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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...Construction and evaluation of a new rat reference assembly, GRCr8, from long reads and long-range scaffolding Kai Li1, Melissa L. Smith2, J. Chris Blazier3, Kelli J. Kochan3, Jonathan M.D. Wood4, Kerstin Howe4, Anne E. Kwitek5, Melinda R. Dwinell5, Hao Chen6, Julia L. Ciosek1, Patrick Masterson7...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...for the massive parallel testing of intrinsic enhancer activity of DNA fragments by cloning these sequences downstream from a core promoter and then quantifying the enhancer activity based on the self-transcription in mRNA transcripts. We generated a library of 11,147 regions, which included 7922 peaks that were...
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LETTER: Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
- Gabriela G. Loots,
- Michaela Kneissel,
- Hansjoerg Keller,
- Myma Baptist,
- Jessie Chang,
- Nicole M. Collette,
- Dmitriy Ovcharenko,
- Ingrid Plajzer-Frick,
- and Edward M. Rubin
Genome Res. July 2005 15: 928-935; Published in Advance June 17, 2005, doi:10.1101/gr.3437105
...bone of neonatal and adult mice (skull, rib, and femur), while all of the SOST vb Δ lines had dramatically reduced levels of human SOST mRNA expression, as determined by rtPCR and qPCR. All lines ( SOST wt and SOST vb Δ ) also consistently expressed human SOST in the adult kidney and heart. Here, we...
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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. March 19, 2026 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...378 per library and 100 bp of single-end sequencing. 379 Standard RNA-seq 380 RNA samples were isolated from 0.5 million HepG2 cells using the RNeasy Plus Kit (Qiagen 74004), 381 and libraries were prepared with the TruSeq Stranded mRNA Library Prep (Illumina) according to 382 the manufacturer...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...using the Qiagen RNeasy kit following the manufacturer's instructions. Stranded mRNA-seq libraries were constructed using an Illumina mRNA prep kit, following the vendor protocol with poly(A) enrichment (Illumina). Libraries were sequenced with 2 × 75 bp paired ends on an Illumina NextSeq 500.CRISPR...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
.... 2024) (original data available from the European Genome-phenome Archive (EGA; https://ega-archive.org) under accession number EGAD50000000015). STARR-seq assesses regulatory sequence activity by cloning them downstream of a minimal promoter; active enhancers self-transcribe, resulting in higher mRNA...
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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...-cell sequencing and long-read sequencing, have greatly expanded. Both have been used in transcriptomics to characterize the mRNA expression profiles of cells. Single-cell sequencing allows transcript molecules to be traced to individual cells, thus preserving cell-type-specific information about expression. Long...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...transcripts. This is in good agreement with the reported difficulty to extract stored mRNAs in Q cells (Aragon et al. 2006). UMAP dimensionality reduction of single-cell RNA-seq data revealed that our gradient-sorted population at 6 days of medium exhaustion shows a bilobate structure (Fig. 3B). Nevertheless...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...is becoming a more viable method (Israeli et al. 2022).Transcript populations can also be explored with these methods as demonstrated by Adamopoulos et al. This group performed mRNA transcript-specific amplification for KRAS, NRAS, and HRAS, which are regulatory genes commonly mutated in various cancers...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...of the CTG repeat, which has been proposed to directly inhibit CTCF occupancy at an upstream element (Filippova et al. 2001). Additionally, decreased DNase I hypersensitivity of the downstream SIX5 promoter has also been observed, along with reduced SIX5 mRNA levels (Klesert et al. 1997). The CpG methylation...

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