For each strain, one cosmid carrying hiC6 was analyzed by physical mapping and sequencing. For construction of physical maps,
cosmids were digested by single or double restriction enzymes, and the sizes of restricted fragments DNA Damage inhibitor were calculated based on their migration distances in agarose gel electrophoresis. hiC6 genes were localized to restriction fragments by PCR. For sequencing of the hiC6 region in the NJ-7 cosmid, a library of 2–4 kb Sau3AI DNA fragments (partial digestion) was constructed by insertion into the BamHI site of pUC19. hiC6-containing subclones were selected by PCR screening and sequenced. The sequence of the NJ-7 hiC6 region was assembled from overlapping subclone sequences. With the reference of the NJ-7 sequence, selleck screening library PCR fragments were generated for the hiC6 region of UTEX259 and sequenced. In addition, restriction fragments of this region in the UTEX259 cosmid were cloned and sequenced. The whole sequence of the UTEX259 hiC6 region was assembled from those of PCR and restriction fragments. In each case, the sequence was confirmed by
a series of PCRs using genomic DNA as the template. DNA sequences were deposited in the NCBI GenBank under accession numbers JF333588 (NJ-7 hiC6 genes) and JF333589 (UTEX259 hiC6 genes). Genomic DNA of C. vulgaris was extracted using the cetyltrimethylammonium bromide (CTAB) method (Murray & Thompson, 1980). A 10-μg aliquot of DNA was digested completely with one or two restriction enzymes. Separation of digested DNA with 0.7% agarose electrophoresis and capillary transfer of the separated DNA fragments onto Immobilon-Ny+ membrane (Millipore) were performed as standard methods (Sambrook et al., 1989). The digoxigenin (DIG)-labeled hiC6 probe for hybridization was prepared by PCR using hiC6-5 and hiC6-6 as primers and genomic DNA of NJ-7 as the template. Labeling,
hybridization and detection were performed with DIG High Prime DNA Labeling and Detection Starter either kit I (Roche) according to the manufacturer’s recommendations. Total RNA was extracted using Trizol reagent (Invitrogen) from C. vulgaris strains according to manufacturer’s instructions, separated by agarose/formaldehyde gel electrophoresis and blotted onto Immobilon-Ny+ membranes by capillary transfer. The hiC6 transcripts were probed by a PCR-generated 322-bp fragment overlapping the 3′-end of hiC6-3/4 cDNA (nt.380-701) of NJ-7. NJ-7 and UTEX259 were grown at 20 °C for 7 days and exposed to 4 °C for 24 h. Total RNA extracted from the algal cells with or without exposure to 4 °C was treated with RNase-free DNase I to remove residual DNA until no DNA could be detected by PCR, and then converted into cDNA using M-MLV reverse transcriptase (Promega). The transcription of each hiC6 gene was shown with RT-PCR with gene-specific primers listed in Supporting Information, Table S1.