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Pharmacological reactivation of inactive genes: the fragile X experience.

The present review on the pharmacological reactivation of inactive genes focuses on our experience with the fragile X syndrome. The fragile X syndrome of mental retardation is the prototype of a series of inherited neurological disorders caused by abnormal expansion of repeated trinucleotide sequences embedded in various genes. In a number of these disorders, such as Huntington disease and several forms of spinocerebellar ataxias, the expanded CAG repeat is translated, resulting in a polyglutamine-containing protein that indirectly causes neurodegeneration. On the contrary, in the fragile X syndrome, the expanded CGG repeat is contained in the regulatory region of the FMR1 gene and causes transcriptional inactivation. The mutation spares the coding region of the FMR1 gene, which potentially would allow synthesis of a normal protein if transcription could be restored. This prompted us to try and reactivate the gene function with different pharmacological regimens. We discuss our successful results with DNA demethylating and histone hyperacetylating drugs and their implications for future treatments of the fragile X syndrome.

Antineoplastic Agents↗

Targeted disruption of Kaposi's sarcoma-associated herpesvirus ORF57 in the viral genome is detrimental for the expression of ORF59, K8alpha, and K8.1 and the production of infectious virus.

Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 regulates viral gene expression at the posttranscriptional level during viral lytic infection. To study its function in the context of the viral genome, we disrupted KSHV ORF57 in the KSHV genome by transposon-based mutagenesis. The insertion of the transposon into the ORF57 exon 2 region also interrupted the 3' untranslated region of KSHV ORF56, which overlaps with the ORF57 coding region. The disrupted viral genome, Bac36-Delta57, did not express ORF57, ORF59, K8alpha, K8.1, or a higher level of polyadenylated nuclear RNA after butyrate induction and could not be induced to produce infectious viruses in the presence of valproic acid, a histone deacetylase inhibitor and a novel KSHV lytic cycle inducer. The ectopic expression of ORF57 partially complemented the replication deficiency of the disrupted KSHV genome and the expression of the lytic gene ORF59. The induced production of infectious virus particles from the disrupted KSHV genome was also substantially restored by the simultaneous expression of both ORF57 and ORF56; complementation by ORF57 alone only partially restored the production of virus, and expression of ORF56 alone showed no effect. Altogether, our data indicate that in the context of the viral genome, KSHV ORF57 is essential for ORF59, K8alpha, and K8.1 expression and infectious virus production.

Cell Line↗

DNA methylation in plants.

DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.

Adenine↗

The TE promoter element of the histone H1t gene is essential for transcription in transgenic mouse primary spermatocytes.

Transcriptional activation of the testis-specific histone H1t gene occurs in pachytene primary spermatocytes during spermatogenesis. Specific binding of testis nuclear proteins to a rat histone H1t promoter sequence, designated the H1t/TE element, correlates with the onset of transcription. This element, located between the H1t/AC box and the H1t/CCAAT box, contains inverted repeats of a shorter element. When the native rat H1t gene along with flanking sequences, including 2453 base pairs (bp) upstream and 3784 bp downstream from the coding region, was microinjected into mouse embryos, the offspring of the resulting transgenic mice transcribed the transgene in a tissue-specific manner and only in primary spermatocytes. In the present study the TE promoter element was deleted and replaced with a heterologous stuffer DNA fragment. When the mutant rat DNA fragment was used to create transgenic mice, offspring of the mice bearing the promoter mutation did not transcribe the rat H1t gene in any tissue. On the other hand, transcription of the rat H4t transgene, which is located approximately 1.5 kilobases downstream from the H1t gene, occurred in these animals. Therefore, these studies support the hypothesis that the TE element is essential for enhanced testis-specific transcription of the H1t gene in primary spermatocytes.

Animals↗

Diverse roles for histone H2A modifications in DNA damage response pathways in yeast.

