short communication ssrd: simple sequence repeats database...

Comparative and Functional GenomicsComp Funct Genom 2003; 4: 342–345.Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.289

Short Communication

SSRD: simple sequence repeats databaseof the human genome

Subbaya Subramanian1, Vamsi M Madgula2, Ranjan George2, Satish Kumar2, Madhusudhan W Pandit1

and Lalji Singh1*1Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India2 Ingenovis, a Division of Ilabs Ltd, 97 Road No. 3, Banjara Hills, Hyderabad, 500 034, India

*Correspondence to:Lalji Singh, Centre for Cellular andMolecular Biology, Uppal Road,Hyderabad 500 007, India.E-mail: [email protected]

Received: 8 November 2003Revised: 24 February 2003Accepted: 28 February 2003

AbstractSimple sequence repeats are predominantly found in most organisms. They playa major role in studies of genetic diversity, and are useful as diagnostic markersfor many diseases. The simple sequence repeats database (SSRD) for the humangenome was created for easy access to such repeats, for analysis, and to be usedto understand their biological significance. The data includes the abundance anddistribution of SSRs in the coding and non-coding regions of the genome, as well astheir association with the UTRs of genes. The exact locations of repeats with respectto genomic regions (such as UTRs, exons, introns or intergenic regions) and theirassociation with STS markers are also highlighted. The resource will facilitate repeatsequence analysis in the human genome and the understanding of the functional andevolutionary significance of simple sequence repeats. SSRD is available through twowebsites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr. Copyright 2003 John Wiley & Sons, Ltd.

Introduction

Among the different types of repeats, transpos-able elements are the most abundant and make upca. 45% of the total human genome. The othermajor type of repeats is simple sequence repeats(SSRs), or microsatellites, which occupy about3% of the human genome (International HumanGenome Sequencing Consortium, 2001). SSRs aredefined as regions within DNA sequences whereshort sequences (1–6 bp; monomers to hexamers)are repeated in tandem arrays. For example, a DNAstretch of GTGTGTGTGTGT would be referred toas (GT)6. Alleles at a specific location (locus) candiffer in the number of repeats. While the biologicalfunction of these SSRs is not known, many serveas a useful source of genetic markers. Microsatel-lites are found in coding and non-coding regions,play a significant role in genome evolution (Kashiet al., 1997), and may influence gene expression.One possible role of such non-coding DNA may beto regulate the expression of neighbouring genes by

means of affecting chromatin organization. Strandslippage during replication has been suggested tobe the most likely mechanism for the generationof mutations and polymorphisms in microsatellites(Pearson and Sinden, 1998). The other importantaspect of these repeats is the instability of certaintrinucleotide repeats that are known to cause neu-rodegenerative diseases and other genetic disorders(Sinden, 2001).

Taking into account the importance of SSRs, itbecomes inevitable that there will be a need toanalyse in detail the distribution of these repeatsand genes associated with these repeats. Althoughthere have been extensive studies on microsatel-lite repeats in humans (Dib et al., 1996; Wrenet al., 2000) and various applications of SSRssuch as studying genetic distance and construct-ing phylogenetic trees have been put forth (Slatkin,1995), a complete inventory of the simple sequencerepeats in the human genome is not available asa single resource. However, with the completionof the sequence of the human genome, this has

Copyright 2003 John Wiley & Sons, Ltd.

SSRD of the human genome 343

become possible, and biologists involved in simplesequence repeat analysis could make extensive useof such a database.

Methods

The complete human genome sequence, down-loaded from the FTP site of Genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes/h sapiens — build num-ber 29; 16 May 2002 release), was used to generatethe simple sequence repeats data. The database con-tains the abundance, distribution and associationof the 501 theoretically possible non-overlappingSSR types of k-mer repeats, where k ranges fromone to six, i.e. monomer to hexamer (Jurka andPethiyagoda, 1995). The number of 501 repeatswas derived using the lowest alphabetical designa-tions (i.e. for AC = CA = GT = TG, AC is givenin the database). In this study, we have analysedthe distribution of perfect simple sequence repeats(without indels) of length ≥12 base pairs (bp). Thissmall cut-off value of 12 bp enables us to cap-ture almost all of the SSRs present in the genome.A JAVA program, based on distributed computingand an exhaustive approach, was developed andused to scan the entire genome to determine theabundance and distribution of these repeats in cod-ing and non-coding regions. The occurrences ofrepeats in genomic regions such as exons, intronsand UTRs were identified based on the annotationof the human genome sequence in Genbank. Suit-able links are provided with the NCBI and Genbankdatabases to the Accession and contig numbersthat are provided in each table. The database willbe updated when the new genome build becomesavailable.

Organization of SSRD

SSRD can be accessed at http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr. The com-plete data set is presented as the following views.

Repeat types across chromosomes

The data provided in this view gives the overallinformation on the repeat number and density forvarious repeat types ranging from monomer tohexamer. For simplicity, the repeats are grouped asper their ‘k’ mer value (e.g., monomer repeats A/T

and G/C are grouped as one type). The table alsoprovides statistics on the total occurrence for allrepeat types across a particular chromosome, andfor all chromosomes, for a particular repeat type.

501 repeats across chromosomes

This view provides details on the occurrence anddensity of each of the 501 repeats across all humanchromosomes. The density of each SSR is tabulatedaccording to the repeat group. The user can selecta chromosome and repeat group of interest to viewthe occurrence and density of a specific repeat type.

Repeat types across genomic regions

This view gives details on the distribution ofSSRs across genomic regions (exons, introns andintergenic regions). First, the sizes of exons, intronsand intergenic regions are calculated for eachchromosome. Next, for each repeat found, theregion to which it belongs is also captured. Thus,for a given chromosome, the density of repeat typesand of specific repeats with respect to genomicregions is presented.

