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International Journal of Biomedical Science : IJBS logoLink to International Journal of Biomedical Science : IJBS
. 2007 Mar;3(1):14–19.

Overlapping of Genes in the Human Genome

Tomohiro Nakayama 1, Satoshi Asai 2, Yasuo Takahashi 2, Oto Maekawa 3, Yasuji Kasama 3
PMCID: PMC3614620  PMID: 23675016

Abstract

Overlapping genes are relatively common in DNA and RNA viruses. There are several examples in bacterial and eukaryotic genomes, but, in general, overlapping genes are quite rare in organisms other than viruses. There have been a few reports of overlapping genes in mammalian genomes. The present study identified all of the overlapping loci and overlapping exons in every chromosome of the human genome using a public database. The total number of overlapping loci on the same and opposite strands was 949 and 743, respectively. Similarly, in every chromosome, the instances in which two loci were located on the same strand was similar to the number of 2 genes observed on opposite strands, except for chromosome 5. The number of 2 exons located on the same strand was higher than that for 2 exons located on opposite strands, indicating the presence of many comprehensive-type overlaps. The mean percentage of overlapping exons on opposite strands in each chromosome was 3.3%, suggesting that parts of the nucleotide sequences of 26,501 exons are used to produce 2 transcribed products from each strand. The ratio of the number of overlapping regions to chromosomal length revealed that, on chromosomes 22, 17 and 19, ratios were high for both types of 2 loci, with exons located on the same and opposite strands. Ratios were low on chromosomes Y, 13 and 18. These results show that all overlapping types are distributed throughout the human genome, but that distributions differ for each chromosome.

Keywords: overlapping genes, human genome, locus, exon, chromosome

INTRODUCTION

Publication of the human genome sequence marked a significant milestone in the field of biology. Significant biological information can also be gained from the analysis of genome organization. Approximately 30,000 protein-coding genes are thought to be present in the human genome, and the positions of genes within chromosomes is currently being established (1-4).

DNA sequences can code for more than one gene product by using different reading frames or different initiation codons. Overlapping genes are relatively common in DNA and RNA viruses (5-9). While several examples exist in bacterial and eukaryotic genomes, overlapping genes appear to be relatively rare in non-viral organisms and few reports have described overlapping genes in mammalian genomes (10-12). Some studies have demonstrated that the overlapping of genes differs among species and have inferred that this can be attributed to differences in evolutionary histories (13-15).

Given that both strands of the human genome are used for transcription, two types of overlapping are thus possible; 2 genes overlapping on the same strand, and 2 genes overlapping on opposing strands. Furthermore, overlapping patterns can be classified by the relative positions of the 2 genes. Little exact information is available regarding overlapping genes in the human genome and their associated overlapping patterns. To investigate this phenomenon and the inherent biological information contained therein further, the number of overlapping genes and their patterns were examined in every chromosome of the human genome.

METHODS

The positions and sequences of each gene were obtained from the National Center for Biotechnology Information (NCBI) database (build 31; published January 15, 2003; http://www.ncbi.nlm.nih.gov/genome/guide/human/HsStats.html). Each locus was defined using both LocusLink and RefSeq, using gene symbols and names established by the nomenclature committee for the genome (http://www.gene.ucl.ac.uk/nomenclature/).

In the LocusLink report, symbols and names were reported under the banner (http://www.ncbi.nlm.nih.gov/). Exons were defined as DNA sequences coding mRNA, rather than considering functions within specific genes or locations within specific genes. This definition allowed for analysis of all possible cases of overlapping. Official gene symbols and names were used as follows: For RefSeq records, symbols were assigned using the LOCUS system. If a symbol had not yet officially been assigned, an interim symbol and name were arbitrarily selected. Arbitrarily selected symbols and names are included at this website http://www.ncbi.nlm.nih.gov/LocusLink/collaborators.html).

