Colin J. Shew
A5035520132- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Single-cell and spatial transcriptomics
- Ubiquitin and proteasome pathways
- Pleistocene-Era Hominins and Archaeology
- Endoplasmic Reticulum Stress and Disease
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Genetic diversity and population structure
- Genomics and Rare Diseases
- Wildlife Ecology and Conservation
- Genetics, Bioinformatics, and Biomedical Research
University of California, Davis
2020-2023
University of California, Los Angeles
2016-2021
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric centromeric repeats, constitute 6.2% the (189.9 megabases). Detailed maps these regions revealed multimegabase structural...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
Significance The Microrchidia (MORC) family of ATPases are important regulators gene silencing in multiple organisms but little is known about their molecular behavior. In this study, we used crystallography and native mass spectrometry to show that MORC3 forms dimers when it binds nonhydrolyzable ATP analogues. We also determined the CW zinc finger-like domain can bind euchromatic histone H3 lysine 4 (H3K4) methylation localizes H3K4me3-marked chromatin. crystal structure provides details...
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led important discoveries related selection within species, demographic history, lineage-specific traits. Structural (SVs), including deletions inversions, comprise a larger proportion of differences between making them an yet understudied source trait divergence. Here, we used combination long-read -range approaches the structural variant landscape two...
Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and important animal model for disease studies. A deep understanding of its genetics therefore required both biomedical evolutionary Among structural variants, inversions represent driving force in speciation play role predisposition. Here we generated genome-wide map between macaque, combining single-cell strand sequencing cytogenetics. We identified 375 total 859 bp 92 Mbp, increasing by eightfold...
Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD are differentially expressed across human cell tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 from 30 families between humans chimpanzees found expression patterns consistent with relaxed selection on or neofunctionalization...
Abstract Existing human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, essential role in chromosome segregation. Here, we present an extensive study newly assembled peri/centromeric representing 6.2% (189.9 Mb) the first complete, telomere-to-telomere assembly (T2T-CHM13). We discovered novel patterns repeat organization, variation, evolution at both large small length scales....
ABSTRACT Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD are differentially expressed across human cell tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 from 30 families between humans chimpanzees found expression patterns consistent with pseudo- or neofunctionalization....