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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...is driven in part by recognition of DNA sequence, genetic variation can influence TF–DNA associations and gene regulation. To identify variants that impact TF binding in human brain tissues, we assessed allele-specific binding (ASB) at heterozygous variants for 94 TFs in nine brain regions from two donors...
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Research: Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression
- Celine L. St. Pierre,
- Juan F. Macias-Velasco,
- Jessica P. Wayhart,
- Li Yin,
- Clay F. Semenkovich,
- and Heather A. Lawson
Genome Res. June 2022 32: 1042-1057; Published in Advance May 2, 2022, doi:10.1101/gr.276193.121
...-by-environment interactions can also alter gene expression patterns in a dynamic and tissue-specific manner without modifying the underlying nucleotide sequence; these effects are missed in a typical sequence-based method. Thus, an allele-specific approach is required to directly measure how cis-regulatory variation impacts...
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Method: Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
- Zeynep Kalender Atak,
- Ibrahim Ihsan Taskiran,
- Jonas Demeulemeester,
- Christopher Flerin,
- David Mauduit,
- Liesbeth Minnoye,
- Gert Hulselmans,
- Valerie Christiaens,
- Ghanem-Elias Ghanem,
- Jasper Wouters,
- and Stein Aerts
Genome Res. June 2021 31: 1082-1096; Published in Advance April 8, 2021, doi:10.1101/gr.260851.120
...for transposase-accessible chromatin using sequencing (ATAC-seq), ChIP against H3K27ac (ChIP-seq), and transcriptome sequencing (RNA-seq) data, we identify allele-specific regulatory changes. To interpret how sequence variation affects the gain or loss of TF binding sites, we used a deep learning model, called...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...composition of transcriptomes obtained from long-read sequencing and to compare quality across preprocessing pipelines and experiments. We show that our choice of ToFU read clustering plus SQANTI filtering for transcriptome curation is a good trade-off between discovery and high quality for novel transcript...
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Research: Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana
- Maximilian O. Press,
- Rajiv C. McCoy,
- Ashley N. Hall,
- Joshua M. Akey,
- and Christine Queitsch
Genome Res. August 2018 28: 1169-1178; Published in Advance July 3, 2018, doi:10.1101/gr.231753.117
..., genotyping 2046 STR loci each, using highly parallel STR sequencing with molecular inversion probes. We found that 95% of examined STRs are polymorphic, with a median of six alleles per STR across these strains. STR expansions (large copy number increases) are found in most strains, several of which have...
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Research: Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes
- Jeremy R.B. Newman,
- Ana Conesa,
- Matthew Mika,
- Felicia N. New,
- Suna Onengut-Gumuscu,
- Mark A. Atkinson,
- Stephen S. Rich,
- Lauren M. McIntyre,
- and Patrick Concannon
Genome Res. November 2017 27: 1807-1815; Published in Advance October 12, 2017, doi:10.1101/gr.217984.116
...of genes implicated in autoimmune disease risk by GWAS, and the subset of these genes specifically implicated in T1D. We performed RNA sequencing and aligned the reads to both the human reference and a catalog of all possible splicing events developed from the , thereby providing a comprehensive evaluation...
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Research: Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
- Nathan C. Sheffield,
- Robert E. Thurman,
- Lingyun Song,
- Alexias Safi,
- John A. Stamatoyannopoulos,
- Boris Lenhard,
- Gregory E. Crawford,
- and Terrence S. Furey
Genome Res. May 2013 23: 777-788; Published in Advance March 12, 2013, doi:10.1101/gr.152140.112
.... This interaction was detected without any knowledge about allele specificity. A web resource for exploring DHS sequences, clusters, and TF motifs The results presented here begin to provide more detailed and informative annotations for 2.7 million DHSs contributing to gene regulation in 112 samples across 72...
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Research: Loss of exon identity is a common mechanism of human inherited disease
- Timothy Sterne-Weiler,
- Jonathan Howard,
- Matthew Mort,
- David N. Cooper,
- and Jeremy R. Sanford
Genome Res. October 2011 21: 1563-1571; Published in Advance July 12, 2011, doi:10.1101/gr.118638.110
...setmay be redundantwith the function of other hexamers and hence more prone to variation across human populations. Alternatively, the polymorphic ESRs identified here may be associated with allele-specific alternative splicing that confers a gain of fitness rather than a disease phenotype (Fraser and Xie...
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Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
- Richa Rashmi,
- Abhinaya Muruganandham,
- Pranita Borkar,
- Sumana Mallick,
- Taylor Hubbs,
- Ari Aviles,
- Daniel Chung,
- and Irtisha Singh
Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
...a regulatory axis connecting epigenetic 23 state and IPA. This finding aligns with emerging evidence that DNA methylation modulates 24 2 alternative polyadenylation via CTCF-mediated chromatin looping. Thus, IPAseek provides a 25 platform to characterize IPA across physiological systems and disease contexts...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...sequences, contribute to evolutionary adaptation but can also confer deleterious effects and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs...
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