All loci and exons registered in NCBI build 31 were examined, using the data describing the position of genes on the chromosome. The information of nucleotide sequences and the positions of each nucleotide in the whole human genome were downloaded and stored in EXCEL file format (Microsoft Corporation, Redmond, Washington). All overlapping loci and overlapping exons could be defined according to the start and end positions of each locus and exon. Data for overlapping loci were produced using data of registered loci, while the data for overlapping exons was produced using data distinct coding regions and mRNA sequences.

RESULTS

The type of overlap was classified into 8 groups (Fig. 1), with 2 loci or exons on the same strand divided into 4 groups, and the same for those on opposite strands. We classified the patterns of overlapping genes by considering the strand-location of respective genes. For example, for Groups 1 and 2, both regions are on the positive (sense) strand and their mRNAs are transcribed using the negative (antisense) strand as the template. Groups 1, 2 and 7 were also different from Groups 3, 4, and 8, respectively.

Figure 1.

Figure 1

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Schema of overlapping patterns among loci or exons. Black arrows indicate locus or exon “1”. Shaded arrows indicate locus or exon “2”. Locus “2” or exon “2” were defined as those with the side of short arm (p) were located downstream of locus 1 or exon 1. A was the length of the flanking region without overlapping, located on the side of short arm (p). B was the length of the overlapping region. C was the length of the flanking region without overlapping, located on the side of long arm (q). a: Schema of 2 loci or exons on the same strand. Groups 1 and 2: both regions are on the positive strand (unidirectional). Groups 3 and 4: both regions are on the negative strand (unidirectional). Groups 2 and 4: region 1 includes region 2 (comprehensive). b: Schema of 2 loci or exons on opposite strands. Group 5: convergent; Group 6: divergent; Groups 7 and 8: comprehensive.

General information for overlapping loci is shown in Table 1. A total of 12,692 loci were present on the positive strand, with 12,442 on the negative strand. The total number of overlapping loci on the same and opposite strands was 949 and 743, respectively. Except for Group 2 of chromosome 5, the number of instances where 2 loci were located on the same strand was similar to the number of 2 loci on opposite strands on every chromosome. This group on chromosome 5 includes the protocadherin (PCDH) cluster located on the positive strand of 5q31. The mean number of overlapping loci was 6.7% of the total loci on each chromosome (range, 2.0-33.7%). The ratio of the number of overlapping loci to chromosome length revealed chromosomal characteristics. On chromosomes 22, 17 and 19, ratios were high when 2 loci were on overlapped both the same and opposite strands. Analysis of overlap type revealed Groups 2 and 6 as occurring relatively frequently.

Table 1.

