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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...In a new window Figure 1. Study overview. (A) Schematics of wild-type CRX protein and the p.R90W and p.E168d2 pathogenic variants, containing a point DNA-binding domain mutation or resulting in truncation of the transcriptional effector domain, respectively. (B) Outline of the experimental procedure...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...functional domains: the N-terminal DNA-binding domain (HD) and the C-terminal transcription effector domain. Disease-associated mutations are distributed across both domains, with amino acid substitutions primarily observed in the CRX HD (Tran and Chen 2014; Zheng and Chen 2024). To understand how HD...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
...authors: liuee1985@sicau.edu.cn, lingzhao.fang@qgg.au.dk, liliang@sicau.edu.cnAbstractPoultry egg production is shaped by the intertwined action of multiple physiological systems, greatly magnifying the complexity of its underlying genetic regulation. Although multitissue mapping of regulatory variants...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...regions underlying disorders like fragile X syndrome (FXS) (Stevanovski et al. 2022). ONT also enables variant phasing for inheritance and de novo mutation analyses (Cretu Stancu et al. 2017) and can distinguish clinically relevant genes from pseudogenes, improving diagnostic accuracy (Leija-Salazar et al...
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Review: A systematic review on the biochemical threshold of mitochondrial genetic variants
- Karan K. Smith,
- Jesse D. Moreira,
- Callum R. Wilson,
- June O. Padera,
- Ashlee N. Lamason,
- Liying Xue,
- Deepa M. Gopal,
- David B. Flynn,
- and Jessica L. Fetterman
Genome Res. March 2024 34: 341-365; Published in Advance April 16, 2024, doi:10.1101/gr.278200.123
...development (Stewart and Chinnery 2015). It is also possible that the biochemical and phenotypic thresholds may not yet have been reached in tissues that would result in a clinical phenotype in the asymptomatic individual, or that other environmental or genetic factors affect the penetrance of this variant...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...individuals (Supplemental Fig. S5A,B), stratifying by drift direction revealed consistent, albeit subtle, age-associated increases in transcriptional levels for genes proximal to both positive and negative drift-CpGs. Notably, only genes near positive drift-CpGs showed increased transcriptional variance...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...of potential large-scale rearrangements and completeness.Long-read sequencing reveals the frequency of structural variantsNext to de novo assembly, long-read sequencing provides an opportunity to detect SVs through mapping to a reference . We mapped the long reads to the reference SC5314 and identified -wide...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...coexpression, potentially fostering tumor progression. On the immunogenic front, HLA-I immunopeptidomics of AsPC-1 cells and DAC13 organoids identify over 11,000 peptides respectively. Althought mutation-derived neoantigens are rare, several peptides are originated from TE-chimeric transcripts, including four...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...classify pathogenic variants into different allelic categories to begin to reveal the underlying pathogenic mechanism of newly discovered clinical conditions. In this Perspective, we will guide clinical researchers to understand how experimental data obtained from flies can support the discovery...
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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. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...RNA-seq on 28 hpf samples. 151 This revealed strong enrichment for transcripts expressed in specific endoderm cell 152 populations including pancreatic, liver and intestinal markers (Fig. 1D, Supplemental Fig. 2, 153 Supplemental Table 1). However, we also note enrichment of markers of fin epithelia...
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