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. Wendt, Single reads were generated of 50 base pairs in length. The quality of DNA sequence was investigated using FASTQC (version 0.11.2), and, when necessary trimmomatic (version 0.32) was used to remove low-quality reads and regions. Quality controlled sequence was aligned to Human genome (hg19) using bowtie (version 1.0.0), and samtools (version 0.1.19) was used to remove reads with mapping quality less than 30, and to keep only aligned reads. Duplicated reads were removed, after alignment, using Picard (version 1.97). For statistics of the ChIP-sequencing see Table S6. Peaks were called using MACS (macs 2) and Peaks were filtered using P value. UCSC tracks were generated after duplicate removal, using HOMER (version 4.3) and deeptools (version 3.0.2). Heatmaps were generated using Deeptools (version 3.0.2) and NGS plot (version 2.61). Peaks were annotated to specific regions using ChIPseeker (Bioconductor package version 1.14.2). The data are accessible at GSE122299. ChIP-qPCR For ChIP-qPCR experiments the ChIP for IgG control, SMC3 and NIPBL (NIPBL #1 antibodies) were performed as described above for the SMC3 ChIP-seq experiment. qPCR analysis using Platinium taq (Thermo Fisher Scientific) was performed according to the manufacturer's instructions and analyzed using a CFX96 C1000 Thermal cycler (Bio-Rad) using the qPCR primers listed in Table S2. Precocious sister chromatid separation assays by chromosome spreading Cells were treated for 90 minutes with 100 ng/ml of nocodazole. Cells were collected and resuspended in 1 mL of medium. 1.5 mL of tap water was added. 6 minutes later 7 mL of Carnoy fixative (3:1, methanol: glacial acetic acid). Cells were then spread on glass slide, dried, brief, cells at 70%-80% confluence were crosslinked with 1% formaldehyde for 10 minutes and quenched with 125 mM glycine. After washing with PBS, cells were resuspended in lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA, 1 mM PMSF and Complete Protease Inhibitor (Roche)) and sonicated (Diagenode Bioruptor, Seraing, Belgium) to around 500 bp DNA fragments. Debris were removed by centrifugation and the lysate was diluted 1:4 with IP dilution buffer (20 mM Tris-HCl pH 8.0, 0.15 M NaCl, 2 mM EDTA, 1% TX-100, protease inhibitors) and precleared with Affi-Prep Protein A support beads, 2008.

. Schmitz, with the exception that cells were fixed as described above and processed for FISH after spreading on glass slides. Only pairs for which the dots could be clearly resolved were considered in the analysis. Microscopic image acquisitions were performed on a Zeiss Axio Imager M2 using 63X oil-immersion objective, DNA FISH was performed as previously described, 2007.

, Whole Genome Sequencing Genomic DNA isolation was performed from blood with the DNeasy Blood & Tissue Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. Genomic DNA quantity was assessed using the Qubit dsDNA BR Assay Kit

M. A. Woburn, The validated libraries were pooled in equimolar quantities and sequenced via 150 bp paired-end on an Illumina HiSeq 4000 platform following Illumina's recommended protocol. Raw data were demultiplexed with the Illumina bcl2fastq 2.17 into individual fastq files. Reads were aligned using the mem algorithm of bwa 0.7.8 and aligned to the hg19 reference into which decoy sequences had been added, PAR regions had been masked and the mitochondrial DNA had been replaced with the rCRS (revised Cambridge Reference Sequence) to match MITOMAP and most publicly available resources for mtDNA variants. Base quality scores were recalibrated using GATK BaseRecalibrator with enlarged context size for SNVs and Indels with respect to default (4 and 8 base pairs instead of 2 and 3). Variant calling was then performed using first HaplotypeCaller, to produce an individual GVCF file, and then multisample calling was performed using CombineGVCFs and then GenotypeGVCFs which produced the actual variant calls. Variant qualities and filters were then assessed with VariantRecalibrator tool using the tracks from GATK bundle and variants from GnomAD. For de novo variants, the Genotype Refinement workflow was applied using GenotypePosteriors to which a PED file with the family relationships, and again, a GnomAD track with allele counts and frequencies were supplied. The two subsequent steps were VariantFiltration to exclude low quality genotypes and VariantAnnotator to annotate possible de novo in the final VCF file. Mammalian two-hybrid assay A fragment of NIPBL containing amino acids 1-300 was inserted into the pCMV-BD expression plasmid (#211342, Agilent Technologies, For library preparation, 1000 ng of genomic DNA were used together with the TruSeq DNA PCR-Free Kit (Illumina) following the manufacturer's recommended protocol. The genomic DNA was fragmented to an average length of 350 bp by sonication on a Covaris E220 instrument

, All measurements were performed in triplicate in at least three independent experiments. Relative luciferase activity, indicating the strength of the interaction, was determined as the triplicate average of the ratio between the Firefly and the Renilla luciferase activity. Gamma irradiation and g-H2AX foci count Patient fibroblasts seeded on a coverslip were exposed to 1 Gy g-irradiation using a 300kV ceramic X-ray tube (RS320 X-ray machine, Xstrahl), Gln310_Ala316del)) were generated by site-directed in vitro mutagenesis with the Quick Change Site-directed mutagenesis kit, according to the manufacturer's instructions (Agilent Technologies). HEK293 cells were transiently transfected in 24-well plates with FuGene-HD (Promega)

. Haack, Briefly, RNA was isolated from whole-cell lysates using the AllPrep RNA Kit (QIAGEN) and RNA integrity number (RIN) was determined with the Agilent 2100, 2013.

;. Bioanalyzer and . Anders, RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies). RNA libraries were sequenced as 150 bp paired-end runs on an Illumina HiSeq4000 platform. The STAR aligner, 2015.

. Love, FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values were calculated using custom scripts. Differential expression analysis was performed using the R Bioconductor package DESeq2, 2014.

. Liao, Gene ontology term enrichment analysis Genes found to be differentially expressed (P value < 0.05, |Fold change| > 2) as compared to wild-type were considered in the analyses. Term enrichment analysis was performed using WEB-based GEne SeT AnaLysis Toolkit in its 2019 version, 2019.

, Over-Representation Analysis method was used on the Biological Processes functional database against genome protein-coding reference set, with default parameters). Redundancy in rendered term list was reduced by weighted set cover method