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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...such as the regulation of tissue-specific gene expression, X Chromosome inactivation, and genomic imprinting, and has been involved in a wide variety of human diseases ranging from developmental disorders to different types of cancer (Portela and Esteller 2010; Smith and Meissner 2013; Monk et al. 2019...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
...Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions Adam R. Prickett 1 , Nikolaos Barkas 1 , Ruth B. Mc...
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Research: Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
- Amber Hogart,
- Jens Lichtenberg,
- Subramanian S. Ajay,
- Stacie Anderson,
- NIH Intramural Sequencing Center,
- Elliott H. Margulies,
- and David M. Bodine
Genome Res. August 2012 22: 1407-1418; Published in Advance June 8, 2012, doi:10.1101/gr.132878.111
...Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites Amber Hogart 1 , Jens Lichtenberg 1 , Subramanian S. Ajay 2 , Stacie Anderson 1 , 3 , NIH...
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Method: A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
- Sanaa Choufani,
- Jonathan S. Shapiro,
- Martha Susiarjo,
- Darci T. Butcher,
- Daria Grafodatskaya,
- Youliang Lou,
- Jose C. Ferreira,
- Dalila Pinto,
- Stephen W. Scherer,
- Lisa G. Shaffer,
- Philippe Coullin,
- Isabella Caniggia,
- Joseph Beyene,
- Rima Slim,
- Marisa S. Bartolomei,
- and Rosanna Weksberg
Genome Res. March 2011 21: 465-476; Published in Advance February 7, 2011, doi:10.1101/gr.111922.110
...by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were...
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LETTER: Computational and experimental identification of novel human imprinted genes
- Philippe P. Luedi,
- Fred S. Dietrich,
- Jennifer R. Weidman,
- Jason M. Bosko,
- Randy L. Jirtle,
- and Alexander J. Hartemink
Genome Res. December 2007 17: 1723-1730; Published in Advance November 30, 2007, doi:10.1101/gr.6584707
..., B.T. , Hu, J.F. , Murphy, S.K. , et al. ( 2002 ) An imprinted PEG1/MEST antisense expressed predominantly in human testis and in mature spermatozoa . J. Biol. Chem. 277 : 13518 – 13527 . ↵ Luedi, P.P. , Hartemink, A.J. , Jirtle, R.L. ( 2005 ) Genome-wide prediction of imprinted murine genes . Genome...
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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
...the expression profiles of two canonically imprinted genes (Peg3 and Grb10) by pyrosequencing (Supplemental Fig. S8). Paternally expressed 3 gene (Peg3) was paternally biased in all three tissues, regardless of context. Its locus had 60 strain-specific variants, but none were predicted as functional. Peg3...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...(Peaston et al. 2004; Pi et al. 2004; Rebollo et al. 2012; Erwin et al. 2014; Friedli and Trono 2015; Garcia-Perez et al. 2016; Thompson et al. 2016; Chuong et al. 2017; Huang et al. 2017). Genome-wide studies demonstrate that a significant portion of transcription factor (TF)-binding sites is derived from...
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Method: Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
- Lulu Yan,
- Jinyu Cheng,
- Qing Nie,
- and Xiaoqiang Sun
Genome Res. June 2025 35: 1400-1414; Published in Advance April 22, 2025, doi:10.1101/gr.279857.124
...it to intracellular targets. We benchmark stMLnet against seven representative methods and find that stMLnet performs better in both intercellular ligand–receptor inference and intracellular target gene prediction. We apply stMLnet to analyze data from diverse ST techniques like seqFISH+, Slide-seq v2, MERFISH...
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LETTER: Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing
- David Monk,
- Alexandre Wagschal,
- Philippe Arnaud,
- Pari-Sima Müller,
- Layla Parker-Katiraee,
- Déborah Bourc’his,
- Stephen W. Scherer,
- Robert Feil,
- Philip Stanier,
- and Gudrun E. Moore
Genome Res. August 2008 18: 1270-1281; Published in Advance May 14, 2008, doi:10.1101/gr.077115.108
...in placenta, in both humans and mouse. A recent bioinformatics screen predicted that this gene would be imprinted based on the unequal frequency of alleles in SNPs in expressed sequence tags ( Seoighe et al. 2006 ). Expression of TFPI2 is almost exclusively found in the placenta, limited...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...not been permeabilized by DTT treatment, and support our prediction that accessible cell-free DNA/chromatin is somatic in origin.View larger version: In this window In a new window Figure 4. Contaminating cell-free DNA is of somatic origin. (A,B) Nano-NOMe-seq data for two imprinting control regions...

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