Targeted disruption of H2B-V encoding a particular H2B histone variant causes changes in protein patterns on two-dimensional polyacrylamide gel electrophoresis in the DT40 chicken B cell line

HDAC2 controls IgM H- and L-chain gene expressions via EBF1, Pax5, Ikaros, Aiolos and E2A gene expressions

We previously reported that histone deacetylase-2 (HDAC2) controls the amount of IgM H-chain at the steps of transcription of its gene and alternative processing of its pre-mRNA in DT40 cells. Here, we showed not only that the HDAC2-deficiency caused repressions of gene expressions for HDAC7, EBF1, Pax5, Aiolos and Ikaros, and elevations of gene expressions for HDAC4, HDAC5, PCAF and E2A, but also that it caused altered acetylation levels of several Lys residues of core histones. Using gene targeting techniques, we generated three homozygous DT40 mutants: EBF1(-/-), Aiolos(-/-) and E2A(-/-), devoid of EBF1, Aiolos and E2A genes, respectively. Semiquantitative RT-PCR analysis of the resultant mutants revealed not only that EBF1 and Aiolos down-regulate expressions of IgM H- and L-chain genes, but also that E2A up-regulates expressions of these two genes. These results, together with others, indicate that HDAC2 controls indirectly expressions of IgM H- and L-chain genes through opposite transcriptional regulations of EBF1, Pax5, Aiolos plus Ikaros and E2A genes.

Different roles of N-terminal and C-terminal halves of HIRA in transcription regulation of cell cycle-related genes that contribute to control of vertebrate cell growth

We reported previously that chicken HIRA, a homolog of Saccharomyces cerevisiae transcriptional co-repressors Hir1p and Hir2p, possesses seven WD dipeptide motifs and an LXXLL motif in its N-terminal and C-terminal halves, respectively, required for transcription regulations. Here, by using the gene targeting technique, we generated the homozygous HIRA-deficient DT40 mutant DeltaHIRA. The HIRA deficiency caused slightly delayed cell growth and affected the opposite transcriptions of cell cycle-related genes, i.e. repressions for P18, CDC25B, and BCL-2, activations for P19 and cyclin A, and histones H2A, H2B, H3, and H4. These altered expressions were completely revived by the artificial stable expression of hemagglutinin-tagged HIRA in DeltaHIRA. The ability to rescue the delayed growth rate was preferentially aided by the N-terminal half instead of the C-terminal half. We cloned the chicken P18 genomic DNA, and we established that its promoter was located surrounding the sequence GCGGGCGC at positions -1157 to -1150. Chromatin immunoprecipitation assay revealed that the N-terminal half interacted directly or indirectly with the putative promoter region of the p18 gene, resulting in up-regulation of the gene. These results indicated that the N-terminal half of HIRA should contribute positively to the growth rate via up-regulation of a set of cell cycle-related genes, whereas the C-terminal half down-regulated another set of them without exhibiting any effect on the cell growth.

GCN5: a supervisor in all-inclusive control of vertebrate cell cycle progression through transcription regulation of various cell cycle-related genes

Histone acetyltransferases (HATs) are involved in the acetylation of core histones, which is an important event for transcription regulation through alterations in the chromatin structure in eukaryotes. To clarify participatory in vivo roles of two such enzymes known as GCN5 and PCAF, we generated homozygous DT40 mutants, DeltaGCN5 and DeltaPCAF, devoid of two alleles of each of the GCN5 and PCAF genes, respectively, with the help of gene targeting technique. While the PCAF-deficiency exhibited no effect on growth rate, the GCN5-deficiency caused delayed growth rate of DT40 cells. FACS analyses revealed not only that the number of cells in S phase decreased, but also that the cell cycle progression was suppressed at G1/S phase transition for DeltaGCN5. RT-PCR analyses revealed that the GCN5-deficiency exhibited opposite influences on transcriptions of G1/S phase transition-related genes, i.e. repressions for E2F-1, E2F-3, E2F-4, E2F-6, DP-2, cyclin A, cyclin D3, PCNA, cdc25B and p107; and activations for p27, c-myc, cyclin D2 and cyclin G1. Similarly, the deficiency influenced oppositely transcriptions of apoptosis-related genes, i.e. decreased expression of bcl-xL and increased expression of bcl-2. Immunoblotting analyses using a number of anti-acetylated histone antisera revealed that the GCN5-deficiency led to decreased acetylation levels of K16/H2B and K9/H3, and increased those of K7/H2A, K18/H3, K23/H3, K27/H3, K8/H4 and K12/H4. These results indicate that GCN5 preferentially acts as a supervisor in the normal cell cycle progression having comprehensive control over expressions of these cell cycle-related genes, as well as apoptosis-related genes, probably via alterations in the chromatin structure, mimicked by changing acetylation status of core histones, surrounding these widely distributed genes.