There are many types of DNA damage that are repaired by a multiplicity of different repair pathways. All damage and repair occur in the context of chromatin, and histone modifications are involved in many repair processes. We have analyzed the roles of H2A and its modifications in repair by mutagenizing modifiable residues in the N- and C-terminal tails of yeast H2A and by testing strains containing these mutations in multiple DNA repair assays. We show that residues in both tails are important for homologous recombination and nonhomologous end-joining pathways of double-strand break repair, as well as for survival of UV irradiation and oxidative damage. We show that H2A serine 122 is important for repair and/or survival in each of these assays. We also observe a complex pattern of H2A phosphorylation at residues S122, T126, and S129 in response to different damage conditions. We find that overlapping but nonidentical groups of H2A residues in both tails are involved in different pathways of repair. These data suggest the presence of a set of H2A "damage codes" in which distinct patterns of modifications on both tails of H2A may be used to identify specific types of damage or to promote specific repair pathways.

Amino Acid Sequence↗

The rat histone H1d gene has intragenic activating sequences that are absent from the testis-specific variant H1t.

In some cases core histone genes in the mouse depend on intragenic sequence elements for high level expression [Gene 176 (1996) 1]. Here we report that the highly expressed gene for rat linker histone H1d also contains an intragenic activating region (IAR). Using transient transfection assays in mouse fibroblast NIH3T3 cells, we showed that rat H1d contains a downstream region (+21 to +116) that imparts a two- to threefold up-regulation of fused reporters. This region also activated expression when moved to the promoter region, though the effect was dependent on its distance from other promoter elements. The IAR contains sequence homologies to the core alpha and Omega elements identified as functional protein binding sites within the mouse H3.2 coding region activating sequence (CRAS). A pair of Omega elements (+32 and +66) accounts for the activating effect of the H1d intragenic region as shown by targeted mutations as well as stepwise deletions. The H1d and H3.2 Omega sequences bound similar and perhaps identical proteins by gel shift analysis. The H1d alpha-like sequence at +56 overlaps the translational start codon and was therefore not mutated. Like the mouse H3.2 alpha element, it bound transcription factor YY1 in gel shift assays. H1t, the gene for the testis-specific linker histone, did not demonstrate an IAR. While H1t has a similar alpha sequence and did bind YY1, it lacks the Omega homologies of H1d. Sequence comparison shows that the YY1/alpha site as well as the adjacent Omega site are likely present in genes for other standard H1 variants, but that the +32 Omega site in the 5' untranslated region (UTR) of H1d is unique. We conclude that the +32 and +66 Omega sequences of the rat H1d gene contribute significantly to its high-level expression.

3T3 Cells↗

Identification of human satellite DNA sequences associated with chemically resistant nonhistone polypeptide adducts.

A fraction of DNA fragments of highly purified and completely unfolded eukaryotic DNA inevitably remains associated with chemically resistant nonhistone DNA-polypeptide complexes. This fraction can be isolated by nitrocellulose filtration because the polypeptide-associated DNA fragments are retained on nitrocellulose filters while bulk DNA passes through the filters. The fraction of AluI-fragmented DNA from human placenta retained on filters as a result of the binding factors (R-DNA, approximately 12%) represents a subset of genomic sequences with a sequence complexity different from unfractionated DNA and DNA recovered in the filtrate (F-DNA). DNA sequences prevalent in the retained fraction were detected by differential plaque hybridization of a recombinant lambda gt10 library with radiolabeled F- and R-DNA fractions. Several recombinant phages showing much stronger hybridization signals with the R-DNA probe than with the F-DNA probe were selected, plaque-purified and analyzed. Analysis of the inserts of such clones showed that repetitive DNA sequences of the alphoid dimeric and tetrameric family, satellite III and satellite III-like sequences are highly enriched in the retained fraction, which indicates that these sequences specifically attract the polypeptides involved in the tightly bound and resistant complexes. This property of repetitive sequences is of interest since tandemly repetitive sequences have been suggested to code for locus-specific fixation and stabilization of the chromatin fiber in the cell nucleus.

Bacteriophage lambda↗

The regulation of expression of histocompatibility antigens on the cell surface; molecular genetic basis.

