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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
...understood. Here, we use comparative genomics, expression across multiple ontogenetic stages and tissues, as well as polymorphism data to investigate MHC evolution in newts. Contrary to earlier suggestions of a massively expanded MHC in salamanders, we find that the core MHC region remains relatively compact...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...and enabling the exploration of the diversity from complex genomic regions (Miga and Wang 2021). This is particularly valuable for detecting links between genetic markers and diseases, facilitating the genetic study of more prevalent pathologies in different populations. Combining long-read sequencing...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
..., California 92093, USA; 2Sanford Stem Cell Institution Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, California 92037, USA; 3Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92093, USA; 4Bioinformatics and Systems Biology...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...the impact of intra-genomic heterogeneity in base composition from that of drift (Fig. 7D). In any case, even though intra-genomic heterogeneity in base composition might explain the weakness of TS in some species, there must be some other factors that affect the intensity of TS. Indeed, among insect species...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...in KS1 and KS2 = 60.01 and 1508.9, respectively.Aging-related regions show preferentially disrupted chromatin accessibility in KS1 and KS2 neurons but not in B or T cellsOur findings yield insights into (1) the genomic distribution of the chromatin defects in KS1 and KS2 and (2) the cell type...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...These authors contributed equally to this work. Corresponding authors: chenhb@bmi.ac.cn, cheng_li@pku.edu.cnAbstractAccurately measuring biological age is crucial for improving healthcare for the elderly population. However, the complexity of aging biology poses challenges in how to robustly estimate aging...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression Howard J. Womersley1,4, Daniel Muliaditan2,3,4, Ramanuj DasGupta3 and Lih Feng Cheow1,2 1Institute for Health Innovation and Technology, National University...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...and Bucher 2022). The T. castaneum has been sequenced and annotated, and a first version of assembly was available in 2008 (Richards et al. 2008). Structural analyses revealed large amounts (>30%) of different classes of repetitive DNA in the assembled regions of the T. castaneum . Among them, the (peri...
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Perspective: Why community consultation matters in genomic research benefit-sharing models
- Sarah LeBaron von Baeyer,
- Rebecca Crocker,
- Rindra Rakotoarivony,
- Jean Freddy Ranaivoarisoa,
- Germain Jules Spiral,
- Stephane Castel,
- Andrew Farnum,
- Holly Vance,
- Noah Collins,
- Keolu Fox,
- and Kaja Wasik
Genome Res. January 2024 34: 1-6; Published in Advance January 31, 2024, doi:10.1101/gr.278308.123
...in human genomic research, established precedents across the private and public spheres are lacking. Moreover, the few existing models for benefit sharing with populations that participate in genomic research are largely limited to intangible or nonfinancial benefits, or to top-down initiatives...
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