Genome Biology
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#1Étienne Fafard-Couture (Université de Sherbrooke)H-Index: 2
#2Danny Bergeron (Université de Sherbrooke)H-Index: 7
Last. Michelle S. Scott (Université de Sherbrooke)H-Index: 29
view all 5 authors...
BACKGROUND Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. RESULTS We used a low structu...
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#1Soo-Ji Park (KU: Korea University)
#2Tae Yeong Jeong (KU: Korea University)
Last. Kyoungmi Kim (KU: Korea University)H-Index: 10
view all 12 authors...
Prime editors, novel genome-editing tools consisting of a CRISPR-Cas9 nickase and an engineered reverse transcriptase, can induce targeted mutagenesis. Nevertheless, much effort is required to optimize and improve the efficiency of prime-editing. Herein, we introduce two strategies to improve the editing efficiency using proximal dead sgRNA and chromatin-modulating peptides. We used enhanced prime-editing to generate Igf2 mutant mice with editing frequencies of up to 47% and observed germline tr...
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#1Claudia VivoriH-Index: 3
Last. Juan ValcárcelH-Index: 60
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BACKGROUND Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem ...
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#1Scott Sherrill-Mix (UPenn: University of Pennsylvania)H-Index: 23
#2Young Sun Hwang (UPenn: University of Pennsylvania)H-Index: 19
Last. Frederic D. Bushman (UPenn: University of Pennsylvania)H-Index: 124
view all 17 authors...
BACKGROUND Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of transmission. Reverse transcription-polymerase chain reaction (RT-PCR) provides a gold standard assay for SARS-CoV-2 RNA, but instrument costs are high and supply chains are potentially fragile, motivating interest in additional assay methods. Reverse transcription and loop-mediated isothermal amplification (RT-LAMP) provides an alternative that uses ort...
1 CitationsSource
#1Nisha Padmanabhan (NUS: National University of Singapore)H-Index: 11
#2Huang Kie Kyon (NUS: National University of Singapore)H-Index: 1
Last. Patrick Tan (NUS: National University of Singapore)H-Index: 89
view all 26 authors...
BACKGROUND CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers including gastric cancer (GC), mechanisms underlying CIMP remain poorly understood. We sought to discover molecular contributors to CIMP in GC, by performing global DNA methylation, gene expression, and proteomics profiling across 14 gastric cell lines, followed by similar integrative...
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#1Xu CaiH-Index: 4
#2Lichun ChangH-Index: 1
Last. Xiaowu WangH-Index: 50
view all 10 authors...
BACKGROUND Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes. RESULTS Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among th...
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#1Paolo Marangio (Edin.: University of Edinburgh)H-Index: 1
#2Ka Ying Toby Law (Edin.: University of Edinburgh)H-Index: 1
Last. Sander Granneman (Edin.: University of Edinburgh)H-Index: 40
view all 4 authors...
Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and variability. We present diffBUM-HMM, a noise-aware model that enables accurate detection of RNA flexibility and conformational changes from high-throughput RNA structure-probing data. diffBUM-HMM is widely compatible, accounting for sampling variation and sequence coverage biases, and displ...
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#1Da-Inn Lee (UW: University of Wisconsin-Madison)H-Index: 2
#2Sushmita Roy (UW: University of Wisconsin-Madison)H-Index: 29
High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene regulatory processes. The sparsity of Hi-C matrices poses a challenge for reliable detection of these units. We present GRiNCH, a constrained matrix-factorization-based approach for simultaneous smoothing and discovery of TADs from sparse contact count matrices. GRiNCH shows superior perform...
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#1Tianyi Sun (UCLA: University of California, Los Angeles)H-Index: 1
#2Dongyuan Song (UCLA: University of California, Los Angeles)H-Index: 3
Last. Jingyi Jessica LiH-Index: 17
view all 4 authors...
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneously achieve three goals: preserving genes, capturing gene correlations, and generating any number of cells with varying sequencing depths. To fill this gap, we propose scDesign2, a transparent simulator that achieves all three goals and generates high-fidelity synthetic data for multiple sing...
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#1Cheng Quan (Protein Sciences)H-Index: 1
#2Yuanfeng Li (Protein Sciences)H-Index: 8
Last. Gangqiao ZhouH-Index: 1
view all 7 authors...
BACKGROUND Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little is known of adaptive introgressed SVs in Tibetans so far. RESULTS Here, we generate a comprehensive catalog of SVs in a Chinese Tibetan (n = 15) and Han (n = 10) population using nanopore sequencing technology. Among a total of 38,216 unique SVs in the catalog, 27% are sequence-...
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