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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...similar to ORF1p. (C) In the mammalian vertebrate RefSeq proteins, two protein-coding genes had alternative ORF1p-like exons. The amino acid sequences encoded by the final coding exons were similar to ORF1p. (D) Protein structures of the ORF1p-like amino acid sequence encoded by the noncanonical exons...
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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
...in the strength of selection occurred along the long branches separating MHC-I-like1 and MHC-I-like2 from other sequences in MHC-I phylogeny, and (ii) whether the number and location of codons under positive/purifying selection differ among the three categories of genes.There was evidence of selection relaxation...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...have at least one G4 sequence per species, followed by bacteria with 6.6% and viruses with 2.2% (Supplemental Fig. 3). Furthermore, if we partition the genes into the two mutually exclusive sets of protein-coding and noncoding, we find in eukaryotic organisms an even higher median overlap of 25...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
....9% of reads started or ended with an MspI cut site. As expected, DNA input fragments were enriched for functionally important areas of the , with 41% located within protein coding sequences, 18% in promoter regions, and 17% in CpG islands (Fig. 1D). As observed in RRBS (Gu et al. 2011), these DNA input...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...evolutionary background of the genomic regions where each element is located, it is necessary to take gBGC into account when testing for lineage-specific acceleration, especially when detecting positively selected elements.MethodsSpecies informationThe final collection of s used in this study contained 201...
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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
...% of the protein-coding genes overlapped with at least one other protein-coding gene (Chen et al. 2019). Most of the time, the overlap involved a noncoding sequence (5′ untranslated region or UTR, 3′ UTR or intronic sequence) and sometimes only a few nucleotides were involved at the 3′ or 5′ end of the genes...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...of completely sequenced s, the large majority of which (>90%) originate from prokaryotes (Reddy et al. 2015). The accurate annotation of all protein-coding genes (interchangeably used with CDSs from here on) is essential to exploit this genomic information at multiple levels: from small, focused experiments, up...
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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...to the genomic target site (protospacer), which also requires the protospacer adjacent motif (PAM) at the 3′end, comprised of an NGG sequence (whereby N is any nucleotide and G is guanine). In addition to the target complementary sequence (spacer), the gRNA also contains a constant CRISPR RNA (crRNA) sequence...
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Research: Overlapping codes within protein-coding sequences
- Shalev Itzkovitz,
- Eran Hodis,
- and Eran Segal
Genome Res. November 2010 20: 1582-1589; Published in Advance September 14, 2010, doi:10.1101/gr.105072.110
...genome sequence. Within protein-coding regions, the redundancy of the genetic code can, in principle, allow for the overlapping encoding of signals in addition to the amino acid sequence, but it is not known to what extent genomes exploit this potential and, if so, for what purpose. Here, we...
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Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
...capacity. In addition, other possible scenarios of exitron origin can exist that are not tested by this approach and can be explored in future. As exitrons are internal regionsof protein-coding exons, selective pressure would prevent substitutions that disrupt their coding capacity, while favoring those...
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