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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...sequence alignment of the C terminus of expressed primate TBC1D3 paralog sequences predicted from Iso-Seq full-length cDNA. All, and only, human-expressed copies contain a 43 bp deletion within the ORF of the terminal exon, resulting in a frameshift, creating an extension of 41 novel amino acids to the C...
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Research: Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
...isoforms encoded by the same gene. Particularly, the fine-tuning of alternative splicing (AS) is a critical mechanism underlying disease and phenotypic evolution (Scotti and Swanson 2016; Bush et al. 2017). Hence, previous research on the conservation of RNA processing events in humans and nonhuman...
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LETTER: Human-specific insertions and deletions inferred from mammalian genome sequences
- Feng-Chi Chen,
- Chueng-Jong Chen,
- Wen-Hsiung Li,
- and Trees-Juen Chuang
Genome Res. January 2007 17: 16-22; Published in Advance November 9, 2006, doi:10.1101/gr.5429606
..., I. , Metzler, D. , Schwarz, C. , Pääbo, S. ( 2002 ) Genomewide comparison of DNA sequences between humans and chimpanzees . Am. J. Hum. Genet. 70 : 1490 – 1497 . ↵ Frazer, K.A. , Chen, X. , Hinds, D.A. , Pant, P.V. , Patil, N. , Cox, D.R. ( 2003 ) Genomic DNA insertions and deletions occur...
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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
...the National Disease Research Interchange (IRB protocol 14378B). Non-human samples were obtained from several sources, including the Yerkes primate center and the Southwest Foundation for Biomedical Research, under IACUC protocol 71619. When possible, samples were collected from adult individuals whose cause...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...and nonrodent species showed significantly narrower HMRs in rodents.To study epigenomic evolution across species, we aligned nonhuman methylomes and HMRs to the human reference at single-CpG resolution (Methods). The genomic composition of the seven-way orthologous is shown in Supplemental Figure S1C...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...–606. Perna NT, Batzer MA, Deininger PL, Stoneking M. 1992. Alu insertion polymorphism: a new type of marker for human population studies. Hum Biol 64: 641–648. Pickeral OK, Makalowski W, Boguski MS, Boeke JD. 2000. Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res 10...
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Perspective: Phylogenomics of primates and their ancestral populations
- Adam Siepel
Genome Res. November 2009 19: 1929-1941; Published in Advance October 3, 2009, doi:10.1101/gr.084228.108
...), to identify and characterize functional sequences present in primates but not other mammals (Boffelli et al. 2003), and to catalog the genomic similarities and differences between humans and nonhuman primates widely used in biomedical research, such as the baboon and rhesus macaque (Rhesus Macaque Genome...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment Martin Ebeling 1 , Erich Küng 2 , Angela See 3 , Clemens Broger 4 , Guido Steiner 1 , Marco Berrera 1 , Tobias Heckel 2...
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Perspective: Neanderthal genomics and the evolution of modern humans
- James P. Noonan
Genome Res. May 2010 20: 547-553; doi:10.1101/gr.076000.108
...of the Neanderthal specimens providing the DNA for whole- sequencing approach this level of preservation (Green et al. 2006, 2008; Briggs et al. 2007). In addition to these challenges, ancient specimens frequently become contaminated with modern human DNAduring handling andDNA extraction (Pa¨a¨bo et al. 2004...
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LETTER: Rapid evolution of an X-linked microRNA cluster in primates
- Rui Zhang,
- Yi Peng,
- Wen Wang,
- and Bing Su
Genome Res. May 2007 17: 612-617; Published in Advance April 6, 2007, doi:10.1101/gr.6146507
..., and inversions) in human ( Newman et al. 2005 ; Pollard et al. 2006 ; Prabhakar et al. 2006 ). Our data add another example by showing rapid evolution of a microRNA cluster in human and nonhuman primates. However, the previously identified fast-evolving regions do not include the X-linked microRNA cluster, which...

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