Journal: iScience
Article Title: Downstream transcription promotes human recurrent CNV associated AT-rich sequence mediated genome rearrangements in yeast.
doi: 10.1016/j.isci.2024.111508
Figure Lengend Snippet: Figure 5. Homologous recombination proteins are involved in the repair of transcription-mediated DSB in AT-rich (A) The sensitivity of AT-rich yeasts to methyl methanesulfonate (MMS) is increased by double deletion of RNH1/201 or single deletion of RAD1. Triple deletion of RAD1 and RNH1/201 further increases the MMS sensitivity of AT-rich yeasts. (B and C) RNH1/201 double deletion significantly increases the number of RR clones in normal AT-rich yeasts and rad1D AT-rich yeasts cultured in YPGal. (D) Breakpoint identification of YPGal-induced rnh1D rnh201D RR yeasts and rnh1D rnh201D rad1D RR yeasts. (E) Deletion of RAD51, but not YKU70, increases the sensitivity of normal AT-rich yeasts and RNH1/201 double-deleted AT-rich yeasts to MMS. (F) The effects of RAD51 or YKU70 deletion on the gross genome rearrangement rates of normal and rnh1D rnh201D AT-rich yeasts.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies cruciform DNA antibody GeneTex Cat#GTX54648 Chemicals, peptides, and recombinant proteins Mouse IgG (H + L) Sangon Cat#D110503 Camptothecin Acmec Cat#7689-03-4 Etoposide Beyotime Cat#SC0173 Methyl methanesulfonate Acmec Cat#66-27-3 Protein A/G beads MCE Cat#HY-K0202 G418 Sangon Cat#A600958 Canavanine sulfate salt Sangon Cat#A606173 5-fluoroorotic acid Macklin Cat#F832427 Zeocin Selection Antibiotic, Sterile MCE Cat#HY-K1053 Hydrogen peroxide solution Macklin Cat#H792073 DNA marker III Tiangen Cat#MD103 Zirconia beads Youlisheng Cat#111178579 Snailase Solarbio #S8280 Critical commercial assays TIANamp Genomic DNA Kit Tiangen Cat#DP304 Es Taq Master Mix CWbio Cat#CW0690 Universal DNA Purification Kit Tiangen Cat#DP214 Hieff Clone Zero TOPO-TA Simple Cloning Kit Yeasen Cat#10908ES20 DNA Purification Kit with Magnetic Beads Beyotime Cat#D0041M Rapid Taq Master Mix Vazyme Cat#P222-01 EZ-10 DNAaway RNA Mini-Preps Kit Sangon Cat#B618133 HiScript III 1st Strand cDNA Synthesis Kit Vazyme Cat#R312-01 AceQ qPCR SYBR Green Master Mix Vazyme Cat#Q111-02 FastPure Cell/Tissue DNA Isolation Mini Kit Vazyme Cat#DC102-01 Deposited data Pacbio HiFi Seq data deposited on Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa) This paper CRA018885 MCF-7 RNA-seq data SRA SRR19737218 MCF-7 END_seq GEO GSE99194 clinvarCNV UCSC https://hgdownload.soe.ucsc.edu/goldenPath/ hg19/database/ Recurrent CNV data ClinGen https://search.clinicalgenome.org/kb/downloads Experimental models: Organisms/strains Yeast strains This paper Table S1 Oligonucleotides Primers This paper Table S2 Recombinant DNA 16p11.2_AT-rich and 16p11.2_Control cassettes in yeast This paper Data S1 22q11.2_AT-rich and 22q11.2_Control cassettes in yeast This paper Data S2 Software and algorithms MACS3 Zhang et al. https://github.com/macs3-project/MACS Integrative Genomics Viewer IGV team https://igv.org/ (Continued on next page) iScience 27, 111508, December 20, 2024 e1
Techniques: Homologous Recombination, Clone Assay, Cell Culture
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