Histocompatibility antigens play a fundamental role in the immune functions by their polymorphic capture structure for binding exogenous and endogenous peptides and presenting them to the appropriate T and B cell receptors. The genetic background of the control of synthesis of the histocompatibility antigens is very complex including several loci controlling the wide polymorphic variation of class I and class II histocompatibility molecules and their regulation of expression. Most significant variability in the presence or absence of histocompatibility antigens could be observed during development, differentiation, and activation. The tissue-specific expression is influenced by pathological events such as malignant transformation, viral infection and genetic defectiveness as well. The research in the field of molecular genetics of the MHC in the last decade revealed, upstream of the coding genes of class I and class II molecules, a very complex regulatory machinery including a series of genes termed enhancer and promoter region. At the DNA level, various gene boxes and regulatory elements were discovered, which are activated by the binding of the appropriate histone proteins, cytokines or hormones responsible for the upregulation and downregulation of histocompatibility antigen expression. Regulation is mainly functioning at the transcriptional level, but other factors such as viral proteins, oncogenes, biomolecules, and physical effects take part, either indirectly or directly affecting the regulatory genes and DNA binding proteins. The increasing knowledge about the regulatory machinery may lead to the introduction of genetic manipulation, either experimental or clinical, with the aim of changing the expression of histocompatibility molecules on the cell surface in order to achieve normal or demanded immune functions.

Animals↗

Control of splicing efficiency by the mouse histone H2a element in a murine leukemia virus-based retroviral vector.

While using various human complementary DNA (cDNA) sequences in the context of the murine leukemia virus (MLV)-based retroviral vector, it was found that a retroviral vector containing some human cDNA sequences produces unusually low viral titer. One of those sequences is that for the human IL-1 receptor antagonist protein (IL1RN). The RNA analysis showed that a cryptic splice acceptor sequence is present in the middle of its coding region, resulting in the deletion of the packaging signal sequence and the removal of some coding sequences that lead to low viral titer and a low level of the transgene product. We tested whether the mouse Hist2h2aa1 element (mH2aE), previously shown to suppress the splicing function, could inhibit the cryptic splicing in the context of MLV-based retroviral vectors. It was found that the mH2aE could efficiently suppress such unwanted splicing event, thus increasing the amount of unspliced transcript, which eventually led to the increase in the level of IL1RN expression and viral titer. The mH2aE could also be used to control unusually high splicing activity. Our data suggested that the mH2aE could be used for the fine-tuning of the splicing process, thus improving the level of gene expression and viral titer in the context of retroviral vectors.

Base Sequence↗

Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene.

We have observed changes in the chromatin structure of a human histone gene promoter that may be functionally related to variations in transcription during the cell cycle. A detailed analysis of the chromatin structure of a cell cycle-dependent human H4 histone gene and its flanking sequences was performed using DNase I, S1 nuclease, and restriction endonucleases. This gene was previously shown to have a DNase I- and S1-sensitive site for which the boundaries varied with the cell cycle, and we have now precisely mapped these modifications. During S phase, the entire coding region of this gene and the 5'-flanking region up to approximately -600 base pairs are sensitive to both DNase I and S1, while during mitosis/G1, accessibility to these enzymes is greatly decreased in regions from -250 to -600 base pairs and downstream of +100 base pairs. DNase I- and S1-hypersensitive sites in the proximal promoter region (which contains two sites of protein-DNA interaction as well as sequence elements necessary for the correct initiation of transcription) are present throughout the cell cycle, as is an additional site sensitive to both DNase I and S1, located at -700 to -800 base pairs. Restriction enzyme analysis confirmed the general openness of the promoter region and relative insensitivity of the 3'-flanking region, while salt wash experiments indicated several discrete sites in the promoter that are candidates for regulatory interactions. The chromatin structure of the proximal promoter region of this H4 gene is different during early S phase when it is maximally transcribed, as indicated by the ability of a high salt wash to render this region inaccessible to the restriction enzyme MspI only at this time of the cell cycle.

Cell Cycle↗

Informational content of the echinoderm egg.

