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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
..., posterior of promoter states is positively correlated with occurrence of annotated TSSs, and the converse is true of quiescent states (Fig. 4D,E; Supplemental Figs. 27, 28).We found that the posterior of the state assignment to the base annotation conveys a great deal of information about what state...
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Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
- Sena A. Gocuk,
- James Lancaster,
- Shian Su,
- Jasleen K. Jolly,
- Thomas L. Edwards,
- Doron G. Hickey,
- Matthew E. Ritchie,
- Marnie E. Blewitt,
- Lauren N. Ayton,
- and Quentin Gouil
Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
...with DeepVariant v1.5.0-gpu (Poplin et al. 2018) on the X Chromosome using the ONT_R104 model and were filtered for high-quality “PASS” calls using BCFtools (Li 2011). The variant call file (VCF) was then phased using WhatsHap v1.7 (Martin et al. 2016) using the merged modbam file. Each sample modbam...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...in highly methylated CpGs. For example, 0.90% of TE bases are annotated with an active promoter, whereas 37% of 5′ UTR bases are in the active promoter. A similar pattern was observed when the proportion of epigenetic states in TE and different genic feature bases were calculated using the union...
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Research: Mosaic loss of Chromosome Y in aged human microglia
- Michael C. Vermeulen,
- Richard Pearse,
- Tracy Young-Pearse,
- and Sara Mostafavi
Genome Res. October 2022 32: 1795-1807; Published in Advance August 30, 2022, doi:10.1101/gr.276409.121
...lymphoma–affected lymph node tissue (10x Genomics 2021; Methods). In total, 7283 nuclei passed initial QC (more than 1500 unique molecular identifiers [UMIs] and more than 800 genes; Methods). Nuclei were clustered and annotated with cell types using GEX levels (Fig. 1A; Supplemental Fig. S1A...
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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
...(https://research.nhgri.nih.gov/HydraAEP/).ResultsGeneration and annotation of two high-quality Hydra assembliesWe sequenced, assembled, and annotated a chromosome-level assembly for the AEP laboratory strain of H. vulgaris (for details, see Supplemental Material; Supplemental Figs. S1, S2; Supplemental...
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Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
- Daniel C. Kraushaar,
- Zuozhou Chen,
- Qingsong Tang,
- Kairong Cui,
- Junfang Zhang,
- and Keji Zhao
Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
...with a certain RefSeq genomic region, i.e., exon, intron, promoter (3 kbp upstream of TSS), 3′ UTR, 5′ UTR, and downstream regions (5 kbp downstream from transcription end site, TES). The RefSeq genomic annotation of mm9 was downloaded from the UCSC Genome Browser.ChIP-seq enrichment calculationA 1 kbp window...
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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...identified within the domestic cat (labeled by chromosome and coordinates), cheetah (AJU), and tiger (PTI). The branches are color-coded based on their predicted chromosome of origin. (B) Ideogram of consensus of Y-linked ERV-like sequences annotated with vestigial ERV genes (below) and the promoter...
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Research: Recurrent epimutations activate gene body promoters in primary glioblastoma
- Raman P. Nagarajan,
- Bo Zhang,
- Robert J.A. Bell,
- Brett E. Johnson,
- Adam B. Olshen,
- Vasavi Sundaram,
- Daofeng Li,
- Ashley E. Graham,
- Aaron Diaz,
- Shaun D. Fouse,
- Ivan Smirnov,
- Jun Song,
- Pamela L. Paris,
- Ting Wang,
- and Joseph F. Costello
Genome Res. May 2014 24: 761-774; Published in Advance April 7, 2014, doi:10.1101/gr.164707.113
.... Here we investigated recurrent, focal hypomethylation in GBM, in annotated and previously unannotated promoters. We mapped full DNA methylomes for five GBMs, encompassing the three most common expression subtypes (proneural, classical, and mesenchymal) and including tumors with canonical genetic...
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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...to annotated TSSs for poly(A)-TSS-seq. RNA isolated from yeast was subjected to poly(A)-TSS-seq using either the original or optimized conditions. The x-axis is centered on the annotated TSS. (C) Fraction (y-axis) of tags located in promoter-proximal regions (–300 to +100 bp from annotated ORF start codons...
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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...copies mapped on the 10 T. freemani chromosomes, fLG2-fLGX, in the Tfree1.0 assembly. The number of annotated copies is color-coded according to the color scale. (C) UpSet plot showing the number of the T. freemani satDNAs with annotated genes, transposable elements (TEs), and/or satDNAs within 10-kb...

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