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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...'s recombination proteins RecA and RecBCD for growth (Sternberg and Hoess 1983). These proteins promote recombination of P1's terminal direct repeats of ∼5–10 kbp when P1's 94.8 kbp linear DNA is injected into the cell. Terminal-repeat recombination forms circular DNA, which is replicated to form the concatemeric...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...U-labeled DNA was then immunoprecipitated, followed by library preparation and sequencing (Fig. 4A).View larger version: In this window In a new window Figure 4. The replication timing profiles of GSC-like and CySC-like cells are distinct. (A) A schematic of the Repli-seq protocol. First, dissected upd tumors...
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Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
- Yanjun Zhang,
- Yin Tang,
- Zhongxing Sun,
- Junqi Jia,
- Yuan Fang,
- Xinyi Wan,
- and Dong Fang
Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
...and reversely mapped to the ssDNA. Two independent replicates from repeat #1 (F) and repeat #2 (G) are shown. The x-axis indicates the 5′-to-3′ direction of the template ssDNA. Forward, reconstructed paired-end sequencing reads mapped to the forward direction of ssDNA. Reverse, reconstructed paired...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...may stall extrusion. Together, cohesin processivity at each side can be unequal and may be facilitated by transcription moving in the same direction. Despite the lack of immediate effect on transcription upon acute SMC-3 and WAPL-1 depletion, the extruded DNA loops encompass multiple cis...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...immunoprecipitated SF3B1 from K562-SF3B1wt/wt and K562-SF3B1K700E/wt cells, yielding together more than 100 million SF3B1 cross-link events (Fig. 6B; Supplemental Table S1). To facilitate direct comparisons, we randomly subsampled the sequencing reads to adjust the library size of the replicates (see Methods). Based...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...CRX HD's dimeric DNA binding (Fig. 1B; Chen et al. 1997, 2002). The BAT-1 sequence is a fragment in the promoter of rhodopsin, a gene that encodes the rod-specific photopigment and is a direct target of CRX in vivo. The BAT-1 fragment contains a central dimeric P3 sequence TAATCATATTA and additional...
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Method: Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
- Romualdas Vaisvila,
- V.K. Chaithanya Ponnaluri,
- Zhiyi Sun,
- Bradley W. Langhorst,
- Lana Saleh,
- Shengxi Guan,
- Nan Dai,
- Matthew A. Campbell,
- Brittany S. Sexton,
- Katherine Marks,
- Mala Samaranayake,
- James C. Samuelson,
- Heidi E. Church,
- Esta Tamanaha,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Eileen T. Dimalanta,
- Thomas C. Evans, Jr.,
- Louise Williams,
- and Theodore B. Davis
Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
.... The library is PCR amplified using EM-seq adaptor primers and can be sequenced on any Illumina sequencer.View larger version: In this window In a new window Figure 3. NA12878 EM-seq libraries. EM-seq and bisulfite libraries were made using 10 ng, 50 ng, or 200 ng of NA12878 DNA (spiked with 2 ng unmethylated...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...levels of read numbers and accuracy, and many, like standard RNA-seq, ChIP-seq, or targeted sequencing of PCR amplified genomic DNA, are unlikely to ever take advantage of the raw read length ONT and PacBio sequencers provide. However, there have been several studies to take advantage of long...
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REVIEW: Sequencing of PCR-amplified DNA.
- I S Bevan,
- R Rapley,
- and M R Walker
Genome Res. May 1992 1: 222-228; doi:10.1101/gr.1.4.222
...DNA sequencing of PCR amplified genomic DNA by the Maxam-Gilbert method. BioTechniques 8 : 366 – 368 . 14. Innis, M.A., , Myambo, K.B. , Gelfand, D.H. , Brow. M.A.D. Innis, M.A., Myambo, K.B. Gelfand, D.H. and Brow. M.A.D. 1988 . DNA sequencing with Thermus aquaticus DNA polymerase and direct...
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Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
- Daniela Nachmanson,
- Shenyi Lian,
- Elizabeth K. Schmidt,
- Michael J. Hipp,
- Kathryn T. Baker,
- Yuezheng Zhang,
- Maria Tretiakova,
- Kaitlyn Loubet-Senear,
- Brendan F. Kohrn,
- Jesse J. Salk,
- Scott R. Kennedy,
- and Rosa Ana Risques
Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
...performed CRISPR/Cas9 digestion of targeted TP53 exons (Fig. 1A) on a range of DNA input amounts (10–250 ng) followed by SPRI size selection to remove undigested high molecular weight DNA fragments (>1 kb in size). The selected DNA fragments were ligated to DS adapters, PCR amplified, and sequenced (Methods...

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