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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...window Figure 1. Characterization of germline and somatic macaque TE insertions. (A) Genomics experimental design. Individual hippocampal neuron (RBFOX3+) nuclei from two rhesus macaques (ON22212 and ON22213) were subjected to whole- amplification (WGA), followed by Illumina scWGS and RC-seq, to identify...
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Resource: The genome of the vervet (Chlorocebus aethiops sabaeus)
- Wesley C. Warren,
- Anna J. Jasinska,
- Raquel García-Pérez,
- Hannes Svardal,
- Chad Tomlinson,
- Mariano Rocchi,
- Nicoletta Archidiacono,
- Oronzo Capozzi,
- Patrick Minx,
- Michael J. Montague,
- Kim Kyung,
- LaDeana W. Hillier,
- Milinn Kremitzki,
- Tina Graves,
- Colby Chiang,
- Jennifer Hughes,
- Nam Tran,
- Yu Huang,
- Vasily Ramensky,
- Oi-wa Choi,
- Yoon J. Jung,
- Christopher A. Schmitt,
- Nikoleta Juretic,
- Jessica Wasserscheid,
- Trudy R. Turner,
- Roger W. Wiseman,
- Jennifer J. Tuscher,
- Julie A. Karl,
- Jörn E. Schmitz,
- Roland Zahn,
- David H. O'Connor,
- Eugene Redmond,
- Alex Nisbett,
- Béatrice Jacquelin,
- Michaela C. Müller-Trutwin,
- Jason M. Brenchley,
- Michel Dione,
- Martin Antonio,
- Gary P. Schroth,
- Jay R. Kaplan,
- Matthew J. Jorgensen,
- Gregg W.C. Thomas,
- Matthew W. Hahn,
- Brian J. Raney,
- Bronwen Aken,
- Rishi Nag,
- Juergen Schmitz,
- Gennady Churakov,
- Angela Noll,
- Roscoe Stanyon,
- David Webb,
- Francoise Thibaud-Nissen,
- Magnus Nordborg,
- Tomas Marques-Bonet,
- Ken Dewar,
- George M. Weinstock,
- Richard K. Wilson,
- and Nelson B. Freimer
Genome Res. December 2015 25: 1921-1933; Published in Advance September 16, 2015, doi:10.1101/gr.192922.115
...conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub...
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Resource: A comparison of gene expression and DNA methylation patterns across tissues and species
- Lauren E. Blake,
- Julien Roux,
- Irene Hernando-Herraez,
- Nicholas E. Banovich,
- Raquel Garcia Perez,
- Chiaowen Joyce Hsiao,
- Ittai Eres,
- Claudia Cuevas,
- Tomas Marques-Bonet,
- and Yoav Gilad
Genome Res. February 2020 30: 250-262; Published in Advance January 17, 2020, doi:10.1101/gr.254904.119
...expression and methylation levels in humans, chimpanzees, and rhesus macaques. Comparative functional genomic studies in primates, including from our own laboratory, often are not designed to test specific hypotheses. Rather, many of these comparative -scale studies aim to build catalogs of similarities...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...brain tissues quantified using RNA-seq data from eight different mammalian species, including human, chimpanzee, rhesus macaque, marmoset, cow, pig, mouse, and rat (Supplemental Tables S1, S2). Here, the brain was chosen as the focus of the current study because it experiences the most extensive...
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Research: Evolution of transcript modification by N⁶-methyladenosine in primates
- Lijia Ma,
- Boxuan Zhao,
- Kai Chen,
- Amber Thomas,
- Jigyasa H. Tuteja,
- Xin He,
- Chuan He,
- and Kevin P. White
Genome Res. March 2017 27: 385-392; Published in Advance January 4, 2017, doi:10.1101/gr.212563.116
.... 2C, four yellow bars) and observed an increase in the percentage of transcripts bearing conserved m6A modifications. Genome-wide, 34.0% of human genes with m6A-modified transcripts (and with chimp and rhesus orthologs) show m6A conservation. When we considered a set of genes defined by ExAC as under...
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Research: Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion
- Brittany L. Daughtry,
- Jimi L. Rosenkrantz,
- Nathan H. Lazar,
- Suzanne S. Fei,
- Nash Redmayne,
- Kristof A. Torkenczy,
- Andrew Adey,
- Melissa Yan,
- Lina Gao,
- Byung Park,
- Kimberly A. Nevonen,
- Lucia Carbone,
- and Shawn L. Chavez
Genome Res. March 2019 29: 367-382; Published in Advance January 25, 2019, doi:10.1101/gr.239830.118
...blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N = 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
...Pic under a Public Domain Dedication 1.0 license, and the silhouette of the macaque is from PhyloPic under a Public Domain Mark 1.0 license.Chromosome distributions and genomic featuresInversions ranged in size from 7 kbp to 17.7 Mbp, with heterozygous events being smaller in size than homozygous inversions...
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Letter: Sex-specific and lineage-specific alternative splicing in primates
- Ran Blekhman,
- John C. Marioni,
- Paul Zumbo,
- Matthew Stephens,
- and Yoav Gilad
Genome Res. February 2010 20: 180-189; Published in Advance December 15, 2009, doi:10.1101/gr.099226.109
...RNA-seq to study transcript regulation in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species, sequencing each sample independently in two lanes of Illumina’s GenomeAnalyzer II (for more details on samples, data collection...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...in human, rhesus macaque, mouse, dog, and rabbit by using BLAT and the UCSC Genome Browser liftOver tool (Kent et al. 2002). From the 67 gibbon BOS, we identified 133 orthologous regions mapped on human (Homo sapiens, hg38), 129 on rhesus (Macaca mulatta, RheMac8), 95 on mouse (Mus musculus, GRC38), 104...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
..., cerebellum, heart, kidney, liver, testis, ovary, placenta) for eight representatives of the three major mammalian lineages (placental mammals: human, chimpanzee, gorilla, orangutan, rhesus macaque, and mouse;marsupials: gray short-tailed opossum;monotremes: platypus) and a bird (nondomesticated chicken...

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