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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...peaks. Switching between narrow peak and mixed peak mode is a simple one argument option in Allo.To create a training set with known labels, we needed MMR-containing regions in which the peak status (i.e., peak vs. nonpeak) is known. We achieved this by artificially shortening ENCODE ChIP-seq reads...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...of these retrogenes occurred more than 3 million years ago (MYA) in the common ancestor of M. caroli and M. musculus (Thybert et al. 2018).To further examine the evolutionary origin of our newly characterized retrogenes, we compared the nucleotide sequences of their ORFs to the sequences of M. musculus and four...
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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
...RSPRDM4 ORF1p and ORF2p that may be less relevant to human L1s, as L1RSPRDM4 retrotransposed most efficiently when both of its native ORFs were present and was far more mobile than L1.3 in human cells and in the more evolutionarily distant context of a rodent cell line. The retrotransposition competence...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...eight chromosomes and containing less than 4000 protein-coding genes in the species examined. Most reduction consists of gene and intron loss, intron shortening, and very short intergenic regions (Abrahamsen et al. 2004; Xu et al. 2004; Kissinger and DeBarry 2011).As the Cryptosporidium field...
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Method: Transcriptional fates of human-specific segmental duplications in brain
- Max L. Dougherty,
- Jason G. Underwood,
- Bradley J. Nelson,
- Elizabeth Tseng,
- Katherine M. Munson,
- Osnat Penn,
- Tomasz J. Nowakowski,
- Alex A. Pollen,
- and Evan E. Eichler
Genome Res. October 2018 28: 1566-1576; Published in Advance September 18, 2018, doi:10.1101/gr.237610.118
...to maintain the isoform structure of the ancestor. Incomplete duplications result in only a portion of the ancestral gene being duplicated. This can lead to a truncated duplicate gene or a fusion transcript, where additional exons are acquired from flanking sequence. For 3′ truncations, transcription may...
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Research: Embryonic LTR retrotransposons supply promoter modules to somatic tissues
- Kosuke Hashimoto,
- Eeva-Mari Jouhilahti,
- Virpi Töhönen,
- Piero Carninci,
- Juha Kere,
- and Shintaro Katayama
Genome Res. November 2021 31: 1983-1993; Published in Advance October 21, 2021, doi:10.1101/gr.275354.121
...in the of the common ancestor of simian primates about 45–65 million years ago. To examine the expression of MLT2A families in early embryos of simian primates, we used publicly available transcriptome data sets of macaque (Wang et al. 2017) and marmoset (Supplemental Fig. S3A; Boroviak et al. 2018). As in human...
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Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
- Sahin Naqvi,
- Daniel W. Bellott,
- Kathy S. Lin,
- and David C. Page
Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
...retains a Y homolog and continues to escape XCI in primates but has lost its Y homolog and is subject to XCI in rodents. These observations could be explained by shortened generation times in the rodent lineage, resulting in longer evolutionary times, during which the forces leading to Y gene decay...
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Research: The frequent evolutionary birth and death of functional promoters in mouse and human
- Robert S. Young,
- Yoshihide Hayashizaki,
- Robin Andersson,
- Albin Sandelin,
- Hideya Kawaji,
- Masayoshi Itoh,
- Timo Lassmann,
- Piero Carninci,
- The FANTOM Consortium,
- Wendy A. Bickmore,
- Alistair R. Forrest,
- and Martin S. Taylor
Genome Res. October 2015 25: 1546-1557; Published in Advance July 30, 2015, doi:10.1101/gr.190546.115
...evolutionary changes, we have set out to discover the extent to which the gain, loss, and divergence of functional promoters contribute to regulatory evolution along both the rodent and human lineages. We have used extensive libraries of cap analysis of gene expression (CAGE) data, which precisely...
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Research: Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
- Arikuni Uchimura,
- Mayumi Higuchi,
- Yohei Minakuchi,
- Mizuki Ohno,
- Atsushi Toyoda,
- Asao Fujiyama,
- Ikuo Miura,
- Shigeharu Wakana,
- Jo Nishino,
- and Takeshi Yagi
Genome Res. August 2015 25: 1125-1134; Published in Advance June 30, 2015, doi:10.1101/gr.186148.114
...successfully sequenced and confirmed in the sequenced individuals, indicating that our high-throughput sequencing analysis was very reliable.In the mutator lines, all of the selected candidates (80 SNVs) were confirmed to be bona fide de novo SNVs, present in the sequenced mouse but not in its ancestors...
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Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
- Sahar Gelfman,
- David Burstein,
- Osnat Penn,
- Anna Savchenko,
- Maayan Amit,
- Schraga Schwartz,
- Tal Pupko,
- and Gil Ast
Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
...analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor...

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