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Title: Sequence and expression analysis of human chromosome 20 gaps      
dateReleased:
04-17-2012
description:
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. 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.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-35405
refinement:
raw
alternateIdentifiers:
35405
keywords:
functional genomics
dateModified:
05-04-2014
availability:
available
types:
gene expression
name:
Homo sapiens
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-35405/E-GEOD-35405.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-35405/E-GEOD-35405.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35405
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress