MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing.

More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses. Key points: We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.

A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations.

Mammalian genomes fold into tens of thousands of long-range loops, but their functional role and physiologic relevance remain poorly understood. Here, using human post-mitotic neurons with rare familial Alzheimer's disease (FAD) mutations, we identify hundreds of reproducibly dysregulated genes and thousands of miswired loops prior to amyloid accumulation and tau phosphorylation. Single loops do not predict expression changes; however, the severity and direction of change in mRNA levels and single-cell burst frequency strongly correlate with the number of FAD-gained or -lost promoter-enhancer loops. Classic architectural proteins CTCF and cohesin do not change occupancy in FAD-mutant neurons. Instead, we unexpectedly find TAATTA motifs amenable to binding by DLX homeodomain transcription factors and changing noncoding RNAPolII signal at FAD-dynamic promoter-enhancer loops. DLX1/5/6 mRNA levels are strongly upregulated in FAD-mutant neurons coincident with a shift in excitatory-to-inhibitory gene expression and miswiring of multi-loops connecting enhancers to neural subtype genes. DLX1 overexpression is sufficient for loop miswiring in wildtype neurons, including lost and gained loops at enhancers with tandem TAATTA arrays and singular TAATTA motifs, respectively. Our data uncover a genome structure-function relationship between multi-loop miswiring and dysregulated excitatory and inhibitory transcriptional programs during lineage commitment of human neurons homozygously-engineered with rare FAD mutations.

Psychological and emotional experiences of participants in a medical school, early assurance admissions program targeting students from groups underrepresented in medicine.

BACKGROUND: There are growing number of pathway programs, with an early assurance of admission, that target undergraduate students from groups underrepresented in medicine (URiM) to enable their competitiveness for and matriculation to medical school, including the Penn Access Summer Scholars (PASS) program. The psychological and emotional experiences of students in these programs, however, have not been previously described. METHODS: Students from the summer 2021 cohort of the PASS program were interviewed using a structured set of questions that explored four specific areas: (i) the application process; (ii) the benefits and value of being in the PASS program; (iii) the emotional and psychological challenges and stresses of being in the PASS program; (iv) feelings and emotions about not taking the MCAT or having to interview at multiple schools. The transcribed, de-identified interviews were then subjected to a qualitative analysis. RESULTS: Students in PASS reported that the program was valuable to them in that it reduced the stress of the pre-medical process; relieved worry and anxiety surrounding the MCAT; enabled development of supportive relationships and provided meaningful exposures to the medical profession and biomedical research. Despite this, students reported feelings of imposterism, guilt, and fear of disappointing, along with varying degrees of regret over not taking the MCAT and not interviewing at more than one medical school. CONCLUSIONS: URiM and other marginalized students participating in early assurance admissions programs likely enter medical school with a range of positive and negative emotions as a result of their participation in these programs. These data can be used to inform the development of programing and other initiatives that further support the transition and success of these students in medical school.

Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.

Short tandem repeat (STR) instability causes transcriptional silencing in several repeat expansion disorders. In fragile X syndrome (FXS), mutation-length expansion of a CGG STR represses FMR1 via local DNA methylation. Here, we find megabase-scale H3K9me3 domains on autosomes and encompassing FMR1 on the X chromosome in FXS patient-derived iPSCs, iPSC-derived neural progenitors, EBV-transformed lymphoblasts, and brain tissue with mutation-length CGG expansion. H3K9me3 domains connect via inter-chromosomal interactions and demarcate severe misfolding of TADs and loops. They harbor long synaptic genes replicating at the end of S phase, replication-stress-induced double-strand breaks, and STRs prone to stepwise somatic instability. CRISPR engineering of the mutation-length CGG to premutation length reverses H3K9me3 on the X chromosome and multiple autosomes, refolds TADs, and restores gene expression. H3K9me3 domains can also arise in normal-length iPSCs created with perturbations linked to genome instability, suggesting their relevance beyond FXS. Our results reveal Mb-scale heterochromatinization and trans interactions among loci susceptible to instability.

Living Alternating Ring-Opening Metathesis Copolymerization of 2,3-Dihydrofuran to Provide Completely Degradable Polymers.

2,3-Dihydrofuran (DHF) has recently been gaining significant attention as a comonomer in metathesis polymerization, thanks to its ability to provide the resultant polymer backbones with stimuli-responsive degradability. In this report, we present living alternating copolymerization of DHF with less reactive endo-tricyclo[4.2.2.02,5 ]deca-3,9-dienes (TDs) and endo-oxonorbornenes (oxoNBs). By carefully controlling the reactivity of both the Ru initiators and the monomers, we have achieved outstanding A, B-alternation (up to 98 %) under near stoichiometric DHF loading conditions. Notably, we have also found that the use of a more sterically hindered Ru initiator helps to attain polymer backbones with higher DHF incorporation and superior A, B-alternation. While preserving the living characteristics of DHF copolymerization, as evidenced by controlled molecular weights (up to 73.9 kDa), narrow dispersities (down to 1.05), and block copolymer formation, our DHF copolymers could be broken down to a single repeat unit level under acidic conditions. 1 H NMR analysis of the model copolymer revealed that after 24 hours of degradation, up to 80 % of the initial polymer was transformed into a single small molecule product, and after purification, up to 66 % of the degradation product was retrieved. This study provides a versatile approach to improve the alternation and degradability of DHF copolymers.

