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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...regulation of mitochondrial–nuclear gene expression (CMNGE) to changing physiological conditions is poorly understood and is limited to certain tissues and organisms. We hypothesized that CMNGE is important for development across vertebrates and, hence, should be conserved. As a first step, we analyzed more...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...@shu.edu.cnAbstractThe spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we present photocleavage and ligation sequencing (PCL-seq), a spatial indexing method utilizing a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...was used on a catalog of polymorphic tandem repeats to genotype tandem repeat copy numbers. A mean neighbor distance-based outlier calling method was used to define extreme repeat expansions. (C) RNA sequencing expression outlier pipeline: transcriptome data from the UDN was processed by quantifying...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...from the chimpanzee (Pan troglodytes) to the zebrafish (Danio rerio) using publicly available transcriptomic data from the Bgee database (Bastian et al. 2021). Of note, except for the chicken (Gallus gallus), all of these vertebrate species show a smaller proportion of predicted expressed sno...
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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
...the proximal side are required for normal regeneration and use spatially resolved transcriptomics (tomo-seq) to understand the molecular and cellular events underlying this process. Analyzing gene expression across the ear and comparing expression modules between proximal and distal wound sides, we identify...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...for this article.] Computational analyses have suggested many conserved structured RNAs in vertebrate s (Washietl et al. 2005; Torarinsson et al. 2008; Parker et al. 2011; Smith et al. 2013). Recent transcriptome-wide experiments also support a diverse RNA structure landscape (Ding et al. 2014; Rouskin et al. 2014...
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Research: The evolution of evolvability in microRNA target sites in vertebrates
- Jin Xu,
- Rui Zhang,
- Yang Shen,
- Guojing Liu,
- Xuemei Lu,
- and Chung-I Wu
Genome Res. November 2013 23: 1810-1816; Published in Advance September 27, 2013, doi:10.1101/gr.148916.112
...to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one—that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)—has rarely been discussed. For such an analysis, we cannot use evolutionary conservation...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...the new s, we show that gars have the slowest rates of genomic structural and sequence evolution of all vertebrates. In species of the two living gar genera Atractosteus and Lepisosteus, 83.35% of the s remain identical even though they diverged over 100 million years ago. Genome size variation among gars...
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Perspective: Functional transcriptomics in the post-ENCODE era
- Jonathan M. Mudge,
- Adam Frankish,
- and Jennifer Harrow
Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
..., the usefulness of comparative annotation depends entirely upon the availability of high-quality sequences and, ideally, large pools of transcriptomic data. In practice, few vertebrate species are comparable with human and mouse in this regard. Toward a functional annotation of lncRNAs Unlike for CDS transcripts...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
..., Jagiellonian University, 30-387 Kraków, Poland; 5Chinese Institutes for Medical Research, Beijing 100069, China; 6Physics of life Excellence Cluster Dresden, 01307 Dresden, Germany Corresponding author: wieslaw.babik@uj.edu.plAbstractMajor Histocompatibility Complex (MHC) molecules are central to vertebrate...

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