Sequential alterations in globin gene chromatin structure during erythroleukemia cell differentiation

β-Actin-dependent global chromatin organization and gene expression programs control cellular identity

During differentiation and development, cell fate and identity are established by waves of genetic reprogramming. Although the mechanisms are largely unknown, during these events, dynamic chromatin reorganization is likely to ensure that multiple genes involved in the same cellular functions are coregulated, depending on the nuclear environment. In this study, using high-content screening of embryonic fibroblasts from a β-actin knockout (KO) mouse, we found major chromatin rearrangements and changes in histone modifications, such as methylated histone (H)3-lysine-(K)9. Genome-wide H3K9 trimethylation-(Me)3 landscape changes correlate with gene up- and down-regulation in β-actin KO cells. Mechanistically, we found loss of chromatin association by the Brahma-related gene ( Brg)/Brahma-associated factor (BAF) chromatin remodeling complex subunit Brg1 in the absence of β-actin. This actin-dependent chromatin reorganization was concomitant with the up-regulation of sets of genes involved in angiogenesis, cytoskeletal organization, and myofibroblast features in β-actin KO cells. Some of these genes and phenotypes were gained in a β-actin dose-dependent manner. Moreover, reintroducing a nuclear localization signal-containing β-actin in the knockout cells affected nuclear features and gene expression. Our results suggest that, by affecting the genome-wide organization of heterochromatin through the chromatin-binding activity of the BAF complex, β-actin plays an essential role in the determination of gene expression programs and cellular identity.-Xie, X., Almuzzaini, B., Drou, N., Kremb, S., Yousif, A., Östlund Farrants, A.-K., Gunsalus, K., Percipalle, P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity.

Atrial natriuretic peptide attenuates elevations in Ca2+ and protects hepatocytes by stimulating net plasma membrane Ca2+ efflux

Elevations in intracellular Ca(2+) concentration and calpain activity are common early events in cellular injury, including that of hepatocytes. Atrial natriuretic peptide is a circulating hormone that has been shown to be hepatoprotective. The aim of this study was to examine the effects of atrial natriuretic peptide on potentially harmful elevations in cytosolic free Ca(2+) and calpain activity induced by extracellular ATP in rat hepatocytes. We show that atrial natriuretic peptide, through protein kinase G, attenuated both the amplitude and duration of ATP-induced cytosolic Ca(2+) rises in single hepatocytes. Atrial natriuretic peptide also prevented stimulation of calpain activity by ATP, taurolithocholate, or Ca(2+) mobilization by thapsigargin and ionomycin. We therefore investigated the cellular Ca(2+) handling mechanisms through which ANP attenuates this sustained elevation in cytosolic Ca(2+). We show that atrial natriuretic peptide does not modulate the release from or re-uptake of Ca(2+) into intracellular stores but, through protein kinase G, both stimulates plasma membrane Ca(2+) efflux from and inhibits ATP-stimulated Ca(2+) influx into hepatocytes. These findings suggest that stimulation of net plasma membrane Ca(2+) efflux (to which both Ca(2+) efflux stimulation and Ca(2+) influx inhibition contribute) is the key process through which atrial natriuretic peptide attenuates elevations in cytosolic Ca(2+) and calpain activity. Moreover we propose that plasma membrane Ca(2+) efflux is a valuable, previously undiscovered, mechanism through which atrial natriuretic peptide protects rat hepatocytes, and perhaps other cell types, against Ca(2+)-dependent injury.

The nuclear matrix and the regulation of chromatin organization and function

Nuclear DNA is organized into loop domains, with the base of the loop being bound to the nuclear matrix. Loops with transcriptionally active and/or potentially active genes have a DNase I-sensitive chromatin structure, while repressed chromatin loops have a condensed configuration that is essentially invisible to the transcription machinery. Core histone acetylation and torsional stress appear to be responsible for the generation and/or maintenance of the open potentially active chromatin loops. The transcriptionally active region of the loop makes several dynamic attachments with the nuclear matrix and is associated with core histones that are dynamically acetylated. Histone acetyltransferase and deacetylase, which catalyze this rapid acetylation and deacetylation, are bound to the nuclear matrix. Several transcription factors are components of the nuclear matrix. Histone acetyltransferase, deacetylase, and transcription factors may contribute to the dynamic attachment of the active chromatin domains with the nuclear matrix at sites of ongoing transcription.

U2-snRNP B" protein gene is an early growth-inducible gene

In this work we isolated mouse U2-snRNP-specific b" clones and analysed the expression of the mouse U2-snRNP-specific b" and U1-snRNP-specific 70K genes in NIH-3T3 fibroblasts. Stimulation of growth-arrested NIH-3T3 cells with serum was found to evoke a rapid increase in the amount of cytoplasmic b" and 70K mRNAs. These increases in mRNA did not require de novo protein synthesis. Moreover, the inhibition of protein synthesis by cycloheximide caused a superinduction in the amounts of the U1-snRNP-specific 70K transcripts. We also found that c-Ha-rasVal12 oncogene-transformed NIH-3T3 cells have higher levels of the b" and 70K mRNAs than the normal 3T3 cells. These data imply that the b" and 70K are early growth response genes, and their enhanced expression might be of significance in the processing of pre-mRNAs into mature mRNAs.