The chicken B cell line DT40: a novel tool for gene disruption experiments

The use of the chicken DT40 B cell line is increasing in popularity due to the ease with which it can be manipulated genetically. It offers a targeted to random DNA integration ratio of more than 1:2, by far exceeding that of any mammalian cell line. The facility with which knockout cell lines can be generated, combined with a short generation time, makes the DT40 cell line attractive for phenotype analysis of single and multiple gene disruptions. Advantage has been taken of this to investigate such diverse fields as B cell antigen receptor (BCR) signaling, cell cycle regulation, gene conversion and apoptosis. In this review, we give a historical introduction and a practical guide to the use of the DT40 cell line, along with an overview of the main topics being researched using the DT40 cell line as a model system. These topics include B cell-specific subjects such as B cell signaling and Ig rearrangement, and subjects common to all cell types such as apoptosis, histones, mRNA modification, chromosomal maintenance and DNA repair. Attention is in each case brought to peculiarities of the DT40 cell line that are of relevance for the subject. Novel applications of the cell line, e.g., as a vector for gene targeting of human chromosomes, are also discussed in this review.

Leucine zipper motif of chicken histone acetyltransferase-1 is essential for in vivo and in vitro interactions with the p48 subunit of chicken chromatin assembly factor-1

We cloned cDNA encoding chicken cytoplasmic histone acetyltransferase-1, chHAT-1, comprising 408 amino acids including a putative initiation Met. It exhibits 80.4% identity to the human homolog and possesses a typical leucine zipper motif. The glutathione S:-transferase (GST) pull-down assay, involving truncated and missense mutants of the chicken chromatin assembly factor-1 (chCAF-1)p48, revealed not only that a region (comprising amino acids 376-405 of chCAF-1p48 and containing the seventh WD dipeptide motif) binds to chHAT-1 in vitro, but also that mutation of the motif has no influence on the in vitro interaction. The GST pull-down assay, involving truncated and missense chHAT-1 mutants, established that a region, comprising amino acids 380-408 of chHAT-1 and containing the leucine zipper motif, is required for its in vitro interaction with chCAF-1p48. In addition, mutation of each of four Leu residues in the leucine zipper motif prevents the in vitro interaction. The yeast two-hybrid assay revealed that all four Leu residues within the leucine zipper motif of chHAT-1 are necessary for its in vivo interaction with chCAF-1p48. These results indicate not only that the proper leucine zipper motif of chHAT-1 is essential for its interaction with chCAF-1p48, but also that the propeller structure of chCAF-1p48 expected to act as a platform for protein-protein interactions may not be necessary for this interaction of chHAT-1.

N-terminal region, C-terminal region, nuclear export signal, and deacetylation activity of histone deacetylase-3 are essential for the viability of the DT40 chicken B cell line

Histone deacetylases (HDACs) are involved in the deacetylation of core histones, which is related to transcription regulation in eukaryotes through alterations in the chromatin structure. We cloned cDNA and genomic DNA encoding a chicken HDAC, chHDAC-3, which was localized in both the nuclei and cytoplasm in DT40 cells. Although one of the two chHDAC-3 alleles could be disrupted with high efficiency, no homozygous mutants were obtained after a second round of the gene-targeting technique due to its necessity for DT40 cells. We introduced a chHDAC-3 transgene under the control of a tetracycline-responsive promoter into the heterozygous mutant and subsequently disrupted the remaining endogenous chHDAC-3 allele to generate the homozygous chHDAC-3-deficient mutant, DeltachHDAC-3/FHDAC3. Inhibition of the expression of the regulatable chHDAC-3 transgene caused apoptotic cell death of the mutant. Complementation experiments involving truncated and missense chHDAC-3 mutant proteins revealed that the 1-23 N-terminal sequence, the 389-417 C-terminal sequence, the nuclear export signal, and the deacetylation activity of chHDAC-3 were essential for the cell viability. Taken together, these results indicate that chHDAC-3 plays an essential role, probably as a scavenger in the cytoplasm, in the proliferation of DT40 cells.

Histone H1 variants play individual roles in transcription regulation in the DT40 chicken B cell line

Thirty-nine of the 44 chicken histone genes are located in a major gene cluster of 110 kb, the others being distributed in four separate regions. All 6 H1 genes, which are present in the cluster and encode different variants, are expressed in the DT40 chicken B cell line, at levels ranging from about 5 to 40%. To clarify differences in the natures of these H1 variants, using gene-targeting techniques, we generated a series of DT40 mutants, which are devoid of each of the 5 H1 genes, respectively. Analyses of six H1-deficient mutants, comprising the latter five and a previously generated H1-deficient mutant, revealed that the protein patterns on 2D-PAGE were definitely different from each other, indicating that each H1 variant plays an individual role in the transcription regulation of specific genes in DT40 cells.

