kb intervals. The results showed that the gene is included in a 1.6 Mb region (Figure 1, chr. 1: 27,600,001–29,200,000) with a very high Alu density (ranging from 27% to 51%). This 1.6 Mb Alu-rich domain is also characterized by a high gene density, resulting in 61.4% of it being made up of exons and introns (the genomic average is 34.3%), with relatively short intergenic sequences. In particular, the 500 kb region (chr. 1: 28,517,396–29,017,396) surrounding YTHDF2 contains nine different protein coding genes (CHC1, SECP43, AF277181, MGC45806, TAF12, GMEB1, YTHDF2, OPRD1, EPB41), most of which are putatively involved in signal transduction, gene expression regulation, and cell division. To evaluate if the high Alu density observed in this genomic region had to be considered exceptional in the context of the whole genome, Alu density was calculated in nonoverlapping 1 Mb windows on each chromosome. The portion of chromosome 1 including YTHDF2 (chr. 1: 28,000,000–28,999,999) resulted among the only four genomic regions of this length (or longer) with an Alu density above 40% (the others are chr. 7: 73,000,000–74,999,999, chr. 19: 10,000,000–10,999,999, and chr. 19: 17,000,000–17,999,999, on 7q11.23, 19p13.2, and 19p13.11, respectively). These four genomic regions with very high Alu density represent only 0.17% of the genome, whereas the large majority (about two thirds) of the genome has an Alu content at least four times lower, below 12% (Figure 2).

Alu Content and Gene Content of the Genomic Region Alu density of a wide genomic region including YTHDF2 gene (chr. 1: 27,500,001–30,100,000) was calculated in 100

The YTHDF2 gene codes for a protein of 579 dues (Swiss-Prot accession no. Q9Y5A9; synonyms:

2ai;&e§Relative freq£e8&8<4 622 1022 1442 1842 2242 2642 9022 9422 9822 >40Alu density (%) 

Table 1. Allelic Frequencies at YTHDF2 (TG)12-27 Locus (rs28969505) in 412 Individuals (Aged 17–109 Years)

Alleles (Repeat Number and Length) and Their Frequency (%) 12–199 bp (0.1) 14–203 bp (5.3) 15–205 bp (30.3) 16–207 bp (26.0) 17–209 bp (5.1) 18–211 bp (0.8) 19–213 bp (0.2) 20–215 bp (5.9) 21–217 bp (7.9) 22–219 bp (13.7) 23–221 bp (3.7) 24–223 bp (0.8) 27–229 bp (0.1)

Figure 2. Frequency of genomic intervals having different Alu density. Density of Alu elements was calculated for 1 Mb nonoverlapping windows along the whole human genome (July 2003 assembly, UCSC version hg16). Height of histograms represents the relative frequency of genomic intervals having the Alu density values indicated under the horizontal axis.

Note: Alleles are named according to the number of repeats.

Characterization of the YTHDF2 Intron 4 (TG)12-27 Polymorphism

The identity between the previously described inter-Alu QM376-400 polymorphism (16) and the polymorphism found in the intron 4 of the YTHDF2 gene was confirmed by performing a PCR assay specific for the YTHDF2 intron 4 (TG)n microsatellite locus, on 20 DNA samples previously analyzed by means of inter-Alu PCR. In fact, the obtained amplification products showed a length variability exactly matching that of the inter-Alu QM376-400 polymorphism (data not shown). Subsequently, a set of 412 novel DNA samples, belonging to two age groups (137 centenarians and 275 control participants), was genotyped using the YTHDF2 intron 4–specific PCR assay. In the whole set of samples, a total number of 13 different alleles was observed, ranging from 199 to 229 bp (Table 1). All the alleles differed from each other by 2 or by a multiple of 2 base pairs. Direct sequencing of different alleles demonstrated that the length variation is produced by the variable number of repeats in the (TG)n microsatellite, ranging from 12 to 27 (Table 1). A reference sequence of the ‘‘16’’ allele (16 repeats, 207 bp) has been deposited in GenBank (accession no. AY626263), and the polymorphism has been submitted to the SNP database at GenBank (accession no. rs28969505).

lymphocytic leukemia-associated antigen KW-14). A BLAST analysis, conducted comparing the YTHDF2 mRNA reference sequence (GenBank accession no. NM_016258) with the human genome sequence, revealed that the YTHDF2 gene spans about 32 kilobases and is composed of five exons. Extensive analysis conducted on publicly available genomic databases and using sequence analysis tools and, in particular, a BLAST search (http:// www.ncbi.nlm.nih.gov/BLAST) and Clustal W multialign- ment (http://www.ebi.ac.uk/clustalw), evidenced that YTHDF2 belongs to a gene family that also includes YTHDF1 on chromosome 20 and YTHDF3 on chromosome 8. In fact, the three genes share a structure composed of five exons of similar length, and high similarity at cDNA and protein sequence level (data not shown). The search in the Protein Family Database showed the presence of a YTH domain (36) in the protein sequences (in position 457–547 on the YTHDF2 protein). Consequently, given that these three genes were previously lacking an official nomenclature, we proposed to the Human Genome Organization (HUGO) Gene Nomenclature Committee the above reported gene names (‘‘YTHDF1, YTH domain family 1’’; ‘‘YTHDF2, YTH domain family 2’’; and ‘‘YTHDF3, YTH domain family 3’’) as official symbols and names, and this proposal was accepted. A protein-translated sequence ‘‘tblastn’’ analysis (available at http://www.ncbi.nlm.nih.gov/BLAST) conducted on public databases collecting cDNA and protein sequences from different organisms revealed that the protein sequence coded by the YTHDF2 gene is highly conserved in vertebrates. In fact, the human YTHDF2 protein contains a stretch of 546 residues (nearly the whole protein) which is virtually identical (similarity 99.7%) to the homologous sequence of mouse (translated protein sequence correspond- ing to GenBank no. BAC28785), and a stretch of 518 amino acids which shares a very high degree (89.8%) of conserved positions with a similar protein (translated protein sequence