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Cars BS, Kessler C, Hoffman EA, Côté SD, Koelsch D, Shafer ABA. Island demographics and trait associations in white-tailed deer. Heredity (Edinb) 2024:10.1038/s41437-024-00685-2. [PMID: 38802598 DOI: 10.1038/s41437-024-00685-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force and results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number (~50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.
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Affiliation(s)
- Brooklyn S Cars
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Camille Kessler
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, 4000, Central Florida Blvd, Orlando, FL, USA
| | - Steeve D Côté
- Département de Biologie and Centre d'Études Nordiques, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Daniel Koelsch
- Fédération des chasseurs de Saint-Pierre et Miquelon, Saint-Pierre et Miquelon, France
- Direction des Territoires de l'Alimentation et de la Mer, service Biodiversité, Saint-Pierre et Miquelon, France
| | - Aaron B A Shafer
- Environmental and Life Sciences Graduate Program, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
- Department of Forensics, Trent University, 2140 East Bank Drive, Peterborough, ON, K9J 7B8, Canada.
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2
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Berglund G, Lennon CD, Badu P, Berglund JA, Pager CT. Zika virus infection in a cell culture model reflects the transcriptomic signatures in patients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595842. [PMID: 38826459 PMCID: PMC11142252 DOI: 10.1101/2024.05.25.595842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection.
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Affiliation(s)
- Gillian Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Claudia D. Lennon
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Pheonah Badu
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - J. Andrew Berglund
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T. Pager
- RNA Institute, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
- Department of Biological Sciences, College of Arts and Sciences, University at Albany-SUNY, Albany, NY 12222, USA
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3
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Kalleberg J, Rissman J, Schnabel RD. Overcoming Limitations to Deep Learning in Domesticated Animals with TrioTrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589602. [PMID: 38659907 PMCID: PMC11042298 DOI: 10.1101/2024.04.15.589602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Variant calling across diverse species remains challenging as most bioinformatics tools default to assumptions based on human genomes. DeepVariant (DV) excels without joint genotyping while offering fewer implementation barriers. However, the growing appeal of a "universal" algorithm has magnified the unknown impacts when used with non-human genomes. Here, we use bovine genomes to assess the limits of human-genome-trained models in other species. We introduce the first multi-species DV model that achieves a lower Mendelian Inheritance Error (MIE) rate during single-sample genotyping. Our novel approach, TrioTrain, automates extending DV for species without Genome In A Bottle (GIAB) resources and uses region shuffling to mitigate barriers for SLURM-based clusters. To offset imperfect truth labels for animal genomes, we remove Mendelian discordant variants before training, where models are tuned to genotype the offspring correctly. With TrioTrain, we use cattle, yak, and bison trios to build 30 model iterations across five phases. We observe remarkable performance across phases when testing the GIAB human trios with a mean SNP F1 score >0.990. In HG002, our phase 4 bovine model identifies more variants at a lower MIE rate than DeepTrio. In bovine F1-hybrid genomes, our model substantially reduces inheritance errors with a mean MIE rate of 0.03 percent. Although constrained by imperfect labels, we find that multi-species, trio-based training produces a robust variant calling model. Our research demonstrates that exclusively training with human genomes restricts the application of deep-learning approaches for comparative genomics.
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Affiliation(s)
- Jenna Kalleberg
- University of Missouri, Division of Animal Sciences, Columbia, MO, 65201 USA
| | - Jacob Rissman
- University of Missouri, Division of Animal Sciences, Columbia, MO, 65201 USA
| | - Robert D Schnabel
- University of Missouri, Division of Animal Sciences, Columbia, MO, 65201 USA
- University of Missouri, Genetics Area Program, Columbia, MO, 65201 USA
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4
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Liddle TA, Majumdar G, Stewart C, Bain MM, Stevenson TJ. Dissociating Mechanisms That Underlie Seasonal and Developmental Programs for the Neuroendocrine Control of Physiology in Birds. eNeuro 2024; 11:ENEURO.0154-23.2023. [PMID: 38548332 PMCID: PMC11007308 DOI: 10.1523/eneuro.0154-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 04/12/2024] Open
Abstract
Long-term programmed rheostatic changes in physiology are essential for animal fitness. Hypothalamic nuclei and the pituitary gland govern key developmental and seasonal transitions in reproduction. The aim of this study was to identify the molecular substrates that are common and unique to developmental and seasonal timing. Adult and juvenile quail were collected from reproductively mature and immature states, and key molecular targets were examined in the mediobasal hypothalamus (MBH) and pituitary gland. qRT-PCR assays established deiodinase type 2 (DIO2) and type 3 (DIO3) expression in adults changed with photoperiod manipulations. However, DIO2 and DIO3 remain constitutively expressed in juveniles. Pituitary gland transcriptome analyses established that 340 transcripts were differentially expressed across seasonal photoperiod programs and 1,189 transcripts displayed age-dependent variation in expression. Prolactin (PRL) and follicle-stimulating hormone subunit beta (FSHβ) are molecular markers of seasonal programs and are significantly upregulated in long photoperiod conditions. Growth hormone expression was significantly upregulated in juvenile quail, regardless of photoperiodic condition. These findings indicate that a level of cell autonomy in the pituitary gland governs seasonal and developmental programs in physiology. Overall, this paper yields novel insights into the molecular mechanisms that govern developmental programs and adult brain plasticity.