Number of overlapping loci

Chromosome Number of loci
 Two loci located on same strand
 Two exons located on the opposite strand
 Total
Positive Negative Positive-Positive
 Negative-Negative
 Total Frequency (%) Ratio of overlapping loci/chromosome Positive-Negative Convergent Group 5 Negative-Positive Divergent Group 6 Positive-Negative Comprehension Group 7 Negative-Positive Comprehension Group 8 Total Frequency (%) Ratio of overlapping loci/chromosome Total Frequency (%) Ratio of overlapping loci/chromosome
Unidirection Group 1 Comprehension Group 2 Unidirection Group 3 Comprehension Group 4
1 1,226 1,178 18 5 21 14 58 2.4 0.26 34 19 8 6 67 2.8 0.30 125 5.2 0.56
2 901 824 9 4 10 5 28 1.6 0.12 20 15 1 2 38 2.2 0.16 66 3.8 0.28
3 688 661 10 2 10 5 27 2.0 0.14 22 11 6 5 44 3.3 0.22 71 5.3 0.36
4 509 527 6 1 3 3 13 1.3 0.07 15 12 2 2 31 3.0 0.17 44 4.2 0.24
5 629 557 10 341 10 4 365 30.8 2.01 17 10 5 3 35 3.0 0.19 400 33.7 2.20
6 640 676 6 1 10 6 23 1.7 0.13 14 12 6 2 34 2.6 0.20 57 4.3 0.33
7 603 580 8 2 13 2 25 2.1 0.17 19 14 2 4 39 3.3 0.27 64 5.4 0.44
8 436 471 6 1 7 5 19 2.1 0.13 10 7 3 3 23 2.5 0.16 42 4.6 0.29
9 489 560 9 4 12 2 27 2.6 0.24 16 8 4 4 32 3.1 0.28 59 5.6 0.52
10 502 472 14 3 15 1 33 3.4 0.25 9 7 2 1 19 2.0 0.15 52 5.3 0.40
11 798 782 5 6 9 6 26 1.6 0.20 22 9 4 6 41 2.6 0.31 67 4.2 0.51
12 616 617 11 6 13 8 38 3.1 0.28 18 9 2 13 42 3.4 0.31 80 6.5 0.59
13 228 258 1 2 5 0 8 1.6 0.08 5 4 3 0 12 2.5 0.12 20 4.1 0.20
14 407 384 8 1 7 0 16 2.0 0.18 11 8 0 1 20 2.5 0.23 36 4.6 0.41
15 402 435 3 2 10 4 19 2.3 0.24 11 9 0 5 25 3.0 0.31 44 5.3 0.55
16 569 471 8 1 9 1 19 1.8 0.25 33 8 1 1 43 4.1 0.57 62 6.0 0.82
17 629 707 11 8 16 9 44 3.3 0.56 33 12 8 5 58 4.3 0.74 102 7.6 1.30
18 217 189 2 1 3 0 6 1.5 0.08 3 4 0 0 7 1.7 0.09 13 3.2 0.17
19 786 750 10 7 13 8 38 2.5 0.66 24 10 1 0 35 2.3 0.60 73 4.8 1.26
20 334 321 6 0 10 5 21 3.2 0.34 10 9 1 6 26 4.0 0.43 47 7.2 0.77
21 150 134 4 7 1 1 13 4.6 0.39 4 1 0 4 9 3.2 0.27 22 7.7 0.66
22 295 298 7 24 6 2 39 6.6 1.08 16 6 18 4 44 7.4 1.22 83 14.0 2.30
X 560 515 21 16 4 1 42 3.9 0.33 5 4 2 7 18 1.7 0.14 60 5.6 0.47
Y 78 75 1 1 0 0 2 1.3 0.11 1 0 0 0 1 0.7 0.05 3 2.0 0.16
Total 12,692 12,442 194 446 217 92 949 3.8 0.33 372 208 79 84 743 3.0 0.26 1692 6.7 0.59
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Given that the organization of several genes has not yet been clarified, insufficient information is currently available for determining the incidence/pervasiveness of overlapping loci in these specific genes. We therefore set about to examine overlapping exons for the human genome as a whole.

The total number of exons on the positive and negative strands was 404,776 and 402,510, respectively (Table 2). The number of 2 exons located on the same strand (3,843,308) differed substantially from the number of 2 exons on opposite strands (26,501). Interestingly, the number of 2 exons located on the same strands (groups 2 and 4) exceeded the number of exons, with comprehensive-type overlaps (Groups 7 and 8). This indicates the presence of numerous comprehensive-type overlaps on the same strands (2 exons located on the same strand with a smaller exon within the larger exon). The percentage of overlapping exons (out of the total number of exons) on opposite strands within each chromosome ranged from 1.1% to 5.5%. The total number of overlapping exons was 26,501 (3.3%) out of 807,286 exons, which suggests that parts of the nucleotide sequences for 26,501 exons are used to produce 2 transcribed products from each strand.

Table 2.

