From 8a57fae619d36065624e67009c0346a0c73dc5ae Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Tue, 5 Sep 2023 09:30:22 +0900 Subject: [PATCH] =?utf8?q?Caf=C3=A9?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- biblio/37402370.mdwn | 39 +++++++++++++++++++++++++++++++++++++++ tags/variants.mdwn | 6 ++++++ 2 files changed, 45 insertions(+) create mode 100644 biblio/37402370.mdwn diff --git a/biblio/37402370.mdwn b/biblio/37402370.mdwn new file mode 100644 index 00000000..d51cc30d --- /dev/null +++ b/biblio/37402370.mdwn @@ -0,0 +1,39 @@ +[[!meta title="Mechanisms of insertions at a DNA double-strand break."]] +[[!tag variants]] + +Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. + +Mol Cell. 2023 Jul 20;83(14):2434-2448.e7. doi: 10.1016/j.molcel.2023.06.016 + +Mechanisms of insertions at a DNA double-strand break. + +[[!pmid 37402370 desc="Indel-seq: double-strand breaks are induced with the +AsiSI endonuclease or CRISPR, and a target locus is studied by targeted +sequencing of PCR amplicons. “the median size of inserts is 120 bp [...] 39% +of inserts originate from repetitive sequences, including telomeres, +centromeres, Alu, and retrotransposon elements” “Inhibition [with NU7441] of +DNA-PK catalytic activity [involved in NHEJ] significantly decreased insertion +events. In contrast, the size and number of deletions increased.” “POLQ +inhibition did not reduce [...] insertions, indicating that insertions were +largely independent of microhomology-mediated end joining (MMEJ)” “Treatment +with CK-666, a small-molecule inhibitor that stabilizes the Arp2/3 complex in +an inactive conformation, resulted in a significant decrease in insertion +events originating from AsiSI-proximal donor sequences” “siRNA-mediated +downregulation of RAD51 did not affect the overall number of insertions but +dramatically [increased] distal (class 3) insertions”. “8.7% of insertions +originated from multiple genomic loci on different chromosomes” “more than 70% +of donor sequences originated from promoters and transcribed gene body regions” +“Donor sequences are spread around the AsiSI sites and span the TSS; however, +insertions preferentially originate from the transcribed side [...]. In +contrast, donor sequences originating from AsiSI-cleaved DSBs within a gene +body or distal intergenic regions did not show any bias” ”[Insertions in] a +Cas9 DSB near the TSS of the BCL6 locus in a [the OCI-Ly7 cell line] were +markedly enriched in the direction of transcription.” “alpha-amanitin +decreased the frequency of insertions, preferentially those originating from +promoter-proximal DSBs [...]. Furthermore, donor sequences in +alpha-amanitin-treated cells were no longer preferentially derived from the +transcribed side.” “[Upregulating transcription of telomeric repeat-containing +RNA at telomerse via] FANCM downregulation resulted in a significant increase +in telomeric insertions.” “RNA-DNA hybrid disruption by RNaseH1 suppressed the +bias of donor sequences that originate preferentially from the direction of +transcription”"]] diff --git a/tags/variants.mdwn b/tags/variants.mdwn index c86aa2db..d23fcca7 100644 --- a/tags/variants.mdwn +++ b/tags/variants.mdwn @@ -83,6 +83,12 @@ the same transposon participate in an aberrant transposition event to a new site”. They give an example where the two transposons are identical copies on sister chromatids in G2 phase. +## Indels + +Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at +double-strand breaks originating from donor regions possibly single-stranded by +transcription (R-loops) or repair. Proximity and contact appear to be important. + ## Software - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long -- 2.47.3