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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...chose 28 hpf as the earliest time point to ensure robust detection of all three fluorescent proteins. To verify that our sorting strategy enriched for endodermal cells in the sox17E population, we performed bulk RNA-seq on 28-hpf samples. This revealed strong enrichment for transcripts expressed...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...taxonomic order. For instance, in annotating D. melanogaster, we used Lepidoptera species, such as butterflies, as the nearest relatives, providing a conservative approximation of the nearest annotated s for a typical new target . Furthermore, despite the availability of numerous RNA-seq libraries (e...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
.... Together with this coordinate track, gene and mRNA annotation tracks are further depicted to provide more functional contexts. Users can find out the name of the displayed genes and mRNAs by mouse clicking (for genes) or hovering (for mRNAs).In the additional feature annotation panel, users can specify one...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...-regulatory elements encompassed CTCF-only, CTCF-bound, PLS, DNase-H3K4me3, dELS, PLS, and pELS terms. We report that human quasi-prime loci are most likely to be found in PLS (Fig. 4B). We also examined the overlap between long noncoding RNA genes and human quasi-prime loci and found a total of 1837 quasi...
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Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
- Christopher Faulk
Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
...methylation patterns and functions in vertebrates. BMC Biol 20: 70. doi:10.1186/s12915-022-01270-x ↵Baeza JA, Molina-Quirós JL, Hernández-Muñoz S. 2021. Genome survey sequencing of an iconic “trophy” sportfish, the roosterfish Nematistius pectoralis: size, repetitive elements, nuclear RNA gene operon...
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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
...vertebrates, we notice that only one-third of all annotated snoRNAs are expressed per , as in humans. Our results suggest that ancestral snoRNAs disseminated within vertebrate s, sometimes leading to the development of new functions and a probable gain in fitness and thereby conserving features favorable...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...In a new window Figure 1. Identification of polyadenylation sites (PASs) using 10x snRNA-seq data. (A) Curve plot showing the coverage of each part of the gene body in 19 different tissues and in each cell type of two representative tissues (skeletal muscle tissue and testicular tissue). The plot...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...first (She et al. 2009).To collect transcriptome evidence, we downloaded the RNA-seq data from NCBI's BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA230881 (tissues include whole embryo, adult gonad, brain, tail, and pooled organs) and mapped them...
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Research: Comparative transcriptomics of primary cells in vertebrates
- Tanvir Alam,
- Saumya Agrawal,
- Jessica Severin,
- Robert S. Young,
- Robin Andersson,
- Erik Arner,
- Akira Hasegawa,
- Marina Lizio,
- Jordan A. Ramilowski,
- Imad Abugessaisa,
- Yuri Ishizu,
- Shohei Noma,
- Hiroshi Tarui,
- Martin S. Taylor,
- Timo Lassmann,
- Masayoshi Itoh,
- Takeya Kasukawa,
- Hideya Kawaji,
- Luigi Marchionni,
- Guojun Sheng,
- Alistair R.R. Forrest,
- Levon M. Khachigian,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Michiel J.L. de Hoon
Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
...to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.Vertebrate organisms consist...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
..., as such, these previous lists underestimate the actual numbers (Frankish et al. 2019). Here, we identify and characterize the host/nested gene pairs in mouse and human using contemporary genomic annotations, RNA sequencing, and single-cell RNA sequencing (scRNA-seq) data, and collate this analysis...
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