Number of overlapping exons

Chromosome Number of exons
 Two exons located on same strand
 Two exons located on the opposite strand
 Total
Positive Negative Positive-Positive
 Negative-Negative
 Total Frequency (%) Ratio of overlapping loci/chromosome Positive-Negative Convergent Group 5 Negative-Positive Divergent Group 6 Positive-Negative Comprehension Group 7 Negative-Positive Comprehension Group 8 Total Frequency (%) Ratio of overlapping loci/chromosome Total Frequency (%) Ratio of overlapping loci/chromosome
Unidirection Group 1 Comprehension Group 2 Unidirection Group 3 Comprehension Group 4
1 40,542 40,285 893 168,929 1,020 194,722 365,564 452.3 1,662 383 265 717 794 2,159 2.7 9.81 367,723 455.0 1,671
2 28,527 31,849 1,145 111,580 5,906 167,407 286,038 473.8 1,192 259 240 693 581 1,773 2.9 7.39 287,811 476.7 1,199
3 24,362 23,336 667 117,639 552 87,753 206,610 433.2 1,033 414 175 621 545 1,755 3.7 8.78 208,365 436.8 1,042
4 14,710 14,759 164 52,399 252 56,197 109,012 369.9 586 65 58 369 475 967 3.3 5.20 109,979 373.2 591
5 19,282 16,553 523 89,258 387 64,222 154,390 430.8 848 171 118 194 300 783 2.2 4.30 155,173 433.0 853
6 19,613 25,094 2,621 98,971 1,269 272,948 375,809 840.6 2,185 430 474 546 670 2,120 4.7 12.33 377,929 845.3 2,197
7 20,190 18,290 433 87,325 612 76,888 165,258 429.5 1,132 208 134 459 440 1,241 3.2 8.50 166,499 432.7 1,140
8 11,752 13,897 247 41,486 269 62,995 104,997 409.4 719 132 75 294 228 729 2.8 4.99 105,726 412.2 724
9 16,063 15,774 342 61,017 418 61,286 123,063 386.5 1,089 269 124 326 335 1,054 3.3 9.33 124,117 389.9 1,098
10 17,280 17,139 329 79,607 333 83,134 163,403 474.7 1,257 99 125 321 238 783 2.3 6.02 164,186 477.0 1,263
11 23,521 21,919 520 111,131 583 94,172 206,406 454.2 1,564 289 151 638 532 1,610 3.5 12.20 208,016 457.8 1,576
12 21,425 21,732 536 113,262 408 84,888 199,094 461.3 1,486 255 210 479 507 1,451 3.4 10.83 200,545 464.7 1,497
13 6,776 7,278 153 21,982 224 24,480 46,839 333.3 473 104 44 96 112 356 2.5 3.60 47,195 335.8 477
14 12,146 14,831 348 44,796 15,341 183,643 244,128 904.9 2,806 178 78 341 203 800 3.0 9.20 244,928 907.9 2,815
15 13,237 14,303 354 57,563 308 57,058 115,283 418.6 1,441 85 96 361 379 921 3.3 11.51 116,204 421.9 1,453
16 19,961 14,845 521 89,625 416 57,171 147,733 424.4 1,970 374 158 800 592 1,924 5.5 25.65 149,657 430.0 1,995
17 21,755 24,413 605 89,629 587 100,913 191,734 415.3 2,458 430 305 735 563 2,033 4.4 26.06 193,767 419.7 2,484
18 5,984 5,333 109 21,236 73 18,906 40,324 356.3 510 19 18 90 74 201 1.8 2.54 40,525 358.1 513
19 24,368 22,916 705 110,770 665 91,434 203,574 430.5 3,510 302 163 575 634 1,674 3.5 28.86 205,248 434.1 3,539
20 11,659 9,879 247 50,843 285 39,595 90,970 422.4 1,491 172 76 102 149 499 2.3 8.18 91,469 427.7 1,499
21 5,610 4,790 158 27,849 157 20,856 49,020 471.3 1,485 42 105 114 66 327 3.1 9.91 49,347 474.5 1,495
22 11,138 8,802 3,221 86,462 245 39,878 129,806 651.0 3,606 143 73 197 403 816 4.1 22.67 130,622 655.1 3,628
X 13,993 13,998 304 56,795 284 63,535 120,918 432.0 945 77 69 195 169 510 1.8 3.98 121,428 433.8 949
Y 882 495 12 2,347 9 967 3,335 242.2 176 2 0 5 8 15 1.1 0.79 3,350 243.3 176
Total 404,776 402,510 15,157 1,792,501 30,603 2,005,047 3,843,308 476.1 1,356 4,902 3,334 9,268 8,997 26,501 3.3 9.35 3,869,809 479.4 1,365
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The ratios for overlapping exons/chromosomal length on chromosomes 22, 19, 14 and 17 were high for 2 exons located on both the same or opposite strands. Ratios were low on chromosomes Y, 13 and 18 for both overlapping types, suggesting that overlapping is not equally distributed among chromosomes. The NIT1/DEDD and ARTS-1/CAST pairs clearly show this overlapping pattern.

