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High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

ABSTRACT: Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. We performed a genome-wide mapping of forum domains termini in human HEK293T cells cultured cells using deep sequencing of the termini. We found that forum domains termini correspond to the fragile sites in human chromosomes and forum domains contain clusters of several or many genes inside. The largest forum domains correspond to the coordinately expressed main clusters of HOX genes genes. Our results indicate that forum domains correspond to big multi-gene chromosomal units some of which could be co-coordinately activated or repressed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE35065 | GEO | 2013/03/31

SECONDARY ACCESSION(S): PRJNA150821

REPOSITORIES: GEO

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High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

Project description:Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. We performed a genome-wide mapping of forum domains termini in human HEK293T cells cultured cells using deep sequencing of the termini. We found that forum domains termini correspond to the fragile sites in human chromosomes and forum domains contain clusters of several or many genes inside. The largest forum domains correspond to the coordinately expressed main clusters of HOX genes genes. Our results indicate that forum domains correspond to big multi-gene chromosomal units some of which could be co-coordinately activated or repressed. 2 sample examined: forum termini from HEK293T cells in two independent experiments

2013-03-31 | E-GEOD-35065 | biostudies-arrayexpress

Tiling path analysis of Drosophila Schneider 2 cultured cells to map forum domains

Project description:Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. <br><br>We performed a genome-wide mapping of forum domains termini in Drosophila Schneider 2 cultured cells using Drosophila melanogaster genomic tiling microarray consisting of overlapping 3 kb fragments. We found that forum domains contain clusters of several or many genes inside. The largest forum domains correspond to the coordinately expressed main clusters of homeotic genes inside BX-C and ANTP-C, cluster of histone genes and clusters of piRNAs. PRE/TRE and binding sites of transcription factors are often reside inside domains, and do not overlap with forum domains termini. The terminal regions of domains often correspond to chromosomal sites containing different classes of mobile elements, binding sites of SuUR protein and regions of intercalary heterochromatin. Our results indicate that forum domains correspond to big multi-gene chromosomal units some of which could be co-coordinately activated or repressed.

2010-11-01 | E-MEXP-2468 | biostudies-arrayexpress

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [DSBs]

Project description:Eukaryotic chromosomes are subjected to spontaneous fragmentation even under quick isolation of DNA in a solid phase by strong treatment with 0.1 M EDTA, 1% SDS and proteinase K (1 mg/ml). The long DNA fragments of excised chromosomal DNA were denoted as forum domains. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. The domains are delimited by hot spots of double-strand breaks (DSBs). We performed a genome-wide mapping of DSBs in human HEK293T cells cultured cells using Illumina deep sequencing of the termini of forum domains. We found that in rDNA units the hot spots of DSBs are distributed non-randomly. Mostly they are located in IGS. Genome-wide mapping of DNA DSBs in HEK293T cells

2014-10-04 | E-GEOD-49302 | biostudies-arrayexpress

Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [DSBs]

2014-10-04 | GSE49302 | GEO

Transcriptional termini of genes on chromosomes 21-22 (RNA mapping)

Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we mapped the poly A + RNA isolated from 12 normal tissues and four cell lines. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-07-28 | GSE17358 | GEO

Whole-genome landscape PARP1 in HEK293T cells

Project description:Poly [ADP-ribose] polymerase 1 (PARP1) is involved in differentiation, proliferation, tumor transformation, in repair of single-stranded DNA and double-stranded DNA breaks (DSBs) in conjunction with BRCA. PARP1 enzyme works modifying nuclear proteins by poly ADP-ribosylation. It was found that PARP1 and HNRNPA2B1 bind at termini of forum domains and may play a role in coordinated regulation of genes in forum domains (Tchurikov et al., 2013). Forum domains are long DNA fragments of excised chromosomal DNA. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. The domains are delimited by hot spots of double-strand breaks (DSBs). This ChIP-Seq is aimed to compare genome-wide binding sites of PARP1 with different genomic features, including the hot spots of DSBs.

2017-02-01 | GSE74954 | GEO

Transcriptional termini of genes on chromosomes 21-22 (RACE mapping)

Project description:The purpose of these experiments was to determine the 5' and 3' transcriptional termini of genes on chromosomes 21-22. Towards this end, we first carried out 5’ and 3’ RACE reactions from 1193 exons from 492 genes in these chromosomes using RNA isolated from 11 normal tissues and 5 cell lines. An average of 3 to 4 RACE reactions (5’ and 3’) was carried out from each gene. The products of the RACE reactions were analyzed by hybridization to tiling arrays interrogating the non-repeat portions of these chromosomes at 17 nucleotide resolution. A total of 26,688 RACE reactions were performed and pooled to be placed on to 1020 tiling arrays For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2009-08-13 | GSE17600 | GEO

Mapping of genome-wide DSBs in HEK293T cells using the RAFT procedure.

Project description:Large DNA fragments (mainly of 50-250 kb, denoted as forum domains) were isolated inside agarose plugs as described below in the extract protocol section. After ligation of 5'-bio-oligos to the blunt DNA termini the digestion with Sau3A enzyme was performed followed by selection of genome-wide preparation of forum domains termini on streptavidin-paramegnetic particles. After ligation of Sau3A adapter the termini were PCR amplified and used for deep sequencing.

2015-03-05 | GSE53811 | GEO

Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes

Project description:Recombination-mediated linking of homologous chromosomes is a unique meiotic feature that enables the halving of chromosomal ploidy in sexual life cycles. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) that are generated by focal multi-protein clusters that condense onto chromosomal axes by poorly understood mechanisms. We discovered in mice that a DBF4-dependent kinase (DDK)–modulated interaction between IHO1 and the chromosomal axis component HORMAD1 effects the formation of axis-bound IHO1 platforms that enhance nucleation of cytologically distinguishable DSB-machinery clusters. This IHO1-HORMAD1-mediated seeding of the DSB-machinery ensures that sufficient DSBs form for efficient pairing of homologous chromosomes. In the absence of IHO1-HORMAD1 interaction, residual DSB activity depends on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, meiotic DSBs are ensured by complementing pathways that differentially effect seeding and growth of DSB-machinery clusters, and that synergistically enable assembly of the DSB machinery on chromosomal axes.

2024-02-23 | PXD042179 | Pride

Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes

2024-02-23 | PXD042221 | Pride

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