Sequence and expression analysis of gaps in human chromosome 20

Sheroy Minocherhomji; Stefan Seemann; Yuan Mang; Zahra Elschich; Mads Bak; Claus Hansen; Nickolas Papadopoulos; Knud Josefsen; Henrik Nielsen; Jan Gorodkin; Niels Tommerup; Asli Silahtaroglu

doi:10.1093/nar/gks302

Sequence and expression analysis of gaps in human chromosome 20

Sheroy Minocherhomji, Stefan Seemann, Yuan Mang, Zahra Elschich, Mads Bak, Claus Hansen, Nickolas Papadopoulos, Knud Josefsen, Henrik Nielsen, Jan Gorodkin, Niels Tommerup, Asli Silahtaroglu

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Abstract

The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and/or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. We found all chr 20 gaps to comprise structured non-coding RNAs (ncRNAs) and to be conserved in primates. We verified expression for 13 candidate ncRNAs, some of which showed tissue specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression in the human brain. Our data suggest that unfinished human genome gaps are likely to comprise numerous functional elements.

Original language	English
Journal	Nucleic Acids Research
Volume	40
Issue number	14
Pages (from-to)	6660-6672
Number of pages	13
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gks302
Publication status	Published - Aug 2012

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Sequence and expression analysis of gaps in human chromosome 20Final published version, 9.22 MBLicence: CC BY-NC

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title = "Sequence and expression analysis of gaps in human chromosome 20",

abstract = "The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and/or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. We found all chr 20 gaps to comprise structured non-coding RNAs (ncRNAs) and to be conserved in primates. We verified expression for 13 candidate ncRNAs, some of which showed tissue specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression in the human brain. Our data suggest that unfinished human genome gaps are likely to comprise numerous functional elements.",

author = "Sheroy Minocherhomji and Stefan Seemann and Yuan Mang and Zahra Elschich and Mads Bak and Claus Hansen and Nickolas Papadopoulos and Knud Josefsen and Henrik Nielsen and Jan Gorodkin and Niels Tommerup and Asli Silahtaroglu",

year = "2012",

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doi = "10.1093/nar/gks302",

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T1 - Sequence and expression analysis of gaps in human chromosome 20

AU - Minocherhomji, Sheroy

AU - Seemann, Stefan

AU - Mang, Yuan

AU - Elschich, Zahra

AU - Bak, Mads

AU - Hansen, Claus

AU - Papadopoulos, Nickolas

AU - Josefsen, Knud

AU - Nielsen, Henrik

AU - Gorodkin, Jan

AU - Tommerup, Niels

AU - Silahtaroglu, Asli

PY - 2012/8

Y1 - 2012/8

N2 - The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and/or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. We found all chr 20 gaps to comprise structured non-coding RNAs (ncRNAs) and to be conserved in primates. We verified expression for 13 candidate ncRNAs, some of which showed tissue specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression in the human brain. Our data suggest that unfinished human genome gaps are likely to comprise numerous functional elements.

AB - The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and/or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum. One of these CpG islands was differentially methylated and paternally hypermethylated. We found all chr 20 gaps to comprise structured non-coding RNAs (ncRNAs) and to be conserved in primates. We verified expression for 13 candidate ncRNAs, some of which showed tissue specificity. Four ncRNAs expressed within the gap at DLGAP4 show elevated expression in the human brain. Our data suggest that unfinished human genome gaps are likely to comprise numerous functional elements.

U2 - 10.1093/nar/gks302

DO - 10.1093/nar/gks302

M3 - Journal article

C2 - 22510267

SN - 0305-1048

VL - 40

SP - 6660

EP - 6672

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 14

ER -

Sequence and expression analysis of gaps in human chromosome 20

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