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Affiliation(s)
- Timothy Adam Liddle
- Laboratory of Seasonal Biology, School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Gaurav Majumdar
- Department of Zoology, University of Allahabad, Allahabad, India
| | - Calum Stewart
- Laboratory of Seasonal Biology, School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Maureen M Bain
- Laboratory of Seasonal Biology, School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Tyler John Stevenson
- Laboratory of Seasonal Biology, School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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5
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Jones T, Sigauke RF, Sanford L, Taatjes DJ, Allen MA, Dowell RD. A transcription factor (TF) inference method that broadly measures TF activity and identifies mechanistically distinct TF networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585303. [PMID: 38559193 PMCID: PMC10980006 DOI: 10.1101/2024.03.15.585303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
TF profiler is a method of inferring transcription factor regulatory activity, i.e. when a TF is present and actively regulating transcription, directly directly from nascent sequencing assays such as PRO-seq and GRO-seq. Transcription factors orchestrate transcription and play a critical role in cellular maintenance, identity and response to external stimuli. While ChIP assays have measured DNA localization, they fall short of identifying when and where transcription factors are actively regulating transcription. Our method, on the other hand, uses RNA polymerase activity to infer TF activity across hundreds of data sets and transcription factors. Based on these classifications we identify three distinct classes of transcription factors: ubiquitous factors that play roles in cellular homeostasis, driving basal gene programs across tissues and cell types, tissue specific factors that act almost exclusively at enhancers and are themselves regulated at transcription, and stimulus responsive TFs which are regulated post-transcriptionally but act predominantly at enhancers. TF profiler is broadly applicable, providing regulatory insights on any PRO-seq sample for any transcription factor with a known binding motif.
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6
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Sigauke RF, Sanford L, Maas ZL, Jones T, Stanley JT, Townsend HA, Allen MA, Dowell RD. Atlas of nascent RNA transcripts reveals enhancer to gene linkages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570626. [PMID: 38105978 PMCID: PMC10723487 DOI: 10.1101/2023.12.07.570626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Gene transcription is controlled and modulated by regulatory regions, including enhancers and promoters. These regions are abundant in unstable, non-coding bidirectional transcription. Using nascent RNA transcription data across hundreds of human samples, we identified over 800,000 regions containing bidirectional transcription. We then identify highly correlated transcription between bidirectional and gene regions. The identified correlated pairs, a bidirectional region and a gene, are enriched for disease associated SNPs and often supported by independent 3D data. We present these resources as an SQL database which serves as a resource for future studies into gene regulation, enhancer associated RNAs, and transcription factors.
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Affiliation(s)
- Rutendo F. Sigauke
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
| | - Lynn Sanford
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
| | - Zachary L. Maas
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
- Computer Science, University of Colorado Boulder, 1111 Engineering Drive, UCB 430, Boulder, 80309, CO, USA
| | - Taylor Jones
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
| | - Jacob T. Stanley
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
| | - Hope A. Townsend
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Ave, UCB 347, Boulder, 80309, CO, USA
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
| | - Robin D. Dowell
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave., UCB 596, Boulder, 80309, CO, USA
- Computer Science, University of Colorado Boulder, 1111 Engineering Drive, UCB 430, Boulder, 80309, CO, USA
- Molecular, Cellular and Developmental Biology, University of Colorado Boulder, 1945 Colorado Ave, UCB 347, Boulder, 80309, CO, USA
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7
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Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC. Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567880. [PMID: 38045327 PMCID: PMC10690208 DOI: 10.1101/2023.11.20.567880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic studies have associated thousands of enhancers with breast cancer. However, the vast majority have not been functionally characterized. Thus, it remains unclear how variant-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3,512 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes. Analysis of >500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of variant-associated enhancers disrupts breast cancer gene programs. We observe variant-associated enhancers that directly or indirectly regulate the expression of cancer genes. We also find one-to-multiple and multiple-to-one network motifs where enhancers indirectly regulate cancer genes. Notably, multiple variant-associated enhancers indirectly regulate TP53. Comparative studies illustrate sub-type specific functions between enhancers in ER+ and ER- cells. Finally, we developed the pySpade package to facilitate analysis of single-cell enhancer screens. Overall, we demonstrate that enhancers form regulatory networks that link cancer genes in the genome, providing a more comprehensive understanding of the contribution of enhancers to breast cancer development.