DISCUSSION

Previous reports (5-12) have counted the number of genes exhibiting the overlapping phenomenon, but no reports have enumerated the number of loci or exons that exhibit this overlap. Furthermore, previous reports (5-12) have only described this overlap phenomenon for opposite strands. The present strategy offers a valuable method for estimating the number of overlapping genes, as the total number of genes in the human genome is yet uncertain. Because the total number of genes in the human genome was estimated 32,000 in 2001 (1, 2), and subsequently estimated in 2004 to 22,000.

The total number of exons in the human genome has been estimated at approximately 320,000 (8.8/gene) (1, 2), whereas the present data indicate the existence of more than twice that number. This discrepancy is due to different methods of enumerating exons. We simply counted all of the exons in the human genome, without considering how many exons comprise a gene. This method can identify all exons (e.g., more than 2 exons identified in the same region) and avoids confusion due to splicing variants.

Overlapping genes may evolve as a result of extensions of open reading frames (ORF) caused by switching to an upstream start codon, substitutions in start or stop codons, or deletions and frame shifts that eliminate initiation or stop codons (13). The necessity for maintaining 2 functional overlapping genes inevitably constrains the extent to which both genes can become optimally adapted. However, such constraints can be alleviated by duplication of the overlapping gene pair, allowing for independent evolution of each gene in the resulting copies. This means that overlapping genes can thus only survive long evolutionary periods when the overlap confers a selective advantage upon the organism. In viruses, overlapping genes are thought to persist due to the considerable constraints on genome size (7). In non-viral organisms, the potential advantages of overlapping genes are less clear, although co-regulation may be involved (4). Results of a comparative study of overlapping genes in the genomes of two closely related bacteria revealed that many overlapping genes arise due to incidental elongation of the coding region (16). Overlapping genes have generally been thought to be relatively rare in the human genome, but the results of the present study show that they are more abundant than was previously thought. Interestingly, overlapping genes do not appear to be the result of evolutionary pressure to minimize the size of the human genome.

Yelin et al. (17) demonstrated by in vitro experiments that antisense transcription occurs widely in the human genome. The resulting data set of 2,667 sense-antisense pairs was evaluated by microarrays containing strand-specific oligonucleotide probes derived from the region of overlap. Verification of specific cases by Northern blot analysis with strand-specific riboprobes confirmed the occurrence of transcription from both DNA strands. While these authors also predicted the existence of approximately 1,600 sense-antisense transcriptional units, transcribed from both DNA strands (13), no overlapping patterns were elucidated.

Adachi-N et al. (18) reported that some genes overlap in a head-to-head manner (transcribed in opposite directions), while Koyanagi-KO et al. (19) recently reported the occurrence of bidirectional gene pairs in some species. However, they did not describe the patterns of the overlapping exons. In our study, this type of overlap was included in the overlapping loci identified. It has also been reported that divergence (bidirectionality) is frequently observed, particularly in genes involved in DNA repair or replication.(18). The functional significance of this is unclear, but divergence may permit two genes to share one CpG island for purposes of coordinated expression. In some bidirectional loci, expression of two divergent genes has been found to be coregulated, and promoters exhibiting bidirectional activity have often been observed (20, 21). To the best of our knowledge, the phenomenon of overlapping exons is not specific in DNA repair or replication, and further studies are needed to clarify the functional significance of overlapping genes.

Clarification of overlapping genes will facilitate the description of roles for each strand of the human genome and will provide insight into the mechanisms of evolution.

These results show that all overlapping types are distributed throughout the human genome, but that distributions differ for each chromosome.

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