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| Status |
Public on Apr 17, 2012 |
| Title |
Sequence and expression analysis of human chromosome 20 gaps |
| Organism |
Homo sapiens |
| Experiment type |
Other
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 currently has three remaining un-sequenced gaps on its q-arm. All three gaps are within gene-dense regions, or overlap loci associated with human disorders, including one gap, which is at DLGAP4. In this study we sequenced, determined the complete sizes and assessed epigenetic landscapes of all three un-sequenced gaps on human chromosome 20 using a methodological approach involving Sanger sequencing, mate-pair paired-end high-throughput sequencing and chromatin and methylation analysis. We found histone H3K27me3 to be distributed across all three gaps in immortalized B-lymphocytes. We found five novel CpG islands in one gap to be highly hypermethylated in genomic DNA from both peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. Furthermore, computational analyses predicted the presence of structured non-coding RNAs (ncRNAs) in all three chromosome 20 gaps. We verified expression for thirteen candidate ncRNAs, some of which showed tissue-specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression particularly in the human brain. Our data suggests that un-sequenced human genome gaps may comprise functional elements.
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| Overall design |
Mate-pair paired end sequencing using genomic DNA from human translocation carriers having chromosomal rearrangments of chromosomes other than chromosome 20 and chromatin, DNA methylation analysis using human peripheral blood lymphocytes and/or human cerebellum tissue. Analysis done for three remaining human chromosome 20 un-sequenced gap regions.
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| Contributor(s) |
Minocherhomji S, Bak M, Tommerup N, Silahtaroglu A |
| Citation(s) |
22510267 |
| Submission date |
Jan 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sheroy Minocherhomji |
| E-mail(s) |
sheroy@sund.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine
|
| Lab |
Ian D. Hickson lab
|
| Street address |
Blegdamsvej 3B, Building 18.1
|
| City |
Copenhagen |
| State/province |
Copenhagen N |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
|
| Samples (7)
|
| GSM867456 |
Mate-Pair reads_chr20_gaps |
| GSM867457 |
Human_Peripheral_Blood_Lymphocytes_5mC |
| GSM867458 |
Human_Peripheral_Blood_Lymphocytes_MRE-Seq |
|
| Relations |
| SRA |
SRP010641 |
| BioProject |
PRJNA152793 |
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