Living Suzuki-Miyaura Catalyst-Transfer Polymerization for Precision Synthesis of Length-Controlled Armchair Graphene Nanoribbons and Their Block Copolymers.

The bottom-up synthesis of graphene nanoribbons (GNRs) offers a promising approach for designing atomically precise GNRs with tuneable photophysical properties, but controlling their length remains a challenge. Herein, we report an efficient synthetic protocol for producing length-controlled armchair GNRs (AGNRs) through living Suzuki-Miyaura catalyst-transfer polymerization (SCTP) using RuPhos-Pd catalyst and mild graphitization methods. Initially, SCTP of a dialkynylphenylene monomer was optimized by modifying boronates and halide moieties on the monomers, affording poly(2,5-dialkynyl-p-phenylene) (PDAPP) with controlled molecular weight (Mn up to 29.8k) and narrow dispersity (D = 1.14-1.39) in excellent yield (>85%). Subsequently, we successfully obtained N = 5 AGNRs by employing a mild alkyne benzannulation reaction on the PDAPP precursor and confirmed their length retention by size-exclusion chromatography. In addition, photophysical characterization revealed that a molar absorptivity was directly proportional to the length of the AGNR, while its highest occupied molecular orbital (HOMO) energy level remained constant within the given AGNR length. Furthermore, we prepared, for the very first time, N = 5 AGNR block copolymers with widely used donor or acceptor-conjugated polymers by taking advantage of the living SCTP. Finally, we achieved the lateral extension of AGNRs from N = 5 to 11 by oxidative cyclodehydrogenation in solution and confirmed their chemical structure and low band gap by various spectroscopic analyses.

Cascade Cyclopolymerization of 5-Ethynyl-1,8-Nonadiyne Derivatives to Synthesize Low Band Gap Conjugated Polyacetylenes Containing a Fused Bicyclic Structure.

Cyclopolymerization is a powerful method for synthesizing polyacetylenes containing four- to seven-membered rings. However, the structure of the repeat unit only consists of mono-cycloalkene due to the single cyclization of diyne monomers. Herein, we demonstrate a novel cascade cyclopolymerization to synthesize polyacetylenes containing fused bicyclic rings from triyne monomers containing bulky dendrons via sequential cascade ring-closing metathesis. These dendrons provided solubility and stability to the rigid bicyclic polyacetylene backbone. In addition, we controlled the regioselectivity of the catalyst approach by altering its structure and synthesized polymers containing fused bicyclo[4,3,0] or [4,4,0] rings with high molecular weights of up to 120 kg mol-1 . Interestingly, the resulting polymers showed narrower band gaps (down to 1.6 eV) than polymers with mono-cycloalkene repeat units due to the planarization of the conjugated segment resulting from the fused bicyclic structure.

Powerful Direct C-H Amidation Polymerization Affords Single-Fluorophore-Based White-Light-Emitting Polysulfonamides by Fine-Tuning Hydrogen Bonds.

The development of white-light-emitting polymers has been actively pursued because of the importance of such polymers in various applications, such as lighting sources and displays. To generate white-light, numerous research efforts have focused on synthesizing multifluorophore-based random copolymers to effectively cover the entire visible region. However, due to their intrinsic synthetic and structural features, this strategy has limitations in securing color reproducibility and stability. Herein, we report the development of single-fluorophore-based white-light-emitting homopolymers with excellent color reproducibility. A powerful direct C-H amidation polymerization (DCAP) strategy enabled the synthesis of defect-free polysulfonamides that emit white-light via excited-state intramolecular proton-transfer (ESIPT). To gain structural insights for designing such polymers, we conducted detailed model studies by varying the electronic nature of substituents that allow facile tuning of the emission colors. Further analysis revealed precise control of the thermodynamics of the ESIPT process by fine-tuning the strength of the intramolecular hydrogen bond. By applying this design principle to polymerization, we successfully produced a series of well-defined polysulfonamides with single-fluorophore emitting white-light. The resulting polymers emitted consistent fluorescence, regardless of their molecular weights or phases (i.e., solution, powder, or thin film), guaranteeing excellent color reproducibility. With these advantages in hand, we also demonstrated practical use of our DCAP system by fabricating a white-light-emitting coated LED.