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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...at Nationwide Children's Hospital, Columbus, Ohio 43205, USA Corresponding author: Parthun.1@osu.eduAbstractA large fraction of the interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in organization and gene regulation across...
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Research: Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease
- Xiaolong Wei,
- Megan A. Murphy,
- Nihal A. Reddy,
- Yi Hao,
- Taylor G. Eggertsen,
- Jeffrey J. Saucerman,
- and Irina M. Bochkis
Genome Res. November/December 2022 32: 1981-1992; Published in Advance December 15, 2022, doi:10.1101/gr.277149.122
...in heterochromatin that are completely reproduced in aging liver.Several studies have reported changes at the nuclear lamina in patients with metabolic disease and NAFLD. Genetic variants in the nuclear lamina-related genes ZMPSTE24 and TMPO, which encode the lamina-associated polypeptide-2 (LAP2), have been...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...was below the threshold (see Methods).FIE genes showed signals of positive selection, assessed using dN/dS (Fig. 2A; Supplemental Note 4), indicating significant enrichment in missense, nonsense, splice, and truncating mutations compared with synonymous variants. Pancancer FIEs showed positive cancer effect...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...–specific, and changes during development in coordination with gene expression. Moreover, RT alterations are linked to abnormal gene expression, instability, and structural variation in multiple diseases, including cancer. However, mechanistic links between RT, large-scale 3D architecture, and transcriptional regulation...
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Research: A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha
- Kevin Gesson,
- Philipp Rescheneder,
- Michael P. Skoruppa,
- Arndt von Haeseler,
- Thomas Dechat,
- and Roland Foisner
Genome Res. April 2016 26: 462-473; Published in Advance January 21, 2016, doi:10.1101/gr.196220.115
..., Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207–210. Gesson K, Vidak S, Foisner R. 2014. Lamina-associated polypeptide (LAP)2α and nucleoplasmic lamins in adult stem cell regulation and disease. Semin Cell Dev Biol...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...experimentally validated as TFs involved in regulatory functions within CD4 naive cells, even though they were not explicitly designated as TFs during the training phase. Among the remaining six genes, ETV3L, a member of the ETS TF family, has not yet been explicitly characterized in the context of CD4 naive...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...beads. To focus on individual candidate genes predicted to be bound by the protein of interest, precipitated DNA can be analyzed using qPCR with primers designed specifically against the regulatory sequences of the GOIs. Alternatively, in ChIP-seq following precipitation, cross-links are reversed...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...), or in controlling alternative splicing in male sex cells of meiosis factor MPS1 (AT5G57880) (Walker et al. 2018). Many genes (10%–20%) (Zhang et al. 2020) in euchromatic arms also harbor DNA methylation but only in the CG context, located in the gene body with a modest bias toward the 3′ end, called gene body...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...in our minigene splicing assays, categorized according to the original MES-based selection criteria (Vallée et al. 2016). (B) Number of variants with alternative transcript products correctly predicted by the updated SpliceAI-10k calculator (SAI-10k-calc). (C,D) Illustration of cryptic donor or acceptor...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...(Saponaro et al. 2014). Factors involved in cotranscriptional RNA processing have also been shown to impact elongation rate. The splicing regulator SRSF2 (also known as SC35) promotes transcription elongation in a gene-specific manner (Lin et al. 2008), and U1 small nuclear ribonucleoprotein (U1 sn...
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