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Next Generation DNA sequencing of telomere fusion events isolated from HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells

ABSTRACT: Next Generation DNA sequencing of telomere fusion events isolated from HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells

PROVIDER: PRJEB6772 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR567599_1.fastq.gz	Fastqsanger.gz
	ERR567599_2.fastq.gz	Fastqsanger.gz
	ERR567600_1.fastq.gz	Fastqsanger.gz
	ERR567600_2.fastq.gz	Fastqsanger.gz
	ERR567601_1.fastq.gz	Fastqsanger.gz

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Next Generation DNA sequencing of telomere fusion events isolated from HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells

Project description:We characterized the DNA sequences spanning telomere fusion junctions focusing on XpYp:17p inter-chromosomal events in HCT116 LIG3-/-:mL3, HCT116 LIG4-/-, WT HCT116 and MRC5HPVE6E7 cells.

2014-07-30 | E-MTAB-2769 | biostudies-arrayexpress

Illumina HiSeq next -generation sequencing of telomere fusion amplicons purified from crisis-stage MCR5HPVE6E7 and TALEN-transfected HCT116 cell lines at 48 and 120 hours post-transfection.

Project description:We sequenced and characterised inter-chromosomal and intra-chromosomal telomere fusions amplified from crisis-stage MCR5HPVE6E7 fibroblasts and DNA repair-compromised HCT116 cell lines nucleofected with plasmids encoding TALEN pairs to induce targeted cleavage at the 17p telomere.

2016-02-24 | E-MTAB-3811 | biostudies-arrayexpress

Telomere dysfunction and fusion during the progression of chronic lymphocytic leukaemia: evidence for a telomere crisis

Project description:We performed single-molecule telomere length and telomere fusion analysis in patients at different stages of chronic lymphocytic leukaemia (CLL). Our work identified the shortest telomeres ever recorded in primary human tissue reinforcing the concept that there is significant cell division in CLL. Furthermore, we provide direct evidence that critical telomere shortening, dysfunction and fusion contribute to disease progression. The frequency of short telomeres and fusion events increased with advanced disease, but importantly these were also found in a subset of early-stage patient samples indicating that these events can precede disease progression. Sequence analysis of fusion events isolated from individuals with the shortest telomeres revealed limited numbers of repeats at the breakpoint, sub-telomeric deletion and microhomology. Array-CGH analysis of individuals displaying evidence of telomere dysfunction revealed large-scale genomic rearrangements that were concentrated in the telomeric regions; this was not observed in samples with longer telomeres. Array CGH was undertaken on six individuals (five CLL stage C and one stage A) that displayed evidence of telomere dysfunction, and four (three CLL stage A and one stage B) that displayed longer and apparently stable telomeres.

2010-05-28 | E-GEOD-22016 | biostudies-arrayexpress

Telomere dysfunction and fusion during the progression of chronic lymphocytic leukaemia: evidence for a telomere crisis

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Seonamhaeicola sp. ML3

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Brucella abortus strain:ML3

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Telomere length effect on genes near the telomere in myoblasts

Project description:We examined differential expression of genes within 10MBs of telomeres in myoblasts with long or short telomeres We offer telomere looping with telomere length as a partial mechanistic explanation for the changes gene expression that is observed. Compare expression of genes within 10MB of the telomere in normal myoblasts with long (15 kb) and short (6 kb) telomeres.

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The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

Project description:BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and, thus, the development of better breeding strategies.RESULTS: The authors assembled a telomere-to-telomere genome by combining PacBio HiFi, ONT ultra- long and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes and genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced two WGD events like the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.CONCLUSIONS: The authors obtained a T2T genome for P. praeruptorum, which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.

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