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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...), NPC lines, and developmental timepoints, to generate a list of putative enhancer regions to investigate using the phNPC model. Whereas other enhancer mapping tools such as massively parallel reporter assays (MPRAs) have been used to identify putative enhancer regions in primary human cortical cells...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...were functionally annotated by mapping them to in-house profiles of the Clusters of Orthologous Genes (COG) database (2020 release) (Galperin et al. 2021) with HMMER v3.1b2 (e-value < 0.001; http://hmmer.org). The 26 major prokaryotic functional categories defined in the COG database were assigned...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...are indeed proximal in physical space and vice versa. A CTG distance matrix is constructed based on the similarity of the diffusion property between genomic loci in the Hi-C contact map. Except for self-distance, the calculation of CTG distance (L1 distance between rows of transition probability matrix...
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Resource: An 11-point time course midgut transcriptome across 72 h after bloodfeeding provides detailed temporal resolution of transcript expression in the arbovirus vector, Aedes aegypti
- Hitoshi Tsujimoto and
- Zach N. Adelman
Genome Res. September 2023 33: 1638-1648; Published in Advance October 6, 2023, doi:10.1101/gr.277808.123
...and mappingFrom our four independent replicates for the 11 time points of prebloodmeal and PBM, Illumina NovaSeq 6000 paired-end sequencing generated 1,160,607,602 fragment pairs (2,321,215,204 reads). We obtained a mean of 26,377,445.5 fragments per sample (ranging from 19,503,828 to 34,008,005 fragments...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...A chromosome-scale epigenetic map of the Hydra reveals conserved regulators of cell state Jack F. Cazet1, Stefan Siebert1,2, Hannah Morris Little1, Philip Bertemes3, Abby S. Primack1, Peter Ladurner3, Matthias Achrainer3, Mark T. Fredriksen4, R. Travis Moreland4, Sumeeta Singh4, Suiyuan Zhang4...
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Resource: Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva,
- Ilia Kurochkin,
- Dingding Han,
- Patricia Guijarro,
- Sabina Kanton,
- Malgorzata Santel,
- Zhengzong Qian,
- Shen Rong,
- Pavel Mazin,
- Marat Sabirov,
- Matvei Bulat,
- Olga Efimova,
- Anna Tkachev,
- Song Guo,
- Chet C. Sherwood,
- J. Gray Camp,
- Svante Pääbo,
- Barbara Treutlein,
- and Philipp Khaitovich
Genome Res. May 2020 30: 776-789; Published in Advance May 18, 2020, doi:10.1101/gr.256958.119
...and chimpanzee cerebral organoids, indicating that cell-type composition can be accurately matched between closely related primate species and expression differences within each type identified (Mora-Bermúdez et al. 2016; Kanton et al. 2019; Pollen et al. 2019).Here, we report transcriptome maps of the human...
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Research: Most chromatin interactions are not in linkage disequilibrium
- Sean Whalen and
- Katherine S. Pollard
Genome Res. March 2019 29: 334-343; Published in Advance January 7, 2019, doi:10.1101/gr.238022.118
...to single nucleotide polymorphisms (SNPs) can impact gene function by altering exonic sequence or by changing gene regulation. Recent studies estimate that 93% of disease-associated variants are in noncoding DNA (Welter et al. 2014) and 60% of causal variants map to regulatory elements (Farh et al. 2015...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...variants and their mechanisms of action in relevant biological systems at scale. The identification of functional variants relative to proxy variants in high linkage disequilibrium (LD) presents an additional challenge. Recent studies have begun to map molecular quantitative trait loci (molQTLs) for gene...
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Research: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
- Rik Kooke,
- Lionel Morgado,
- Frank Becker,
- Henriëtte van Eekelen,
- Rashmi Hazarika,
- Qunfeng Zheng,
- Ric C.H. de Vos,
- Frank Johannes,
- and Joost J.B. Keurentjes
Genome Res. January 2019 29: 96-106; Published in Advance November 30, 2018, doi:10.1101/gr.232371.117
...and quantitative metabolic variationTo gain deeper insight into the regulation of plant metabolism within the epiRIL population, QTLepi analysis was performed on all metabolites using a genetic map based on differentially methylated regions as physical markers (Colome-Tatche et al. 2012). To verify that these DMRs...
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Research: Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing
- Frederic Faucon,
- Isabelle Dusfour,
- Thierry Gaude,
- Vincent Navratil,
- Frederic Boyer,
- Fabrice Chandre,
- Patcharawan Sirisopa,
- Kanutcharee Thanispong,
- Waraporn Juntarajumnong,
- Rodolphe Poupardin,
- Theeraphap Chareonviriyaphap,
- Romain Girod,
- Vincent Corbel,
- Stephane Reynaud,
- and Jean-Philippe David
Genome Res. September 2015 25: 1347-1359; Published in Advance July 23, 2015, doi:10.1101/gr.189225.115
...ones. Sequencing metrics and coverage The use of target enrichment technology followed by multiplexed Illumina sequencing allowed obtaining an average of 4.35 million 75-bp reads per sample (Supplemental Table 1). Filtering them according to read pairing, sequence quality, and mapping quality Faucon et...
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