regulation of gene expression. Histone H1 in mammals is a family of closely related, single-gene encoded proteins, including five somatic subtypes (from H1.1 to H1.5) and a terminally differentiated expressed isoform (H1.0). It is not well known whether the different variants have distinct roles or if they regulate specific promoters. We have explored this by inducible knock-down of each of the H1 variants in breast cancer cells. A different subset of genes is altered in each H1 knock-down, and depletion has different effects on cell survival. Interestingly, H1.2 and H1.4 depletion specifically caused arrest of cell proliferation. Concomitant with this, H1.2 depletion caused decreased global nucleosome spacing and repressed expression of a number of cell cycle genes. Thus, specific phenotypes are observed in breast cancer cells depleted of individual histone H1 variants.

Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement

Yeast SWI/SNF is a multisubunit, 1.14-MDa ATP-dependent chromatin-remodeling enzyme required for transcription of a subset of inducible genes. Biochemical studies have demonstrated that SWI/SNF uses the energy from ATP hydrolysis to generate superhelical torsion, mobilize mononucleosomes, enhance the accessibility of nucleosomal DNA and remove H2A-H2B dimers from mononucleosomes. Here we describe the ATP-dependent activities of a SWI/SNF sub complex that is composed of only three subunits, Swi2p, Arp7p and Arp9p. Whereas this sub complex is fully functional in most remodeling assays, Swi2p-Arp7p-Arp9p is defective for ATP-dependent removal of H2A-H2B dimers. We identify the acidic N terminus of the Swi3p subunit as a novel H2A-H2B-binding domain required for ATP-dependent dimer loss. Our data indicate that H2A-H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, and furthermore they suggest that SWI/SNF is composed of at least four interdependent modules.

Chromatin Remodeling and Control of Cell Proliferation by Progestins via Cross Talk of Progesterone Receptor with the Estrogen Receptors and Kinase Signaling Pathways

Transcription from the mouse mammary tumor virus (MMTV) promoter can be induced by glucocorticoids or progestins. Progesterone treatment of cultured cells carrying an integrated single copy of an MMTV transgene leads to recruitment of progesterone receptor (PR), SWI/SNF, and SNF2h-related complexes to MMTV promoter. Recruitment is accompanied by selective displacement of histones H2A and H2B from the nucleosome B. In nucleosomes assembled on promoter sequences, SWI/SNF displaces histones H2A and H2B from MMTV nucleosome B, but not from other MMTV nucleosomes or from an rDNA promoter nucleosome. Thus, the outcome of nucleosome remodeling by purified SWI/SNF depends on the DNA sequence. On the other hand, 5 min after hormone treatment, the cytoplasmic signaling cascade Src/Ras/Erk is activated via an interaction of PR with the estrogen receptor, which activates Src. As a consequence of Erk activation PR is phosphorylated, Msk1 is activated, and a ternary complex PR-Erk-Msk1 is recruited to MMTV nucleosome B. Msk1 phosphorylates H3 at serine 10, which is followed by acetylation at lysine 14, displacement of HP1gamma, and recruitment of Brg1, PCAF, and RNA polymerase II. Blocking Erk activation or Msk1 activity prevents induction of the MMTV transgene. Thus, the rapid nongenomic effects of progestins are essential for their transcriptional effects on certain progestin target genes. In rat endometrial stromal cells, picomolar concentrations of progestins trigger the cross talk of PR with ERbeta that activates the Erk and Akt kinase pathways leading to cell proliferation in the absence of direct transcriptional effects of the ligand-activated PR. Thus, depending on the cellular context rapid kinase activation and transcriptional effect play different roles in the physiological response to progestins.

