Searching journal content for articles similar to Lay et al. 24 (4): 545.

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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
..., the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type–specific chromatin...
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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: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China Corresponding author: weilei92@tsinghua.edu.cnAbstractReprogramming cell state transitions provides the potential for cell engineering and regenerative therapy. Finding the reprogramming transcription factors (TFs...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...-specific networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...be responsible for wiring tissue or cell type-specific regulatory networks (Chuong et al. 2017; Trizzino et al. 2018) and have acquired tissue-specific epigenetic regulations (Bourque et al. 2008; Chuong et al. 2013; Wang et al. 2015). Studies have also revealed that TE DNA methylation is dynamic during...
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Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
- Rylee Genner,
- Stuart Akeson,
- Melissa Meredith,
- Pilar Alvarez Jerez,
- Laksh Malik,
- Breeana Baker,
- Abigail Miano-Burkhardt,
- CARD-long-read Team,
- Benedict Paten,
- Kimberley J. Billingsley,
- Cornelis Blauwendraat,
- and Miten Jain
Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
...). While these improvements present promising opportunities for future genomics studies, they pose certain challenges for ongoing, multiyear sequencing projects. The NIH Intramural Center for Alzheimer's and Related Dementias (CARD) is in the process of sequencing thousands of brain tissue samples from...
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Research: Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
- Jia Huang,
- Wenjun Chen,
- Fan Zhou,
- Zhichang Pang,
- Luoluo Wang,
- Tao Pan,
- and Xiaoyun Wang
Genome Res. June 2021 31: 947-957; Published in Advance April 15, 2021, doi:10.1101/gr.272153.120
...investigated host-microbiome interactions via the tRNA profiling of four tissue types from germ-free and specific pathogen-free mice. Our analyses reveal that cytosolic and mitochondrial tRNA expression and tRNA modifications in the host are reprogrammed in a tissue-specific and microbiome-dependent manner...
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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
...that transcriptional co-occurrence is often tissue specific. This coexpression was especially prevalent within the transcriptionally permissive tissue, testis. We use this developmental system and scRNA-seq analysis to demonstrate that the coexpression of pairs can occur in single cells and transcription in the same...
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Research: Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
- Aarthi Venkat,
- Maximillian J. Carlino,
- Betty R. Lawton,
- Manju L. Prasad,
- Matthew Amodio,
- Courtney E. Gibson,
- Caroline J. Zeiss,
- Scott E. Youlten,
- Smita Krishnaswamy,
- and Diane S. Krause
Genome Res. June 2024 34: 837-850; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123
...+, but in others, unstable physiological levels of Ca2+ can lead to severe symptoms including muscle cramping, tetany, convulsions, and chronic fatigue (Gafni and Collins 2019). In surgical cases in which inadvertent damage to PT glands or their vascular supply may occur, fragments of functional PT tissue can...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...Departament de Genètica, Microbiologia i Estadística and IRBio, Universitat de Barcelona, 08028 Barcelona, Spain Corresponding author: yiguan.wang@ed.ac.ukAbstractThe rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses...
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