Cell transformation by c-Ha-rasVal12 oncogene is accompanied by a decrease in histone H1 zero and an increase in nucleosomal repeat length

The activated c-Ha-rasVal12 oncogene is often involved in the genesis of human malignancies. We show here that in c-Ha-rasVal12 oncogene-transformed mouse NIH 3T3 fibroblasts the copy number and expression level of the mutant ras oncogene correlates with the degree of chromatin decondensation, as assessed by micrococcal nuclease (MNase) and DNase I digestion. MNase and DNase I analyses further revealed that the nucleosomal repeat lengths were different in the normal and ras oncogene-transformed cells, 162.3 bp and 178.1 bp, respectively. These chromatin changes were accompanied by alterations in the content of histone H1 zero. Furthermore, using DNase I as a probe, we discovered that serum stimulation of normal and transformed cells, synchronized by serum starvation, induces rapid reversible changes in the structure of bulk chromatin that may be linked to transcriptional activation. Our data thus indicate that cell transformation by ras is associated with specific changes in chromatin structure that make it more vulnerable, and prone to additional mutations characteristic of cancer development in vivo.

Methylation status and chromatin structure of an early response gene (ornithine decarboxylase) in resting and stimulated NIH-3T3 fibroblasts

The early response gene ornithine decarboxylase (odc) is indispensable for normal and malignant cell growth. Although DNA methylation is generally associated with chromatin condensation and gene inactivation, the odc gene is heavily methylated at CCGG-sequences in animal cell lines. In this work we analyzed the chromatin structure and the DNA methylation status at the CpG-rich promoter sequences at the odc locus in mouse 3T3 fibroblasts. We show that the proximal promoter region of the odc locus is not hypermethylated, while the distal promoter sequences appear to have a few methylated CCGG-sites and display methylation polymorphism. Furthermore, it was found that the 5' promoter region of odc is constitutively more sensitive to micrococcal nuclease than the coding and 3' regions of the odc gene. Stimulation of the cells with serum resulted in an appearance of a DNase I sensitive site at the promoter region. The chromatin structure of the mid-coding and 3' regions of the odc gene also underwent structural changes that were accompanied by the rapid accumulation of odc mRNA. Such changes were not detected in the chromatin structure of glyceraldehyde-3-phosphate dehydrogenase (gadph) gene, whose expression remains invariant upon serum stimulation. These data suggest that the chromatin structure may play an important role in the rapid transcriptional activation of odc and other immediate early genes during serum stimulation.

Reverse transformation, genome exposure, and cancer

The reverse transformation reaction whereby malignant cells are restored to a more normal phenotype has been reviewed. The primary causative action is ascribed to the genome exposure reaction in which a peripheral nuclear DNA region is restored to high sensitivity to DNase I, like that in normal cells. Various aspects of genome exposure around the nucleoli and the nuclear periphery are considered. The special role of the cytoskeleton in regulating exposure resulting in normal differentiation on the one hand and malignant transformation on the other is discussed. The action of the two-level system for regulation of the mammalian genome previously proposed is reviewed in relation to normal differentiation and malignancy with brief indication of roles played by various metabolites, transcription factors, protooncogenes, cell organelles, and processes like specific phosphorylation and dephosphorylation. Possible implications for cancer therapy and prevention and for the fields of genetic disease and toxicology are indicated.

Selective suppression of endogenous beta-globin gene expression by transferred beta-globin/TK chimeric gene in murine erythroleukemia cells

To examine the effect of gene transfer on expression of the endogenous beta-globin gene in murine erythroleukemia (MEL) cells, a beta-globin/TK chimeric gene was introduced into MEL cells. In some of the transformants, expression of the endogenous beta-globin gene was only weakly induced with the addition of DMSO, while expression of the introduced beta-globin/TK chimeric gene was well induced. Suppression of the endogenous beta-globin gene is selective for beta-globin gene, since expression of alpha-globin gene was only weakly affected in its induction in the transformants. Analysis of nine individual transformants indicated that suppression of the endogenous gene correlates more closely with the transcriptional activity than the copy number of the exogenous gene. Thus, the selective suppression can be explained by competition of positive trans-acting factor(s), present in limiting amounts, with high copy number of the exogenous gene the conformation of which is active.

5' structural motifs and Xenopus beta globin gene activation

We have analysed the structure of the Xenopus beta globin gene 5' flanking region in erythroid and non-erythroid chromatin, in supercoiled plasmids and in minichromosomes assembled in HeLa cell transfections. We have identified two erythroid chromatin-specific, nuclease-hypersensitive sites (HSs), one centred on the cap site, the other located 1000 base-pairs further upstream. An (AT)n tract is located 200 base-pairs upstream from each of these sites. In supercoiled plasmids, the (AT)n tracts, and not the chromatin HSs, are preferentially cleaved by single strand and double strand-specific nucleases. Using restriction enzymes, we have looked at the structure of the cap site HS in minichromosomes assembled in HeLa cell transfections. We find that the structure is indistinguishable from that found in erythroid chromatin, thus reinforcing our previous suggestion, based only on DNase I studies, that the formation of this HS is not dependent on erythroid-specific factors. In view of this close structural mimicry of the situation in vivo, we have used the HeLa cell model system to study the sequences required for cap site HS formation. We find that deletion of the (AT)n tract immediately upstream influenced neither the formation of the HS nor transcription of the globin gene. Indeed, these features remained unaffected by further deletion of upstream sequences, including 50 base-pairs of the HS itself. In this construct, the dimensions of the HS remained the same as in the undeleted construct, with the plasmid sequences that replaced the deleted Xenopus sequences becoming hypersensitive. Thus, HS formation is directed by sequences downstream from --116 acting over a distance of at least 50 base-pairs.