The dynamics of chromatin remodeling at promoters

The nucleosome, the structural unit of chromatin, is known to play a central role in regulating gene transcription from promoters. The last seven years have spawned a vast amount of data on the enzymes that remodel and modify nucleosomes and the rules governing how transcription factors interact with the epigenetic code on histones. Yet despite this effort, there has yet to emerge a unifying mechanism by which nucleosomes are remodeled during gene regulation. Recent advances have allowed nucleosome dynamics on promoters to be studied in real time, dramatically changing how we think about gene regulation on chromatin templates.

DNA instructed displacement of histones H2A and H2B at an inducible promoter

Regulation of gene expression requires dynamic changes in chromatin, but the nature of these changes is not well understood. Here, we show that progesterone treatment of cultured cells leads to recruitment of progesterone receptor (PR) and SWI/SNF-related complexes to Mouse Mammary Tumor Virus (MMTV) promoter, accompanied by displacement of histones H2A and H2B from the nucleosome containing the receptor binding sites, but not from adjacent nucleosomes. PR recruits SWI/SNF to MMTV nucleosomes in vitro and facilitates synergistic binding of receptors and nuclear factor 1 to the promoter. In nucleosomes assembled on MMTV or mouse rDNA promoter sequences, SWI/SNF catalyzes ATP-dependent sliding of the histone octamer followed only on the MMTV promoter by displacement of histones H2A and H2B. In MMTV nucleosome arrays, SWI/SNF displaces H2A and H2B from nucleosome B and not from the adjacent nucleosome. Thus, the outcome of nucleosome remodeling by SWI/SNF depends on DNA sequence.

Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract

We describe a cell-free chromatin assembly system derived from the yeast Saccharomyces cerevisiae, which efficiently packages DNA into minichromosomes in a reaction dependent on exogenous core histones and an ATP-regenerating system. Both supercoiled and relaxed plasmid DNA serve as templates for nucleosomal loading in a gradual process that takes at least 6 h for completion at 30 degrees C. Micrococcal nuclease digestion of the assembled minichromosomes displays an extended nucleosomal ladder with a repeat length of 165 bp. The purified minichromosomes contain the four core histones in stoichiometric proportion and exhibit phased nucleosomes over the mouse mammary tumour virus (MMTV) promoter. The progesterone receptor and NF1 synergize on these minichromosomes resulting in efficient cell-free transcription. The ease of manipulation and the potential use of yeast strains carrying mutations in the chromatin handling machinery make this system suitable for detailed mechanistic studies.

Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin

Histone H1 and the high-mobility group (HMG) proteins are chromatin binding proteins that regulate gene expression by modulating the compactness of the chromatin fiber and affecting the ability of regulatory factors to access their nucleosomal targets. Histone H1 stabilizes the higher-order chromatin structure and decreases nucleosomal access, while the HMG proteins decrease the compactness of the chromatin fiber and enhance the accessibility of chromatin targets to regulatory factors. Here we show that in living cells, each of the three families of HMG proteins weakens the binding of H1 to nucleosomes by dynamically competing for chromatin binding sites. The HMG families weaken H1 binding synergistically and do not compete among each other, suggesting that they affect distinct H1 binding sites. We suggest that a network of dynamic and competitive interactions involving HMG proteins and H1, and perhaps other structural proteins, constantly modulates nucleosome accessibility and the local structure of the chromatin fiber.

Linker Histone H1 Modulates Nucleosome Remodeling by Human SWI/SNF

Chromatin, a combination of nucleosomes and linker histones, inhibits transcription by blocking polymerase movement and access of factors to DNA. ATP-dependent remodeling complexes such as SWI/SNF and RSC alter chromatin structure to increase or decrease this repression. To further our understanding of how human SWI/SNF (hSWI/SNF) "remodels" chromatin we examined the octamer location, nature, and template specificity of hSWI/SNF-remodeled mononucleosomes when free or bound by linker histone H1. We find that, in the absence of H1, hSWI/SNF consistently moves nucleosomes to DNA ends, regardless of template sequence. On some sequences the repositioned histone octamer appears to be moved approximately 45 bp off the DNA edge, whereas on others it appears to be normal, suggesting that the nature of the remodeled nucleosome can be influenced by DNA sequence. By contrast, in the presence of histone H1, hSWI/SNF slides octamers to more central positions and does not promote nucleosome movement off the ends of the DNA. Our results indicate that the nature and position of hSWI/SNF products may be influenced both by DNA sequence and linker histone, and shed light on the roles of H1 and hSWI/SNF in modulating chromatin structure.