The sea urchin egg contains a store of mRNA synthesized during oogenesis but translated only after fertilization, which accounts for a large, rapid increase in the rate of synthesis of largely the same set of proteins synthesized by eggs. Starfish oocytes contain a population of stored maternal mRNA that becomes actively translated upon GVBD and codes for a set of proteins distinct from that synthesized by oocytes. The sequence complexity of RNA in echinoderm eggs is about 3.5 x 10(8) nucleotides, enough to code for about 12,000 different mRNAs averaging 3 kb in length. About 2-4% of the egg RNA functions as mRNA during early embryonic development; most of the sequences are rare, represented in a few thousand copies per egg, but some are considerably more abundant. Many of the stored RNA sequences accumulate during the period of vitellogenesis, which lasts a few weeks. The mechanisms of storage and translational activation of maternal mRNA are not well understood. Histone mRNAs are sequested in the egg pronucleus until first cleavage, but other mRNAs are widely distributed in the cytoplasm. The population of maternal RNA includes many very large molecules having interspersed repetitive sequence transcripts colinear with single-copy sequences. The structural features of much of the cytoplasmic maternal RNA is thus reminiscent of incompletely processed nuclear precursors of mRNA. The functional role of these strange molecules is not understood, but many interesting possibilities have been considered. For instance, they may be segregated into different cell lineages during cleavage and/or they may become translationally activated by selective processing during development. Maternal mRNA appears to be underloaded with ribosomes when translated, possibly because the coding sequences are short relative to the size of the mRNA. Most abundant and many rare mRNA sequences persist during embryonic development. The rare sequence molecules are replaced by newly synthesized RNA, but some abundant maternal transcripts appear to persist throughout embryonic development. Most of the proteins present in the egg do not change significantly in mass during development, but a few decline or accumulate substantially. Together, these observations indicate that much of the information for embryogenesis is stored in the egg, although substantial changes in gene expression occur during development.

Animals↗

The expression of human H2A-H2B histone gene pairs is regulated by multiple sequence elements in their joint promoters.

The majority of human H2A and H2B histone genes are organized as gene pairs: 14 H2A-H2B gene pairs, one solitary H2A gene and three solitary H2B genes have been described. Two of the H2A genes and two of the H2B genes arranged within gene pairs are pseudogenes. The gene pairs are organized with divergent transcriptional orientation, and the coding regions of the respective H2A and H2B genes are separated by about 320 nucleotide pairs that form overlapping promoter regions. Comparison of promoters of H2A-H2B gene pairs has previously shown that these belong to two different groups (groups I and II) which are characterized by specific patterns of conserved sequence elements. We have constructed a reporter gene vector that allows the simultaneous analysis of both genes regulated by the divergent promoters belonging to group I or II, respectively. Firefly-luciferase and beta-galactosidase genes were taken as reporter genes. Site directed mutagenesis performed at individual promoter elements revealed that individual sequence elements within both groups of promoters functionally depend on each other and may contribute to a coordinate expression of paired H2A and H2B genes through assembly of their joint promoter into a mutually dependent promoter complex. Group II promoters are characterized by the presence of an E2F binding site upstream of the H2A gene-proximal TATA box. Immediately upstream of the E2F element, we have identified a highly conserved octanucleotide CACAGCTT (RT-1) that exists in all human group II H2A-H2B gene promoters. Protein binding studies at the RT-1 element indicate factor binding to this sequence. Site directed mutagenesis indicates that both the E2F element and the RT-1 motif are essential for full promoter activity.

Base Sequence↗

A mouse histone H1 variant, H1b, binds preferentially to a regulatory sequence within a mouse H3.2 replication-dependent histone gene.

H1 histones, found in all multicellular eukaryotes, associate with linker DNA between adjacent nucleosomes, presumably to keep the chromatin in a compact, helical state. The identification of multiple histone H1 subtypes in vertebrates suggests these proteins have specialized roles in chromatin organization and thus influence the regulation of gene expression in the multicellular organism. The mechanism by which the association of H1 with nucleosomal DNA is regulated is not completely understood, but affinity for different DNA sequences may play a role. Here we report that a specific H1 subtype in the mouse, namely H1b, selectively binds to a regulatory element within the protein-encoding sequence of a replication-dependent mouse H3.2 gene. We have previously shown that this coding region element, Omega, is the target of very specific interactions in vitro with another nuclear factor called the Omega factor. This element is required for normal gene expression in stably transfected rodent cells. The mouse H1b protein interacts poorly (100-fold lower affinity) with the comparable "Omega" sequence of a replication-independent mouse H3.3 gene. This H3.3 sequence differs at only 4 out of 22 nucleotide positions from the H3.2 sequence. Our findings raise the possibility that this H1b protein plays a specific role in regulation of expression of the replication-dependent histone gene family.

Amino Acid Sequence↗

A common mechanism of action for three mood-stabilizing drugs.

