Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness

Schneider, Aksana D.; Hiller, Michael; Buchholz, Frank

doi:10.1101/683565

Cited by 3 publications

(1 citation statement)

References 35 publications

(37 reference statements)

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“…Because of their extraordinary sequence conservation, ultraconserved elements were initially assumed to be essential for life 12 . However, deletion of many ultraconserved enhancers has no effects on mouse organismal or cell viability [62][63][64][65] . Although poison exons are similar to enhancers with respect to their gene regulatory activities, we found that many poison exons exert robust effects on cell viability.…”

Section: Discussionmentioning

confidence: 99%

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

et al. 2020

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While RNA-seq has enabled comprehensive quantification of alternative splicing, no correspondingly high-throughput assay exists for functionally interrogating individual isoforms. We describe pgFARM (paired guide RNAs for alternative exon removal), a CRISPR/Cas9-based method to manipulate isoforms independent of gene inactivation. This approach enabled rapid suppression of exon recognition in polyclonal settings to identify functional roles for individual exons, such as an SMNDC1 cassette exon that regulates pan-cancer intron retention. We generalized this method to a pooled screen to measure the functional relevance of "poison" cassette exons, which disrupt their host genes' reading frames yet are frequently ultraconserved. Many poison exons were essential for the growth of both cultured cells and lung adenocarcinoma xenografts, while a subset had clinically relevant tumor suppressor activity. The essentiality and cancer relevance of poison exons likely contribute to their unusually high conservation and contrast with the dispensability of other ultraconserved elements for viability.Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

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Section: Discussionmentioning

confidence: 99%

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

et al. 2020

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Application of CRISPR screens to investigate mammalian cell competition

Paraskevopoulos¹,

McGuigan²

2021

Briefings in Functional Genomics

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Cell competition is defined as the context-dependent elimination of cells that is mediated by intercellular communication, such as paracrine or contact-dependent cell signaling, and/or mechanical stresses. It is considered to be a quality control mechanism that facilitates the removal of suboptimal cells from both adult and embryonic tissues. Cell competition, however, can also be hijacked by transformed cells to acquire a ‘super-competitor’ status and outcompete the normal epithelium to establish a precancerous field. To date, many genetic drivers of cell competition have been identified predominately through studies in Drosophila. Especially during the last couple of years, ethylmethanesulfonate-based genetic screens have been instrumental to our understanding of the molecular regulators behind some of the most common competition mechanisms in Drosophila, namely competition due to impaired ribosomal function (or anabolism) and mechanical sensitivity. Despite recent findings in Drosophila and in mammalian models of cell competition, the drivers of mammalian cell competition remain largely elusive. Since the discovery of CRISPR/Cas9, its use in functional genomics has been indispensable to uncover novel cancer vulnerabilities. We envision that CRISPR/Cas9 screens will enable systematic, genome-scale probing of mammalian cell competition to discover novel mutations that not only trigger cell competition but also identify novel molecular components that are essential for the recognition and elimination of less fit cells. In this review, we summarize recent contributions that further our understanding of the molecular mechanisms of cell competition by genetic screening in Drosophila, and provide our perspective on how similar and novel screening strategies made possible by whole-genome CRISPR/Cas9 screening can advance our understanding of mammalian cell competition in the future.

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A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

Hecker

Hiller

2020

GigaScience

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Background Multiple alignments of mammalian genomes have been the basis of many comparative genomic studies aiming at annotating genes, detecting regions under evolutionary constraint, and studying genome evolution. A key factor that affects the power of comparative analyses is the number of species included in a genome alignment. Results To utilize the increased number of sequenced genomes and to provide an accessible resource for genomic studies, we generated a mammalian genome alignment comprising 120 species. We used this alignment and the CESAR method to provide protein-coding gene annotations for 119 non-human mammals. Furthermore, we illustrate the utility of this alignment by 2 exemplary analyses. First, we quantified how variable ultraconserved elements (UCEs) are among placental mammals. Leveraging the high taxonomic coverage in our alignment, we estimate that UCEs contain on average 4.7%–15.6% variable alignment columns. Furthermore, we show that the center regions of UCEs are generally most constrained. Second, we identified enhancer sequences that are only conserved in placental mammals. We found that these enhancers are significantly associated with placenta-related genes, suggesting that some of these enhancers may be involved in the evolution of placental mammal-specific aspects of the placenta. Conclusion The 120-mammal alignment and all other data are available for analysis and visualization in a genome browser at https://genome-public.pks.mpg.de/and for download at https://bds.mpi-cbg.de/hillerlab/120MammalAlignment/.

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Large-scale dissection suggests that ultraconserved elements are dispensable for mouse embryonic stem cell survival and fitness

Cited by 3 publications

References 35 publications

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

Application of CRISPR screens to investigate mammalian cell competition

A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers

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