Congrats to Dr. Colin Shew & Dr. Daniela Soto: Our first Dennis lab PhD Grads!

Halloween Genome Center symposium

The lab took part in the UC Davis Genome Center Halloween Symposium (first time in-person since 2019). Our Bob-Ross-themed costumes secured our place as team and individual costume winners this year (was stiff competition, as usual!), as well as 3rd place for our Neanderthal-themed pumpkins. Was nice to see faculty, staff, and trainees in person again to discuss topics related to diversity!

Dennis lab at (in-person) ASHG!

We were excited to attend ASHG in-person in LA, to catch up with old friends and make new ones. Four lab members presented their work:

  • Postdoc Sierra Nishizaki platform talk: “Novel genes associated with the severe autism subphenotype disproportionate megalencephaly”

  • Grad student José Uribe-Salazar poster: “Parallel functional screening of human duplicated genes in neurodevelopment at single-cell resolution using zebrafish”

  • Grad student Colin Shew poster: “Dissecting mechanisms underlying expression divergence of human duplicated genes”

  • Grad student Daniela Soto poster: “Population diversity and selection of recent gene duplications detected using a complete human genome sequence”

Good news: Graduations and grad school!

Three junior trainees from the lab are heading to grad school starting in Fall 2022:

  • Genetics and genomics undergrad Cole Ingamells will be starting the M.S. Bioinformatics program at UC Berkeley.

  • UC Davis PREP scholar Tasha Mariano is starting in the Ph.D. Molecular Biology and Genetics program at Cornell University.

  • Former undergrad Aditya Sriram completed his M.S. in Epidemiology from the University of Washington and will be starting in the Ph.D. Human Genetics program at University of Pittsburgh.

We also have farewells and graduations to celebrate:

  • IGG student Aedric Lim completed his M.S. on “3D Genome Organization in the Developing Macaque Brain” with future plans to pursue a career in genetic counseling. He is currently seeking out clinical research opportunities. Feel free to reach out to Aedric.

  • Postdoc Sierra Nishizaki completed their ARTP fellowship focused on the genetics of ASD with megalencephaly (with a preprint on the way, stay tuned!) and is currently on the job market as a Bioinformatician (see tweet for more info and feel free to reach out to Sierra).

  • Former undergrad and postbac KaeChandra Weyenberg completed her M.S. in Public Health from East Tennessee University and is now lead supervisor epidemiologist at the Tennessee Department of Health.

  • Former undergrad Dhriti Jagannathan completed her M.S. in Genetic Counseling at the University of Minnesota and is now Program Manager and General/Pediatrics Genetic Counselor at Columbia University working with the All Of Us study and eMERGE network.

The complete sequence of a human genome!

A historical scientific milestone has been achieved: the first complete sequence of a human genome (!) published in a special issue of Science. Scientists of the Telomere-to-Telomere (T2T) Consortium sequenced a fully homozygous human cell line, CHM13, generated by the erroneous fertilization of an enucleated egg, to reconstruct the complete genome. The new assembly, named T2T-CHM13, includes 8% of heterochromatin completely missing from the previous human genome assembly (GRCh38). Besides the original Human Genome Project, this is the second most significant progress in our sequencing and understanding of the human genome.

Summary abstract from “A complete reference genome improves analysis of human genetic variation”

Dennis lab members, including Megan and graduate students Colin Shew and Daniela Soto, contributed to a number of the published studies, including:

  • “A complete reference genome improves analysis of human genetic variation,” where the impact of the complete genome in the analysis of human genetic variation was thoroughly assessed. This was a truly collaborative effort led by four labs (Schatz, McCoy, Zook, and ours). In particular, Daniela performed genome-wide analysis of collapsed duplication in GRCh38, finding 8 Mbp of sequence incorrectly represented in GRCh38 and fixed in T2T-CHM13. Further, we helped demonstrate significant improvements in variant calling across medically-relevant genes.

  • “Complete genomic and epigenetic maps of human centromeres” by generating CHM13 RNA-seq data, with Colin analyzing transcript abundance across the T2T-CHM13 transcriptome and showing expression of numerous genes near centromeres.

  • “The complete sequence of a human genome”, with Megan performing comparative genomic analysis of the expanded FRG1 primate-specific gene expansion, which has several missing copies in GRCh38 that are resolved in T2T-CHM13.

This new genome opens many possibilities for scientists who can now explore the most repetitive sequence of the human genome, such as centromeres. Particularly interesting for us is the full resolution of segmental duplications, large historical duplicated segments that are a hallmark of great ape evolution and harbor genes associated with neurodevelopment. Moving forward, we are fully embracing T2T-CHM13 to answer questions regarding the evolution and disease implication of human-specific duplicated genes at unprecedented resolution (and hope many of you will too!).

Additional resources available for the new T2T-CHM13 genome include:

  • A UCSC Genome Browser

  • CHM13 open-access data available via GitHub

  • Dennis lab analysis available via GitHub

  • Genome stratifications of reference artefacts (incl. collapsed dups) are here

  • Variant calls can be found here as well as on AnVIL

You can read Megan’s commentary about the implications of this scientific achievement in a perspective published in Genome Research. Also, our work, in addition to contributions by Prof Chuck Langley, were highlighted by UC Davis here.

