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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...in prenatal screening, where the methylation profile of fetal cfDNA correlates with placental methylation, allowing for the differentiation of maternal from fetal cfDNA without depending on genotypic information (Sun et al. 2015). Methylation patterns in circulating tumor DNA (ctDNA), analyzed through unique...
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Research: Pervasive polymorphic imprinted methylation in the human placenta
- Courtney W. Hanna,
- Maria S. Peñaherrera,
- Heba Saadeh,
- Simon Andrews,
- Deborah E. McFadden,
- Gavin Kelsey,
- and Wendy P. Robinson
Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
...-independent mechanism of establishment. Genome Res 24: 554–569. ↵Das R, Lee YK, Strogantsev R, Jin S, Lim YC, Ng PY, Lin XM, Chng K, Yeo GS, Ferguson-Smith AC, et al. 2013. DNMT1 and AIM1 imprinting in human placenta revealed through a -wide screen for allele-specific DNA methylation. BMC Genomics 14: 685. ↵Docherty LE...
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Resource: Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
- Mei Zhang,
- Shaojun Xie,
- Xiaomei Dong,
- Xin Zhao,
- Biao Zeng,
- Jian Chen,
- Hui Li,
- Weilong Yang,
- Hainan Zhao,
- Gaokui Wang,
- Zongliang Chen,
- Silong Sun,
- Andrew Hauck,
- Weiwei Jin,
- and Jinsheng Lai
Genome Res. January 2014 24: 167-176; Published in Advance October 16, 2013, doi:10.1101/gr.155879.113
...in different development stages (vegetative and reproductive) exhibit high tissue specificity, which is similar as in Arabidopsis (Weinhofer et al. 2010). We developed a protocol to screen for allele-specific H3K27me3 peaks (see Methods). With our stringent criteria, 1131 parent-oforigin dependent H3K27me3...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...331 gene, and the second coincides with exon 2 of DIRAS3 (Supplemental Fig. S2C). Genome-wide methylation profiling identifies novel imprinted domains To determine if there are additional imprintedDMRs in the human , we screened for regions of intermediate methylation common to lymphocyte, brain...
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Methods: Genome-wide prediction of imprinted murine genes
- Philippe P. Luedi,
- Alexander J. Hartemink,
- and Randy L. Jirtle
Genome Res. June 2005 15: 875-884; doi:10.1101/gr.3303505
...and maternally expressed. Increased maternal transmission of male homosexuality has previously been observed ( Hamer et al. 1993 ), and it is proposed to result in part from imprinted genes ( Bocklandt and Hamer 2003 ). A -wide screen for methylated CpG islands found a germline differentially methylated region...
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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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ARTICLE: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes
- Liora Z. Strichman-Almashanu,
- Richard S. Lee,
- Patrick O. Onyango,
- Elizabeth Perlman,
- Folke Flam,
- Matthew B. Frieman,
- and Andrew P. Feinberg
Genome Res. April 1, 2002 12: 543-554; Published in Advance March 20, 2002, doi:10.1101/gr.224102
...A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes Liora Z. Strichman-Almashanu 1 , 4 , 5 , Richard S. Lee 1 , 5 , Patrick O. Onyango 1 , Elizabeth Perlman 2 , Folke Flam 3...
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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
...are dependent on serum response factor . Mol. Cell. Biol. 16 : 6065 – 6074 . ↵ Strichman-Almashanu, L.Z. , Lee, R.S. , Onyango, P.O. , Perlman, E. , Flam, F. , Frieman, M.B. , Feinberg, A.P. ( 2002 ) A -wide screen for normally methylated human CpG islands that can identify novel imprinted genes . Genome Res...
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LETTER: The Binding Sites for the Chromatin Insulator Protein CTCF Map to DNA Methylation-Free Domains Genome-Wide
- Rituparna Mukhopadhyay,
- WenQiang Yu,
- Joanne Whitehead,
- JunWang Xu,
- Magda Lezcano,
- Svetlana Pack,
- Chandrasekhar Kanduri,
- Meena Kanduri,
- Vasudeva Ginjala,
- Alexander Vostrov,
- Wolfgang Quitschke,
- Igor Chernukhin,
- Elena Klenova,
- Victor Lobanenkov,
- and Rolf Ohlsson
Genome Res. August 2004 14: 1594-1602; Published in Advance July 15, 2004, doi:10.1101/gr.2408304
...those with known functions in oncogenesis. Additional loci are described in Table 1 and in the Supplemental material. View this table: In this window In a new window Table 1. Selected Genes At or Adjacent To Newly Identified CTCF Target Sites A Genome-Wide Screen of Insulator Function by a Novel Assay...
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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
.... 2008), and only 26 candidate imprinted DMRs were identified in a screen for maternal methylation in parthenogenetic mouse embryos (Smith Figure 5. Allelic expression analysis for the new candidate imprinted gene Axl in mouse. Shown here are cDNA amplified using Axl primers digested with Hpy188III...

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