Histone H1 and the dynamic regulation of chromatin function

Eukaryotic DNA is organized in a complex structure called chromatin. Although a primary function of chromatin is compaction of DNA, this must done such that the underlying DNA is potentially accessible to factor-mediated regulatory responses. Chromatin structure clearly plays a dominant role in regulating much of eukaryotic transcription. The demonstration that reversible covalent modification of the core histones contribute to transcriptional activation and repression by altering chromatin structure and the identification of numerous ATP-dependent chromatin remodeling enzymes provide strong support for this view. Chromatin is much more dynamic than was previously thought and regulation of the dynamic properties of chromatin is a key aspect of gene regulation. This review will focus on recent attempts to elucidate the specific contribution of histone H1 to chromatin-mediated regulation of gene expression.

Histone H1 enhances synergistic activation of the MMTV promoter in chromatin

Minichromosomes assembled on the mouse mammary tumor virus (MMTV) promoter in vitro exhibit positioned nucleosomes, one of which covers the binding sites for progesterone receptor (PR) and nuclear factor 1 (NF1). Incorporation of histone H1 into MMTV minichromosomes improves the stability of this nucleosome and decreases basal transcription from the MMTV promoter, as well as its response to either PR or NF1. However, histone H1-containing minichromosomes display better PR binding and support a more efficient synergism between PR and NF1, leading to enhanced transcription initiation. A mutant MMTV promoter lacking positioned nucleosomes does not display enhanced transcriptional synergism in the presence of H1. Binding of PR leads to phosphorylation of H1, which leaves the promoter upon transcription initiation. Thus, H1 assumes a complex and dynamic role in the regulation of the MMTV promoter.

Complex role of histone H1 in transactivation of MMTV promoter chromatin by progesterone receptor

Transcription from the mouse mammary tumor virus (MMTV) promoter can be induced by glucocorticoids or progestins. The corresponding receptors bind to a cluster of hormone responsive elements (HREs) and activate the promoter by synergistic interactions with ubiquitous transcription factors, in particular nuclear factor 1 (NF1). Synergism between hormone receptors and NF1 depends on the precise positioning of the promoter sequences on the surface of a histone octamer in chromatin, but how linker histones participate in the process is unclear. Asymmetric binding of histone H1 to chromatin organized MMTV promoter sequences compacts the nucleosomal structure and leads to repression of basal transcription and to reduced binding of NF1. In contrast, H1 containing MMTV chromatin binds PR with higher affinity and is transcribed more efficiently in the presence of PR and NF1 than chromatin free of linker histone. Thus histone H1 represses hormone independent transcription and enhances the synergism between PR and NF1 resulting in tighter hormonal regulation. This positive effect of H1 is likely due to a better defined nucleosome positioning over the MMTV promoter. Upon binding of PR to the promoter chromatin a hitherto unidentified kinase is recruited or activated that phosphorylates H1. This is not sufficient for transcriptional activation but is likely a requisite for the action of ATP-dependent chromatin remodelling complexes. Following remodelling and in the presence of NF1, which maintains the open nucleosome conformation, additional PR molecules bind, transactivation takes place and H1 is displaced from the promoter during transcription initiation. Therefore, H1 plays a key role during the initial hormonal activation of the MMTV promoter in native chromatin, which includes recruitment by PR of a histone H1 kinase and an ATP-dependent chromatin remodelling complex, followed by NF1 binding, increased PR binding, transcription initiation and H1 displacement.