Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review

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Bonaldi, Adriano ^[1] ; Kashiwabara, Andre ^[2] ; de Araujo, Erica S. ^[3] ; Pereira, Lygia V. ^[1] ; Paschoal, Alexandre R. ^[2] ; Andozia, Mayra B. ^[1] ; Villela, Darine ^[1] ; Rivas, Maria P. ^[1] ; Suemoto, Claudia K. ^{[4, 5]} ; Pasqualucci, Carlos A. ^{[4, 6]} ; Grinberg, Lea T. ^{[4, 7]} ; Brentani, Helena ^[8] ; Maria-Engler, Silvya S. ^[9] ; Carraro, Dirce M. ^[3] ; Vianna-Morgante, Angela M. ^[1] ; Rosenberg, Carla ^[1] ; Vasques, Luciana R. ^[1] ; Krepischi, Ana ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inst Biosci, Dept Genet & Evolutionary Biol, Rua Matao 277, BR-05508090 Sao Paulo, SP - Brazil

^[2] Univ Tecnol Fed Parana, Dept Computat, Ave Alberto Carazzai 1640, BR-86300000 Cornelio Procopio, PR - Brazil

^[3] AC Camargo Canc Ctr, Int Ctr Res, Rua Tagua 440, BR-01508010 Sao Paulo, SP - Brazil

^[4] Univ Sao Paulo, Sch Med, Dept Pathol, Brazilian Aging Brain Study Grp LIM22, Av Dr Arnaldo 455, BR-01246903 Sao Paulo, SP - Brazil

^[5] Univ Sao Paulo, Sch Med, Div Geriatr, Av Dr Arnaldo 455, BR-01246903 Sao Paulo, SP - Brazil

^[6] Univ Sao Paulo, Sch Med, Dept Pathol, Av Dr Arnaldo 455, BR-01246903 Sao Paulo, SP - Brazil

^[7] Univ Calif San Francisco, Dept Neurol, Memory & Aging Ctr, 1500 Owens St, San Francisco, CA 94143 - USA

^[8] Univ Sao Paulo, Sch Med, Dept Psychiat, LIM23, Av Dr Arnaldo 455, BR-01246903 Sao Paulo, SP - Brazil

^[9] Univ Sao Paulo, Sch Pharmaceut Sci, Av Prof Lineu Prestes 580, BR-05508000 Sao Paulo, SP - Brazil

• Tipo de documento: Artigo de Revisão
• Fonte: EPIGENOMES; v. 1, n. 2 SEP 2017.
• Citações Web of Science: 2

Resumo

Large-scale transcriptome and methylome data analyses obtained by high-throughput technologies have been enabling the identification of novel imprinted genes. We investigated genome-wide DNA methylation patterns in multiple human tissues, using a high-resolution microarray to uncover hemimethylated CpGs located in promoters overlapping CpG islands, aiming to identify novel candidate imprinted genes. Using our approach, we recovered similar to 30% of the known human imprinted genes, and a further 168 candidates were identified, 61 of which with at least three hemimethylated CpGs shared by more than two tissue types. Thirty-four of these candidate genes are members of the protocadherin cluster on 5q31.3; in mice, protocadherin genes have non-imprinted random monoallelic expression, which might also be the case in humans. Among the remaining 27 genes, ZNF331 was recently validated as an imprinted gene, and six of them have been reported as candidates, supporting our prediction. Five candidates (CCDC166, ARC, PLEC, TONSL, and VPS28) map to 8q24.3, and might constitute a novel imprinted cluster. Additionally, we performed a comprehensive compilation of known human and mice imprinted genes from literature and databases, and a comparison among high-throughput imprinting studies in humans. The screening for hemimethylated CpGs shared by multiple human tissues, together with the extensive review, appears to be a useful approach to reveal candidate imprinted genes. (AU)

• Processo FAPESP: 13/07480-8 - Fatores genéticos e epigenéticos na etiologia do melanoma cutâneo
• Beneficiário: Ana Cristina Victorino Krepischi
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 09/00898-1 - Desequilíbrios genômicos submicroscópicos em quadros clínicos específicos de anomalias congênitas e deficiência mental
• Beneficiário: Carla Rosenberg
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 13/08028-1 - CEGH-CEL - Centro de Estudos do Genoma Humano e de Células-Tronco
• Beneficiário: Mayana Zatz
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs