Browsing by keyword "Computational biology and bioinformatics"

Now showing items 1-3 of 3

    • A Cas9 with PAM recognition for adenine dinucleotides
      Chatterjee, Pranam; Lee, Jooyoung; Nip, Lisa; Koseki, Sabrina R. T.; Tysinger, Emma; Sontheimer, Erik J.; Jacobson, Joseph M.; Jakimo, Noah (2020-05-18)
      CRISPR-associated (Cas) DNA-endonucleases are remarkably effective tools for genome engineering, but have limited target ranges due to their protospacer adjacent motif (PAM) requirements. We demonstrate a critical expansion of the targetable sequence space for a type II-A CRISPR-associated enzyme through identification of the natural 5[Formula: see text]-NAAN-3[Formula: see text] PAM preference of Streptococcus macacae Cas9 (SmacCas9). To achieve efficient editing activity, we graft the PAM-interacting domain of SmacCas9 to its well-established ortholog from Streptococcus pyogenes (SpyCas9), and further engineer an increased efficiency variant (iSpyMac) for robust genome editing activity. We establish that our hybrids can target all adenine dinucleotide PAM sequences and possess robust and accurate editing capabilities in human cells.

    • Highly structured homolog pairing reflects functional organization of the Drosophila genome
      AlHaj Abed, Jumana; Erceg, Jelena; Goloborodko, Anton; Nguyen, Son C.; McCole, Ruth B.; Saylor, Wren; Fudenberg, Geoffrey; Lajoie, Bryan R.; Dekker, Job; Mirny, Leonid A.; et al. (2019-10-03)
      Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks.

    • The case for altruism in institutional diagnostic testing
      Specht, Ivan; Sani, Kian; Botti-Lodovico, Yolanda; Hughes, Michael; Heumann, Kristin; Bronson, Amy; Marshall, John; Baron, Emily; Parrie, Eric; Glennon, Olivia; et al. (2022-02-03)
      Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members' close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18 to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.