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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
...-seq-constructed libraries by different amounts of Tn5 are shown. cDNAs were tagmented with the indicated amounts of Tn5, PCR amplified, and analyzed by TBE gel. Mg2+ was required for the enzymatic activity of Tn5 transposon. Samples treated without Mg2+, which inhibited the Tn5 transposon activity, were used as negative...
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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
...called “fountains,” which have also been reported in zebrafish and mice. These are population average reflections of DNA loops originating from distinct genomic regions and are ∼20–40 kb in C. elegans. Hi-C analysis upon cohesin and WAPL-1 depletion supports the idea that cohesin is preferentially loaded...
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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
...essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of a paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation...
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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
...and treatment options. We applied long-read transcriptome sequencing (LRTS) to 44 MDS and CLL patients, as well as two pairs of isogenic cell lines with and without SF3B1 mutations, and found >60% of novel isoforms. Splicing alterations were largely shared between cancer types and specifically affected...
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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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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...devised new methods to map DNA supercoiling and single-stranded DNA in Caenorhabditis elegans embryos and diapause larvae. To map supercoiling, we quantified the incorporation of biotinylated psoralen into DNA using high-throughput sequencing. To map single-stranded DNA, we combined permanganate treatment...
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REVIEW: Strategies for direct sequencing of PCR-amplified DNA.
- V B Rao
Genome Res. August 1994 4: S15-S23
...Strategies for direct sequencing of PCR-amplified DNA. V B Rao Department of Biology, Catholic University of America, Washington, D.C. 20064, USA. Abstract Footnotes Copyright © Cold Spring Harbor Laboratory Press VB Rao Rao, V.B V.B. Rao...
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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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