Yasunari Takami

Dicer is essential for formation of the heterochromatin structure in vertebrate cells

RNA interference is an evolutionarily conserved gene-silencing pathway in which the nuclease Dicer cleaves double-stranded RNA into small interfering RNAs. The biological function of the RNAi-related pathway in vertebrate cells is not fully understood. Here, we report the generation of a conditional loss-of-function Dicer mutant in a chicken–human hybrid DT40 cell line that contains human chromosome 21. We show that loss of Dicer results in cell death with the accumulation of abnormal mitotic cells that show premature sister chromatid separation. Aberrant accumulation of transcripts from α-satellite sequences, which consist of human centromeric repeat DNAs, was detected in Dicer-deficient cells. Immunocytochemical analysis revealed abnormalities in the localization of two heterochromatin proteins, Rad21 cohesin protein and BubR1 checkpoint protein, but the localization of core kinetochore proteins such as centromere protein (CENP)-A and -C was normal. We conclude that Dicer-related RNA interference machinery is involved in the formation of the heterochromatin structure in higher vertebrate cells.

Activation of Cdh1-dependent APC is required for G1 cell cycle arrest and DNA damage-induced G2 checkpoint in vertebrate cells

Anaphase‐promoting complex (APC) is activated by two regulatory proteins, Cdc20 and Cdh1. In yeast and Drosophila, Cdh1‐dependent APC (Cdh1–APC) activity targets mitotic cyclins from the end of mitosis to the G1 phase. To investigate the function of Cdh1 in vertebrate cells, we generated clones of chicken DT40 cells disrupted in their Cdh1 loci. Cdh1 was dispensable for viability and cell cycle progression. However, similarly to yeast and Drosophila, loss of Cdh1 induced unscheduled accumulation of mitotic cyclins in G1, resulting in abrogation of G1 arrest caused by treatment with rapamycin, an inducer of p27Kip1. Further more, we found that Cdh1−/− cells fail to maintain DNA damage‐induced G2 arrest and that Cdh1–APC is activated by X‐irradiation‐induced DNA damage. Thus, activation of Cdh1–APC plays a crucial role in both cdk inhibitor‐dependent G1 arrest and DNA damage‐induced G2 arrest.

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, ΔchHDAC-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.

Role of NAD‐dependent deacetylases SIRT1 and SIRT2 in radiation and cisplatin‐induced cell death in vertebrate cells

Yeast Sir2 is a nicotinamide adenine dinucleotide (NAD)‐dependent histone deacetylase that plays a central role in transcriptional silencing, chromosomal stability, DNA damage response and aging. In mammals, Sir2‐like genes constitute a seven‐member family whose function is largely unknown. To investigate the role of the Sir2 family in vertebrates, we have disrupted Sir2 homologues SIRT1 and SIRT2 in the p53‐deficient chicken cell line DT40. Both SIRT1−/− and SIRT2−/− cells had mild growth defects. Colony survival assays showed moderate and mild sensitivity to cisplatin in SIRT1−/− and SIRT2−/− cells, respectively, while SIRT1−/−, but not SIRT2−/− cells, were sensitive to ionizing radiation (IR). Cells rendered doubly deficient in SIRT1 and SIRT2 exhibited the same levels of IR and cisplatin sensitivity as SIRT1−/− cells. SIRT1−/− cells appeared to be defective neither in DNA double strand break repair nor in G2/M checkpoints, but were more susceptible to cell death induction following IR than wild‐type cells. Furthermore, both SIRT1‐ and SIRT2‐deficient cells were more sensitive to pro‐apoptotic stimuli including cisplatin and staurosporine. Our results indicate that SIRT1 and SIRT2 regulate stress‐induced cell death pathways in a p53‐independent manner.

Asf1 Is Required for Viability and Chromatin Assembly during DNA Replication in Vertebrate Cells

Asf1 (anti-silencing function 1), a well conserved protein from yeast to humans, acts as a histone chaperone and is predicted to participate in a variety of chromatin-mediated cellular processes. To investigate the physiological role of vertebrate Asf1 in vivo, we generated a conditional Asf1-deficient mutant from chicken DT40 cells. Induction of Asf1 depletion resulted in the accumulation of cells in S phase with decreased DNA replication and increased mitotic aberrancy forming multipolar spindles, leading to cell death. In addition, nascent chromatin in Asf1-depleted cells showed increased nuclease sensitivity, indicating impaired nucleosome assembly during DNA replication. Complementation analyses revealed that the functional domain of Asf1 for cell viability was confined to the N-terminal core domain (amino acids 1-155) that is a binding platform for histones H3/H4, CAF-1p60, and HIRA, whereas Asf1 mutant proteins, abolishing binding abilities with both p60 and HIRA, exhibit no effect on viability. These results together indicate that the vertebrate Asf1 plays a crucial role in replication-coupled chromatin assembly, cell cycle progression, and cellular viability and provide a clue of a possible role in a CAF-1- and HIRA-independent chromatin-modulating process for cell proliferation.

