Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

Weissbein, Uri; Schachter, Maya; Egli, Dieter; Benvenisty, Nissim

doi:10.1038/ncomms12144

Cited by 56 publications

(59 citation statements)

References 41 publications

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“…Our approach to RNA digital karyotyping relies solely on expression values from each sample and does not require SNP genotyping, which can require deep sequencing (Weissbein et al 2016;Licciardi et al 2018). As such, this approach is translatable to lighter-sequencing schemes in addition to being computationally accessible.…”

Section: Rna-seq For Evaluating Human Embryo Competencementioning

confidence: 99%

RNA-seq as a tool for evaluating human embryo competence

et al. 2019

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The majority of embryos created through in vitro fertilization (IVF) do not implant. It seems plausible that rates of implantation would improve if we had a better understanding of molecular factors affecting embryo competence. Currently, the process of selecting an embryo for uterine transfer uses an ad hoc combination of morphological criteria, the kinetics of development, and genetic testing for aneuploidy. However, no single criterion can ensure selection of a viable embryo. In contrast, RNA-sequencing (RNA-seq) of embryos could yield high-dimensional data, which may provide additional insight and illuminate the discrepancies among current selection criteria. Recent advances enabling the production of RNAseq libraries from single cells have facilitated the application of this technique to the study of transcriptional events in early human development. However, these studies have not assessed the quality of their constituent embryos relative to commonly used embryological criteria. Here, we perform proof-of-principle advancement to embryo selection procedures by generating RNA-seq libraries from a trophectoderm biopsy as well as the remaining whole embryo. We combine state-of-the-art embryological methods with low-input RNA-seq to develop the first transcriptome-wide approach for assessing embryo competence. Specifically, we show the capacity of RNA-seq as a promising tool in preimplantation screening by showing that biopsies of an embryo can capture valuable information available in the whole embryo from which they are derived. Furthermore, we show that this technique can be used to generate a RNA-based digital karyotype and to identify candidate competence-associated genes. Together, these data establish the foundation for a future RNA-based diagnostic in IVF.

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Section: Rna-seq For Evaluating Human Embryo Competencementioning

confidence: 99%

RNA-seq as a tool for evaluating human embryo competence

et al. 2019

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“…Chromosome loss in aneuploidy results in CNV of RNA transcript levels as well as LOH. When we performed eSNP karyotyping 41 for expressed genes to validate CNV results, we found a lower frequency of heterozygous SNPs on chromosome 7 in patients compared with healthy donors (supplemental Figure 5). Furthermore, LOH was evident for chromosome 7 on examination of individual denominated monosomy 7 cells compared with diploid cells from the same patient, as described above (supplemental Figure 6A).…”

Section: Aneuploid Cells Detected From Patients' Hspcsmentioning

confidence: 99%

Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells

Zhao

Gao

et al. 2017

Blood

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“…Previous studies reporting chromosomal breakpoints in human or mouse PGA p(MII)ESC lines used either (1) DNA genotyping of p(MII)ESCs derived from an F1 mouse cross similar to the DNA genotyping performed here used as a control (Additional file 2: Fig. S6) [10]; (2) the signature of heterozygous and homozygous signals over SNPs as obtained by DNA-based genotyping [41] or by RNA-seq [71]. The latter method takes advantage of the fact that p(MII) ES cells retain pericentromeric homozygosity but show distal regions of heterozygosity due to crossing-over in the oocyte [10,41] and is particularly powerful if parental genotypes are unknown.…”

Section: Discussionmentioning

confidence: 99%

Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states

Dirks

Mierlo

Kerstens

et al. 2019

Epigenetics & Chromatin

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Background: Genomic imprinting, resulting in parent-of-origin specific gene expression, plays a critical role in mammalian development. Here, we apply allele-specific RNA-seq on isogenic B6D2F1 mice to assay imprinted genes in tissues from early embryonic tissues between E3.5 and E7.25 and in pluripotent cell lines to evaluate maintenance of imprinted gene expression. For the cell lines, we include embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) derived from fertilized embryos and from embryos obtained after nuclear transfer (NT) or parthenogenetic activation (PGA). Results: As homozygous genomic regions of PGA-derived cells are not compatible with allele-specific RNA-seq, we developed an RNA-seq-based genotyping strategy allowing identification of informative heterozygous regions. Global analysis shows that proper imprinted gene expression as observed in embryonic tissues is largely lost in the ESC lines included in this study, which mainly consisted of female ESCs. Differentiation of ESC lines to embryoid bodies or NPCs does not restore monoallelic expression of imprinted genes, neither did reprogramming of the serum-cultured ESCs to the pluripotent ground state by the use of 2 kinase inhibitors. Fertilized EpiSC and EpiSC-NT lines largely maintain imprinted gene expression, as did EpiSC-PGA lines that show known paternally expressed genes being silent and known maternally expressed genes consistently showing doubled expression. Notably, two EpiSC-NT lines show aberrant silencing of Rian and Meg3, two critically imprinted genes in mouse iPSCs. With respect to female EpiSC, most of the lines displayed completely skewed X inactivation suggesting a (near) clonal origin. Conclusions: Altogether, our analysis provides a comprehensive overview of imprinted gene expression in pluripotency and provides a benchmark to allow identification of cell lines that faithfully maintain imprinted gene expression and therefore retain full developmental potential.

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Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

Cited by 56 publications

References 41 publications

RNA-seq as a tool for evaluating human embryo competence

RNA-seq as a tool for evaluating human embryo competence

Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells

Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states

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