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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...to decipher tissue-specific codes of gene regulation for individual and groups of TFs using available single-cell gene expression data in both species. Studying key conserved factors in worm and fly greatly will enhance analysis, interpretation, and the broader relevance of data gathered in ENCODE and other...
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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
...(Yanai et al. 2005). The value of τ varies between 0 for housekeeping genes (or broadly expressed genes) and 1 for tissue-specific genes. In both mouse and human, we observed that host genes are more broadly expressed and nested genes are more tissue specific than the rest of the (Fig. 4B), suggesting...
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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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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
...the features learned from single-cell omics data can capture other dimensions of biological aging.Here, we developed single-cell aging-level estimator (SCALE), a tissue-specific measure that quantifies aging in individual cells using single-cell RNA-sequencing (scRNA-seq) data (Fig. 1). Unlike other clocks...
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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
...Iris Zhu and David Landsman National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA Corresponding author: zhuz2@nih.govAbstractHousekeeping genes are considered to be regulated by common enhancers across different...
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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
...expression. We find that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, whereas housekeeping genes are more often controlled by intergenic enhancers, common to many tissues. Notably, an intergenic...
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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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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...of the C. elegans embryo (Packer et al. 2019) and second larval stage (L2) (Cao et al. 2017) provide a survey of the full complement of genes expressed in each major cell type, and even some cells present only once in the worm (e.g., the ASEL and ASER gustatory neurons). Now, to understand how these tissue-specific...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...component of mole-rat adaptations. Last, we investigated the contribution of repetitive elements to lineage-specific gene regulation in the mole-rat clade.ResultsComparative epigenomics of liver and heart regulatory activities in mole-ratsTo investigate the contribution of enhancer evolution to tissue-specific...
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Research: Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs
- Jake Yeung,
- Jérôme Mermet,
- Céline Jouffe,
- Julien Marquis,
- Aline Charpagne,
- Frédéric Gachon,
- and Felix Naef
Genome Res. February 2018 28: 182-191; Published in Advance December 18, 2017, doi:10.1101/gr.222430.117
...equally to this work. Corresponding author: felix.naef@epfl.chAbstractTemporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs...
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