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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...MHC in newts illuminates the evolutionary dynamics of complex regions in giant s Wiesław Babik1, Katarzyna Dudek1, Gemma Palomar1,2, Marzena Marszałek1,3, Grzegorz Dubin4, Maximina H. Yun5,6 and Magdalena Migalska1 1Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University...
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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 variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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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
...equally to this work. Corresponding author: sgillett@cornellcollege.eduAbstractGenome-wide association studies (GWASs) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. Here...
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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
...expression. We find that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, whereas housekeeping genes are more often controlled by intergenic enhancers, common to many tissues. Notably, an intergenic...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...preferentially in the promoter of nonexpressed alleles of imprinted genes. Furthermore, we found that most of the paternal specifically positioned nucleosomes (pat-nucleosomes) were associated with parent-of-origin-dependent differential methylated regions, suggesting a functional link between the maternal...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...in KS1 and KS2 = 60.01 and 1508.9, respectively.Aging-related regions show preferentially disrupted chromatin accessibility in KS1 and KS2 neurons but not in B or T cellsOur findings yield insights into (1) the genomic distribution of the chromatin defects in KS1 and KS2 and (2) the cell type...
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Research: The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
...betweenmaternal and paternal imprinting and differential expression between males and females (Supplemental Fig. S22). Allele-specific methylation of differentially methylated regions (DMRs) is the primary epigenetic mechanism of imprinting, controlling monoallelic expression (Supplemental Fig. S6; Skaar et al...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events Marin Volarić1,2, Evelin Despot-Slade1,2, Damira Veseljak1, Brankica Mravinac1 and Nevenka Meštrović1 1Ruđer Bošković Institute, 10000 Zagreb, Croatia...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...The aberrant epi of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory Varsha Poondi Krishnan1, Barbara Morone1, Shir Toubiana2, Monika Krzak3,6, Salvatore Fioriniello1, Floriana Della Ragione1...

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