Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.
The human genome is 99% complete. This study contributes to filling the 1% gap by enriching previously unknown repeat regions called microsatellites (MST). We devised a Global MST Enrichment (GME) kit to enrich and nextgen sequence 2 colorectal cell lines and 16 normal human samples to illustrate its utility in identifying contigs from reads that do not map to the genome reference. The analysis of these samples yielded 790 novel extra-referential concordant contigs that are observed in more than one sample. We searched for evidence of functional elements in the concordant contigs in two ways: (1) BLAST-ing each contig against normal RNA-Seq samples, (2) Checking for predicted functional elements using GlimmerHMM. Of the 790 concordant contigs, 37 had an exact match to at least one RNA-Seq read; 15 aligned to more than 100 RNA-Seq reads. Of the 249 concordant contigs predicted by GlimmerHMM to have functional elements, 6 had at least one exact RNA-Seq match. BLAST-ing these novel contigs against all publically available sequences confirmed that they were found in human and chimpanzee BAC and FOSMID clones sequenced as part of the original human genome project. These extra-referential contigs predominantly contained pentameric repeats, especially two motifs: AATGG and GTGGA.
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Natalie C
NC
Fonville
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Karthik Raja
KR
Velmurugan
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Hongseok
H
Tae
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Zalman
Z
Vaksman
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Lauren J
LJ
McIver
Via Bioinformatics and Clinical Genetics Network, Edward Via College of Osteopathic Medicine, 2265 Kraft Dr, Blacksburg, VA 24060, USA.
Harold R
HR
Garner
D000465:Algorithms; D000818:Animals; D002460:Cell Line; D020451:Contig Mapping; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D018895:Microsatellite Repeats; D002679:Pan troglodytes / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*