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Affiliation(s)
- Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | | | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Huan Zhao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Current address: Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences
- Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390
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8
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Dussex N, Kurland S, Olsen RA, Spong G, Ericsson G, Ekblom R, Ryman N, Dalén L, Laikre L. Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Commun Biol 2023; 6:1035. [PMID: 37848497 PMCID: PMC10582009 DOI: 10.1038/s42003-023-05385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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Affiliation(s)
- Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden.
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden.
- Norwegian University of Science and Technology, University Museum, Trondheim, NO-7491, Norway.
| | - Sara Kurland
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, SE-171 21, Solna, Sweden
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Göran Ericsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Robert Ekblom
- Wildlife Analysis Unit, Swedish Environmental Protection Agency, SE-106 48, Stockholm, Sweden
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, SE-106 91, Stockholm, Sweden.
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9
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Mestre-Tomás J, Liu T, Pardo-Palacios F, Conesa A. SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554392. [PMID: 37662216 PMCID: PMC10473693 DOI: 10.1101/2023.08.23.554392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Long-read RNA-seq has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile utility that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field. We demonstrate the effectiveness of SQANTI-SIM by benchmarking five transcriptome reconstruction pipelines using the simulated data.
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Affiliation(s)
- Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council, Catedràtic Agustín Escardino Benlloch, Paterna, 46980, Spain
| | - Tianyuan Liu
- Institute for Integrative Systems Biology, Spanish National Research Council, Catedràtic Agustín Escardino Benlloch, Paterna, 46980, Spain
| | - Francisco Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council, Catedràtic Agustín Escardino Benlloch, Paterna, 46980, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Catedràtic Agustín Escardino Benlloch, Paterna, 46980, Spain
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534962. [PMID: 37066272 PMCID: PMC10103937 DOI: 10.1101/2023.03.30.534962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The invasive trophoblast cell lineage in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model to study hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus (sn) ATAC-seq data from gestation day (gd) 15.5 and 19.5 rat uterine-placental interface tissues and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial, and smooth muscle cells, and compared invasive trophoblast chromatin accessibility to extravillous trophoblast (EVT) cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO, 64108
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
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11
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Pinto BJ, Gamble T, Smith CH, Keating SE, Havird JC, Chiari Y. The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.523807. [PMID: 36712019 PMCID: PMC9882329 DOI: 10.1101/2023.01.20.523807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .
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Affiliation(s)
- Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Tony Gamble
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
- Bell Museum of Natural History, University of Minnesota, St Paul, MN USA
| | - Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Shannon E. Keating
- Department of Biological Sciences, Marquette University, Milwaukee WI USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
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12
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Bonar M, Anderson SJ, Anderson CR, Wittemyer G, Northrup JM, Shafer ABA. Genomic correlates for migratory direction in a free-ranging cervid. Proc Biol Sci 2022; 289:20221969. [PMID: 36475444 PMCID: PMC9727677 DOI: 10.1098/rspb.2022.1969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Animal migrations are some of the most ubiquitous and one of the most threatened ecological processes globally. A wide range of migratory behaviours occur in nature, and this behaviour is not uniform among and within species, where even individuals in the same population can exhibit differences. While the environment largely drives migratory behaviour, it is necessary to understand the genetic mechanisms influencing migration to elucidate the potential of migratory species to cope with novel conditions and adapt to environmental change. In this study, we identified genes associated with a migratory trait by undertaking pooled genome-wide scans on a natural population of migrating mule deer. We identified genomic regions associated with variation in migratory direction, including FITM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. Such a genetic basis for a migratory trait contributes to the adaptive potential of the species and might affect the flexibility of individuals to change their behaviour in the face of changes in their environment.
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Affiliation(s)
- Maegwin Bonar
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada K9L 0G2
| | - Spencer J. Anderson
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada K9L 0G2
| | - Charles R. Anderson
- Mammals Research Section, Colorado Parks and Wildlife, Fort Collins, CO 80523, USA
| | - George Wittemyer
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph M. Northrup
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada K9L 0G2,Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources & Forestry, Peterborough, Ontario, Canada K9J 3C7
| | - Aaron B. A. Shafer
- Environmental & Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada K9L 0G2
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