Welcome new lab members!

This past year, we have welcomed two new undergrads, Jeffrey Zang (Computer Science) and Gabriana La (Biochemistry), and a new grad student, Sean McGinty (Integrative Genetics & Genomics).

Gabriana was recently awarded the UC Davis Genome Center Charles and Nanci Cooper Undergraduate Award. Sean received a UC Davis Dean’s Distinguished Graduate Fellowship.

Welcome!!

Evaluating CRISPR tools in zebrafish

Our recent paper “Evaluation of CRISPR gene-editing tools in zebrafish” led by grad student José Uribe-Salazar is out in BMC Genomics. Several others from the lab contributed including lab manager Gulhan Kaya, volunteer Aadithya Sekar, and postbacs/undergrads KaeChandra Weyenberg and Cole Ingamells.


Some highlights:

  • We tested editing accuracy and predictability of 50 guide RNAs (from IDT) with SpCas9 using in vivo, in silico, and in vitro methods.

  • Large discrepancies existed between in silico editing predictive tools and empirical in vivo cutting efficiencies. The most accurate prediction resulted from using CRISPRScan against a reference specific to our zebrafish strain.

  • We observed low frequency of off-target mutations with no method (in silico or in vitro) effectively predicting these. More analyses are needed to understand the variability involved in off-target cutting events.

  • To characterize commonly-used controls in zebrafish CRISPR experiments, we evaluated larvae solely injected with SpCas9 (enzyme or mRNA) and found no evidence of an excess of somatic mutations in these injected larvae.

  • Performing RNA-seq of injection controls revealed notable variability in gene expression profiles compared to uninjected controls, including genes involved in several metabolic pathways that highlight a potential lasting effect of the microinjection. We recommend caution if performing characterizations of these particular genes in mosaic crispants.

Overall, our hope is for this resource to be helpful for the zebrafish/CRISPR community while they plan their future awesome experiments!

RapID semi-automated cell counter

Our recent paper “RapID Cell Counter: Semi-automated and mid-throughput estimation of cell density within diverse cortical layers” was published in eNeuro co-led by IGG grad students Aarthi Sekar and Thiago Sanches and in collaboration with the amazing Simó lab at UC Davis. After struggling to manually count neurons from images of in utero electroporation of mouse neocortex, we decided to make an easy-to-use automated tool that can quantify fluorescently-labeled cells across defined layers. The method is called RapID and is available here.

Some highlights of our study:

  • RapID runs as an easy-to-use GUI, with step-by-step instructions on how to install and run as supplementary materials and on the Github. Our hope is that the tool will be useful to the community with install and implementation representing only a small hurdle. Please reach out to us if you encounter difficulties!

  • Users define parameters for images based on expected cell size, density, and brightness. RapID subsequently will quantify labeled cells within a user-defined quadrangle (split by set number of layers). Parameters used for diverse cell types by our groups are included in the study as a starting point for users.

  • We successfully show that RapID results match manual “click” identification using Fiji’s Cell Counter and apply it to diverse cell images, including astrocytes and dopaminergic neurons.

As an added bonus: the beautiful images of dopaminergic neurons, made by the talented Keiko Hino and Sergi Simó, were selected as an official Zoom backdrop for the Society for Neuroscience available for download on their website!

Three of our former undergrads heading to grad school

We are so proud of former Dennis lab undergrads heading off to grad school this fall!

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  • Matangi Kumar will be starting in the Vision Science Ph.D. program at UC Berkeley. She also received a UC Davis Distinguished Scholar award as one of the top Genetics and Genomics undergrads in her graduating class!

  • Mira Mastoras is joining the Biomolecular Engineering and Bioinformatics Ph.D. program at UC Santa Cruz.

  • Eva Ferino was accepted to the Genetic Counseling master’s program at UCSF.

Regulatory mechanisms of recent human gene duplications

Our recent study “Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes” was published in Molecular Biology and Evolution led by IGG grad student Colin Shew, with support from various current/former Dennis lab members Paulina Carmona-Mora, Daniela Soto, Mira Mastoras, Elizabeth Roberts, Joseph Rosas, and Gulhan Kaya and collaborator Henriette O’Geen. Using diverse functional genomic datasets, we characterized expression of recent human gene duplicates to better understand their functional fates and mechanisms underlying altered paralog expression.

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Major highlights of the study:

  • Most human derived duplicate genes diverge in expression from their human and chimp counterparts, suggesting they’re undergoing neofunctionalization or pseudogenization.

  • In some cases derived genes may have usurped function of their ancestral paralogs or function through increased gene dosage.

  • Evolutionary age, post-transcriptional mechanisms, copy-number, and truncation status cannot completely explain observed diverged expression of genes in lymphoblastoid cell lines

  • ChIP-seq datasets miss most histone marks in duplicated regions that we recover using a modified bioinformatic pipeline that allows multiple read mappings.

  • We did not detect global differences in regulatory signatures between ancestral and derived paralogs, but rather, individual differences in cis regulatory elements, which we validate using reporter assays.