Details of each repeat

This view provides details of each SSR found inthe human genome. For a given repeat, the repeatnumber and total length of the repeated sequenceare given, along with the starting position of therepeat with respect to both the contig ID and thespecific Accession ID. If the repeat is found ina particular gene, the name of the gene and therespective regions are displayed. In the event thata repeat lies in an intergenic region, the nearestdownstream (sequence towards the 3′ region of theSSR) gene and the distance between the repeatand the gene is given. We have also presentedthe association of SSRs with sequence tagged sites(STSs) in terms of the distance between SSR andthe known STS marker.

Details of repeats within genes

This view tabulates the genes that contain SSRs intheir coding regions. This table is expected to give acomprehensive list of genes that may be associatedwith disease phenotypes, and will be helpful in theidentification of novel genes that are involved indiseases related to repeat expansion.

Copyright 2003 John Wiley & Sons, Ltd. Comp Funct Genom 2003; 4: 342–345.

344 S. Subramanian et al.

Details of each repeat for a specific gene

A search tool that fetches the details of microsatel-lite repeats for a specific gene is given in this view.The user can enter a gene name of interest to getthe details of microsatellites that flank the gene, orrepeats which are present within the gene. Repeatsthat are present both within the gene and in theflanking sequence of the gene are included in thesearch. In the case of repeats within the gene, thepresence of SSRs in exons, introns and UTRs aretabulated. In the case of the SSRs that flank thegene, we have not specified any cut-off for theflanking sequence; instead we have included thoseSSRs in the flanking sequence on both sides ofthe gene until the end or the beginning of the nextgene is encountered in the sequence. In this way,one can search for all of the SSRs that flank aparticular gene.

Discussion

SSRs are found in most genomes, with vary-ing abundance (Toth et al., 2000; Gur-Arie et al.,2000). The analysis of various properties of SSRswill be helpful in understanding their biologi-cal significance. The density of each repeat type(length in base pairs contributed/Mb of genome)will reveal the abundance of each particular repeattype and the probable association of these repeattypes with specific chromosomes. In our earlierstudies we have found that the densities of SSRsacross the human chromosomes are relatively uni-form. However, the overall density of SSRs wasfound to be high on chromosome 19 (Subramanianet al., 2003). Thangaraj et al. (2003) reported thatthe pentameric repeat GGAAT is predominantlyassociated with the human Y chromosome, in theYq centromeric and heterochromatic regions, andmay be involved in intrachromosomal recombina-tion. Information on the abundance of SSRs, cou-pled with their distribution patterns in the coding aswell as non-coding regions of the genome and theirassociations with genes and STS markers will shedmore light on the function of SSRs in gene regu-lation. The location of the repeats with respect tocontigs and accession numbers will serve as a mapof these SSRs in the human genome, thereby asso-ciating them with particular disease phenotypes anddeveloping newer molecular markers. As the STS

markers are locus-specific, the distances (bp) pro-vided in the database for those repeats which areappearing near such markers will be further help-ful in mapping the location of the SSRs to theirgenomic locus.

The presence of microsatellites in the codingregions and regulatory regions of the genome caninfluence gene expression. The allelic variationof HUMTH01 (TCAT repeats) has been shownto be correlated with quantitative and qualita-tive changes in the binding of the ZNF191 pro-tein, which contributes significantly to the con-trol of the expression of quantitative genetic traits(Albanese et al., 2001). Studies on GT tandemrepeats on human chromosome 22 revealed thatthese repeats are associated with high recombi-nation frequency (Majewski and Ott, 2000). Onepossible role of such non-coding DNA may beto regulate the expression of neighbouring genesby affecting chromatin organization. Hui et al.(2003) demonstrated that CA repeats in intron 13of the human endothelial nitric oxide synthase(eNOS) gene function as an unusual intronic splic-ing enhancer, whose activity depends on the CArepeat number.

While there is no direct correlation betweenmicrosatellite content and genome size, it is gen-erally believed that the microsatellite content ofa genome depends on its size (Primmer et al.,1997). Many markers have been developed fromknown sequences containing these repeats (avail-able from databases and derived by screeninggenomic libraries). In spite of the recognition ofsimple repeats as markers and their association withgene regulation, the mechanisms underlying theallelic diversity of microsatellites are still poorlyunderstood. Questions such as why certain repeatmotifs are more common than others, and whythere is variation of such repeats across taxa, areimportant from an evolutionary point of view.

Acknowledgements

The authors would like to thank Sreedhar, Kavitha, SivaPrasad and Saritha for their support in developing theSSRD database. We are grateful to Rakesh Mishra andRamesh Aggarwal for providing helpful discussions. Wealso thank the anonymous referees for their valuablesuggestions. Financial support from CSIR and DBT isduly acknowledged.


SSRD of the human genome 345

References

Albanese V, Biguet NF, Kiefer H, et al. 2001. Quantitative effectson gene silencing by allelic variation at a tetranucleotidemicrosatellite. Hum Mol Genet 10: 1785–1792.

Dib C, Faure S, Fizames C, et al. 1996. A comprehensive geneticmap of the human genome based on 5264 microsatellites. Nature380: 149–152.

Gur-Arie R, Cohen CJ, Eitan Y, et al. 2000. Simple sequencerepeats in Escherichia coli : abundance, distribution, composi-tion, and polymorphism. Genome Res 10: 62–71.

Hui J, Stangl K, Lane WS, Bindereif A. 2003. HnRNP Lstimulates splicing of the eNOS gene by binding to variable-length CA repeats. Nature Struct Biol 10: 33–37.

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