Chicken histone deacetylase-2 controls the amount of the IgM H-chain at the steps of both transcription of its gene and alternative processing of its pre-mRNA in the DT40 cell line

Histone deacetylases (HDACs) are involved in the deacetylation of core histones, which is an important event in transcription regulation in eukaryotes through alterations in the chromatin structure. We cloned cDNAs and genomic DNAs encoding two chicken HDACs (chHDAC-1 and -2), which are preferentially localized in nuclei. Treatment with trichostatin A reduced the HDAC activities in immunoprecipitates obtained with anti-chHDAC-1 and -2 antisera. Using gene targeting techniques, we generated homozygous DT40 mutants, DeltachHDAC-1 and -2, devoid of two alleles of the chHDAC-1 and -2 genes, respectively. The protein patterns on two-dimensional PAGE definitely changed for DeltachHDAC-2, and the amounts of the IgM H- and L-chains increased in it. Of the two IgM H-chain forms, the secreted form mu(s) increased in DeltachHDAC-2, but the membrane-bound form mu(m) decreased. The IgM H-chain gene was transcribed more in DeltachHDAC-2 than in DT40 cells. In the mutant, the alternative processing of IgM H-chain pre-mRNA preferentially occurred, resulting in an increase in the amount of mu(s) mRNA, whereas the stability of the two types of mRNA, mu(s) and mu(m), was unchanged. In DT40 cells, treatment with trichostatin A increased both the amounts of IgM H-chain mRNAs and the switch from mu(m) to mu(s) mRNAs. Based on these results, we propose a model for a role of chHDAC-2 in both the transcription and alternative processing steps, resulting in control of the amount of the mu(s) IgM H-chain in the DT40 cell line.

WD repeats of the p48 subunit of chicken chromatin assembly factor-1 required for in vitro interaction with chicken histone deacetylase-2

Chromatin assembly factor-1 (CAF-1) is essential for chromatin assembly in eukaryotes, and comprises three subunits of 150 kDa (p150), 60 kDa (p60), and 48 kDa (p48). We cloned and sequenced cDNA encoding the small subunit of the chicken CAF-1, chCAF-1p48. It consists of 425 amino acid residues including a putative initiation Met, possesses seven WD repeat motifs, and contains only one amino acid change relative to the human and mouse CAF-1p48s. The immunoprecipitation experiment followed by Western blotting revealed that chCAF-1p48 interacts with chicken histone deacetylases (chHDAC-1 and -2) in vivo. The glutathione S-transferase pulldown affinity assay revealed the in vitro interaction of chCAF-1p48 with chHDAC-1, -2, and -3. We showed that the p48 subunit tightly binds to two regions of chHDAC-2, located between amino acid residues 82-180 and 245-314, respectively. We also established that two N-terminal, two C-terminal, or one N-terminal and one C-terminal WD repeat motif of chCAF-1p48 are required for this interaction, using deletion mutants of the respective regions. These results suggest that chCAF-1p48 is involved in many aspects of DNA-utilizing processes, through alterations in the chromatin structure based on both the acetylation and deacetylation of core histones.

One allele of the major histone gene cluster is enough for cell proliferation of the DT40 chicken B cell line

Thirty-nine of the 44 chicken histone genes are located in a major histone gene cluster of 110 kb, the others residing in four separate regions. We generated a heterozygous chicken DT40 mutant, 1/2 delta110 kb, devoid of one allele of the cluster, using gene targeting techniques. Analyses of the mutant revealed that the growth rate of DT40 cells was unchanged even in the absence of one allele of the cluster. Moreover, analyses involving a RNase protection assay, SDS-PAGE or Triton-acid-urea-PAGE revealed not only that in the 1/2 delta110 kb mutant the steady-state levels of total mRNAs of gene families H1, H2A, H2B, H3 and H4 remained constant, but also that the amounts of histones H1, H2A, H2B, H3 and H4 were not changed. A comparison by 2D-PAGE revealed no changes in total cellular protein patterns of the mutant. These observations demonstrate that all the histone gene families have the inherent ability to compensate for the disruption of one allele of the gene cluster, with no influence on cell functions.

Neither HMG-14a nor HMG-17 gene function is required for growth of chicken DT40 cells or maintenance of DNaseI-hypersensitive sites

HMG-14 and HMG-17 form a family of ubiquitous non-histone chromosomal proteins and have been reported to bind preferentially to regions of active chromatin structure. Our previous studies demonstrated that the chicken HMG-17 gene is dispensable for normal growth of the DT40 chicken lymphoid cell line. Here it is shown that the major chicken HMG-14 gene,HMG-14a, is also dispensable and, moreover, that DT40-derived cells lacking both HMG-17 and HMG-14a proteins show no obvious change in phenotype with respect to the parental DT40 cells. Furthermore, no compensatory changes in HMG-14b or histone protein levels were observed in cells lacking both HMG-14a and HMG-17, nor were any alterations detected in such hallmarks of chromatin structure as DNaseI-hypersensitive sites or micrococcal nuclease digestion patterns. It is concluded that the HMG-14a and HMG-17 proteins are not required for normal growth of avian cell linesin vitro, nor for the maintenance of DNaseI-hypersensitive sites in chromatin.