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, ΔchHDAC-1 and -2, devoid of two alleles of the chHDAC-1and -2 genes, respectively. The protein patterns on two-dimensional PAGE definitely changed for ΔchHDAC-2, and the amounts of the IgM H- and L-chains increased in it. Of the two IgM H-chain forms, the secreted form (μs) increased in ΔchHDAC-2, but the membrane-bound form (μm) decreased. The IgM H-chain gene was transcribed more in ΔchHDAC-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 μs mRNA, whereas the stability of the two types of mRNA, μs and μm, was unchanged. In DT40 cells, treatment with trichostatin A increased both the amounts of IgM H-chain mRNAs and the switch from μm to μs 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 μs IgM H-chain in the DT40 cell line.

The Histone Chaperone Facilitates Chromatin Transcription (FACT) Protein Maintains Normal Replication Fork Rates

Ordered nucleosome disassembly and reassembly are required for eukaryotic DNA replication. The facilitates chromatin transcription (FACT) complex, a histone chaperone comprising Spt16 and SSRP1, is involved in DNA replication as well as transcription. FACT associates with the MCM helicase, which is involved in DNA replication initiation and elongation. Although the FACT-MCM complex is reported to regulate DNA replication initiation, its functional role in DNA replication elongation remains elusive. To elucidate the functional role of FACT in replication fork progression during DNA elongation in the cells, we generated and analyzed conditional SSRP1 gene knock-out chicken (Gallus gallus) DT40 cells. SSRP1-depleted cells ceased to grow and exhibited a delay in S-phase cell cycle progression, although SSRP1 depletion did not affect the level of chromatin-bound DNA polymerase α or nucleosome reassembly on daughter strands. The tracking length of newly synthesized DNA, but not origin firing, was reduced in SSRP1-depleted cells, suggesting that the S-phase cell cycle delay is mainly due to the inhibition of replication fork progression rather than to defects in the initiation of DNA replication in these cells. We discuss the mechanisms of how FACT promotes replication fork progression in the cells.

Histone H1 null vertebrate cells exhibit altered nucleosome architecture

In eukaryotic nuclei, DNA is wrapped around an octamer of core histones to form nucleosomes, and chromatin fibers are thought to be stabilized by linker histones of the H1 type. Higher eukaryotes express multiple variants of histone H1; chickens possess six H1 variants. Here, we generated and analyzed the phenotype of a complete deletion of histone H1 genes in chicken cells. The H1-null cells showed decreased global nucleosome spacing, expanded nuclear volumes, and increased chromosome aberration rates, although proper mitotic chromatin structure appeared to be maintained. Expression array analysis revealed that the transcription of multiple genes was affected and was mostly downregulated in histone H1-deficient cells. This report describes the first histone H1 complete knockout cells in vertebrates and suggests that linker histone H1, while not required for mitotic chromatin condensation, plays important roles in nucleosome spacing and interphase chromatin compaction and acts as a global transcription regulator.

A single copy of linker H1 genes is enough for proliferation of the DT40 chicken B cell line, and linker H1 variants participate in regulation of gene expression

There is general agreement that large numbers of histone H1 are necessary for maintenance of the higher order structure of chromatin in higher eukaryotes. The chicken H1 gene family comprises six members per haploid genome, the total copy number being 12, and they encode six H1 variants which are considerably different from each other in amino acid sequence. We recently established that in two chicken DT40 mutants (1/2Δ110kb and Δ57kb), which lack, respectively, one allele of the gene cluster of 110 kb carrying six H1 genes, plus 33 core histone genes, and two copies each of four of the six H1 genes included in an ≈ 57 kb segment of the cluster, expression of the remaining H1 genes is increased, resulting in constant steady‐state levels of total H1 mRNAs. These results gave rise to the simple questions of how many H1 genes and how many H1 variants, at minimum, are necessary for the viability of DT40 cells.

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.