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Genome-wide maps of chromatin state in buffalo fibroblasts with different cloning efficency

ABSTRACT: We report the distribution of histone acetylation at global genomic level in donor cells with different cloning efficiency. By obtaining over 40 million clean reads from immunoprecipitated DNA, we generated genome-wide chromatin-state maps of two buffalo fibroblast cell lines. We find that high cloning efficiency BFFs also had more regions enriched with H3K9ac sites near to the upstream of genes related to glycolysis. This study provides a framework for the application of comprehensive chromatin profiling towards donor cells with different cloning efficiency. We report the landscape of chromatin accessibility in donor cells with different cloning efficiency by transposase-accessible chromatin sequencing (ATAC-seq). We found that the landscape of chromatin accessibility was similar in both BFF1 and BFF2. Most loci defined by ATAC-seq was abundant just on the upstream of transcription start sites (TSS), but the signals in BFF2 were stronger than BFF1. GO analysis showed that most differential loci annotated genes were involved in developmental process, cellular process and metabolic process. This study provides a framework for the application of landscape of chromatin accessibility towards donor cells with different cloning efficiency.

ORGANISM(S): Bubalus bubalis

PROVIDER: GSE157250 | GEO | 2020/09/02

REPOSITORIES: GEO

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Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.

Project description:Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity, rendering a decline in cloning. To test this possibility, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning. Our plan included the control hybridizations (self to self) of 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency. Results We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cloning efficiency cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). Conclusions Our findings reveal that large copy number genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline. 9 custom 2.1M high density aCGH were performed to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning, accommodating the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency.