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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...of Michigan, Ann Arbor, Michigan 48109, USA; 9Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA Corresponding author: mohlke@med.unc.eduAbstractChromatin accessibility quantitative trait locus (caQTL) studies have identified regulatory...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
.... By integrating transcription factor (TF)–target gene relationships, chromatin accessibility, and genetic variation, this framework aims to elucidate the cell type–specific regulatory mechanisms underlying AD progression, link genetic risk variants to cis-regulatory elements and target genes, and prioritize...
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Method: Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
- Brendan L. O'Connell,
- Ruth V. Nichols,
- Dmitry Pokholok,
- Jerushah Thomas,
- Sonia N. Acharya,
- Andrew Nishida,
- Casey A. Thornton,
- Marissa Co,
- Andrew J. Fields,
- Frank J. Steemers,
- and Andrew C. Adey
Genome Res. February 2023 33: 208-217; Published in Advance February 15, 2023, doi:10.1101/gr.276655.122
...ATAC produces high-coverage profiles. (A) Single-end indexed adapter design for nanowell sciATACv3. (B) UMAP of 21,239 mouse brain chromatin accessibility profiles produced using nanowell sciATACv3. Dashed line indicates interneuron cell clusters. (C) Cell type module scoring for clusters in panel A. (D) Marker...
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Method: A unified analysis of atlas single-cell data
- Hao Chen,
- Nam D. Nguyen,
- Matthew Ruffalo,
- and Ziv Bar-Joseph
Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
...the ability of GIANT on integrating data from different modalities, we collected single-cell mouse brain data from the Allen Brain Cell Atlas (Yao et al. 2023), which contains 2,341,350 cells from scRNA-seq and 3,938,808 cells from MERFISH spatial transcriptomics (Chen et al. 2015). Both modalities were...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...-based measurements of genomic activity, including ChIP-seq measurement of transcription factor binding and histone modifications and DNaseseq and ATAC-seq measurement of chromatin accessibility (Luo et al. 2020; Moore et al. 2020; Snyder et al. 2020). The fourth and final phase of ENCODE has greatly expanded the set...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...a bivalent chromatin-state configuration at the tail of the embryo and a coenrichment signature of the histone modifications H3K4me3 and H3K27ac at the medial level of the spinal cord (Fig. 4m), in agreement with gene expression revealed by in situ hybridization (Allen Developing Mouse Brain Atlas) (Fig. 4n...
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Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
- Khang Ma and
- Rinki Ratnapriya
Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
...and distinguishable groups (Fig. 2F). Taken together, our analyses shows that the transcriptome profile of retina microglia closely resembles that of brain microglia.Chromatin accessibility is similar in retina and brain microgliaRNA expression is regulated by the changes in chromatin accessibility at gene promoters...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...targets for PB and potentially other brain tumors.ResultsPan-transcriptomic and accessibility maps of PB progressionTo investigate gene expression and chromatin accessibility dynamics that occur during initiation and progression of PB, we extracted pineal glands from a well-characterized mouse model...
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Method: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
- Shelsa S. Marcel,
- Austin L. Quimby,
- Melodie P. Noel,
- Oscar C. Jaimes,
- Marjan Mehrab-Mohseni,
- Suud A. Ashur,
- Brian Velasco,
- James K. Tsuruta,
- Sandeep K. Kasoji,
- Charlene M. Santos,
- Paul A. Dayton,
- Joel S. Parker,
- Ian J. Davis,
- and Samantha G. Pattenden
Genome Res. December 2021 31: 2327-2339; Published in Advance November 23, 2021, doi:10.1101/gr.275219.121
....Tumor-type-specific chromatin accessibility in xenografts reflects primary tumor chromatin accessibilityNext, we tested whether chromatin accessibility detected in the xenografted tumors reflected that in primary human tumors. The Cancer Genome Atlas Program applied ATAC-seq in frozen primary human tumors to identified...
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Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
...to this work. Corresponding authors: yhloh@imcb.a-star.edu.sg, Li.Hu@mayo.eduAbstractJoint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different...
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