Lithium, carbamazepine and valproic acid are effective mood-stabilizing treatments for bipolar affective disorder. The molecular mechanisms underlying the actions of these drugs and the illness itself are unknown. Berridge and colleagues suggested that inositol depletion may be the way that lithium works in bipolar affective disorder, but others have suggested that glycogen synthase kinase (GSK3) may be the relevant target. The action of valproic acid has been linked to both inositol depletion and to inhibition of histone deacetylase (HDAC). We show here that all three drugs inhibit the collapse of sensory neuron growth cones and increase growth cone area. These effects do not depend on GSK3 or HDAC inhibition. Inositol, however, reverses the effects of the drugs on growth cones, thus implicating inositol depletion in their action. Moreover, the development of Dictyostelium is sensitive to lithium and to valproic acid, but resistance to both is conferred by deletion of the gene that codes for prolyl oligopeptidase, which also regulates inositol metabolism. Inhibitors of prolyl oligopeptidase reverse the effects of all three drugs on sensory neuron growth cone area and collapse. These results suggest a molecular basis for both bipolar affective disorder and its treatment.

Animals↗

Interactions of U2 gene loci and their nuclear transcripts with Cajal (coiled) bodies: evidence for PreU2 within Cajal bodies.

The Cajal (coiled) body (CB) is a structure enriched in proteins involved in mRNA, rRNA, and snRNA metabolism. CBs have been shown to interact with specific histone and snRNA gene loci. To examine the potential role of CBs in U2 snRNA metabolism, we used a variety of genomic and oligonucleotide probes to visualize in situ newly synthesized U2 snRNA relative to U2 loci and CBs. Results demonstrate that long spacer sequences between U2 coding repeats are transcribed, supporting other recent evidence that U2 transcription proceeds past the 3' box. The presence of bright foci of this U2 locus RNA differed between alleles within the same nucleus; however, this did not correlate with the loci's association with a CB. Experiments with specific oligonucleotide probes revealed signal for preU2 RNA within CBs. PreU2 was also detected in the locus-associated RNA foci, whereas sequences 3' of preU2 were found only in these foci, not in CBs. This suggests that a longer primary transcript is processed before entry into CBs. Although this work shows that direct contact of a U2 locus with a CB is not simply correlated with RNA at that locus, it provides the first evidence of new preU2 transcripts within CBs. We also show that, in contrast to CBs, SMN gems do not associate with U2 gene loci and do not contain preU2. Because other evidence indicates that preU2 is processed in the cytoplasm before assembly into snRNPs, results point to an involvement of CBs in modification or transport of preU2 RNA.

3' Untranslated Regions↗

Preliminary characterization of the transcriptional and translational products of the Saccharomyces cerevisiae cell division cycle gene CDC28.

The CDC28 gene was subcloned from a plasmid containing a 6.5-kilobase-pair segment of Saccharomyces cerevisiae DNA YRp7(CDC28-3) by partial digestion with Sau3A and insertion of the resulting fragments into the BamHI sites of YRp7 and pRC1. Recombinant plasmids were obtained containing inserts of 4.4 and 3.1 kilobase pairs which were capable of complementing a cdc28(ts) mutation. R-loop analysis indicated that each yeast insert contained two RNA coding regions of about 0.8 and 1.0 kilobase pairs, respectively. In vitro mutagenesis experiments suggested that the smaller coding region corresponded to the CDC28 gene. When cellular polyadenylic acid-containing RNA, separated by agarose gel electrophoresis after denaturation with glyoxal and transferred to nitrocellulose membrane, was reacted with labeled DNA from the smaller coding region, and RNA species of about 1 kilobase in length was detected. Presumably, the discrepancy in size between the R-loop and electrophoretic determinations is due to a segment of polyadenylic acid which is excluded from the R-loops. By using hybridization of the histone H2B mRNAs to an appropriate probe as a previously determined standards, it was possible to estimate the number of CDC28 mRNA copies per haploid cell as between 6 and 12 molecules. Hybrid release translation performed on the CDC29 mRNA directed the synthesis of a polypeptide of 27,000 daltons, as determined by polyacrylamide gel electrophoresis in sodium dodecyl sulfate. This polypeptide was not synthesized when mRNA prepared from a cdc28 nonsense mutant was translated in a parallel fashion. However, if the RNA from a cell containing the CDC28 gene on a plasmid maintained at a high copy number was translated, the amount of in vitro product was amplified fivefold.

