Project description:Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.

2019-01-17 | GSE125207 | GEO

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 [III]

2019-01-17 | GSE125209 | GEO

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 [II]

2019-01-17 | GSE125208 | GEO

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.

Project description:DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.

| S-EPMC6438178 | biostudies-literature

Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-17 | GSE125210 | GEO

UNG shapes the specificity of AID-induced somatic hypermutation

Project description:This SuperSeries is composed of the following subset Series: GSE39108: UNG shapes the specifity of AID-induced somatic hypermutation in non B cells GSE39114: UNG shapes the specifity of AID-induced somatic hypermutation in B cells Refer to individual Series

2012-07-04 | E-GEOD-39115 | biostudies-arrayexpress

Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome

Project description:This SuperSeries is composed of the following subset Series: GSE36626: Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome (mRNA-Seq) GSE36629: Dynamic Deposition of the Histone H3.3 Variant Accompanies Developmental Remodeling of Arabidopsis Transcriptome (ChIP-Seq) Refer to individual Series

2012-05-15 | E-GEOD-36631 | biostudies-arrayexpress

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