Base Sequence↗

Bile salt excretory pump: biology and pathobiology.

Bile acids are the major determinant and driving force for the generation of bile flow. Bile acid transport across the canalicular membrane is primarily an ATP-dependent process. The predominant transporter is the bile salt excretory pump (BSEP, ABCB11), a member of the adenosine triphosphate-binding cassette (ABC) family of transporters. Regulatory mechanisms that can coordinate the genes encoding bile acid transport proteins are critically important to avoid hepatocyte damage from intracellar accumulation of bile acids. Bile salts are natural ligands for several nuclear hormone receptors expressed in liver and intestine. Nuclear receptors are transcription factors that bind specific ligands such as bile acids and regulate gene expression according to the metabolic requirements of the cell. In cloning of the BSEP gene, we found a binding site in the promoter for the farnesoid X receptor (FXR), a nuclear receptor for bile acids. FXR activity requires heterodimerization with the 9-cis retinoid receptor (RXR alpha), and when bound by bile acids and retinoic acid, the complex effectively activates the transcription of BSEP. There is a growing body of evidence for the activation of nuclear hormone receptors through the remodeling of chromatin by histone modification involving acetylation, in concert with methylation of H3 and H4 histones. We have recently demonstrated a role for the coactivator-associated arginine methyltransferase 1 (CARM1), as a coactivator of the FXR/RXR receptor and regulator of FXR responsive genes such as BSEP. Chromatin immunoprecipitation showed that the bile acid-dependent activation of the human BSEP is associated with a simultaneous increase of FXR and CARM1 occupation of the BSEP promoter. The increased occupation of the BSEP locus by CARM1 also corresponds with the increased deposition of Arg-17 methylation and Lys-9 acetylation of histone H3 within the FXR DNA-binding element of BSEP. Our work on the role of nuclear receptors in regulation of bile acid homeostasis has led to an increased understanding of the pathogenesis of the disorder, progressive familial intrahepatic cholestasis, type 1 (PFIC1) or Byler disease. The gene mutated in PFIC1 is called FIC1 and codes for a type IV P-type ATPase whose function is unknown. Increased ileal apical sodium-dependent bile acid transporter messenger RNA (mRNA) expression was detected in 3 patients with PFIC1. Ileal FXR and short heterodimer partner (an inhibitory nuclear receptor) messenger RNA levels were reduced in the same 3 patients. In studies of cells after antisense-mediated knock-down of endogenous FIC1, the activity of the ileal apical bile acid transporter promoter was enhanced, whereas the activities of the human FXR and BSEP promoters were reduced. Nuclear but not cytoplasmic localization of FXR is markedly decreased in FIC1-negative cells, indicating that FIC1 is necessary for posttranslational modifications necessary for the nuclear translocation of FXR. This defect leads to enhanced ileal bile salt uptake and impaired canalicular bile salt secretion by BSEP. In PFIC1, an increased load of bile acids is retained in the liver leading to cholestasis and progressive liver injury.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Histone H3.3 deposition at E2F-regulated genes is linked to transcription.

The histone variant H3.3 can be incorporated in chromatin independently of DNA synthesis. By imaging using green fluorescent protein-tagged histones, H3.3 deposition has been found to be linked with transcriptional activation. Here, we investigated H3.3 incorporation during G1 progression on cell-cycle-regulated E2F-dependent genes and on some control loci. We transiently transfected resting cells with an expression vector for tagged H3.3 and we analysed its presence by chromatin immunoprecipitation. We found that replication-independent H3.3 deposition occurred on actively transcribed genes, but not on silent loci, thereby confirming its link with transcription. Interestingly, we observed similar levels of H3.3 occupancy on promoters and on the coding regions of the corresponding genes, indicating that H3.3 deposition is not restricted to promoters. Finally, H3.3 occupancy correlated with the presence of transcription-competent RNA polymerase II. Taken together, our results support the hypothesis that H3.3 is incorporated after disruption of nucleosomes mediated by transcription elongation.

Animals↗