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Brunst KJ, Tignor N, Just A, Liu Z, Lin X, Hacker MR, Bosquet Enlow M, Wright RO, Wang P, Baccarelli AA, Wright RJ. Cumulative lifetime maternal stress and epigenome-wide placental DNA methylation in the PRISM cohort. Epigenetics 2018; 13:665-681. [PMID: 30001177 DOI: 10.1080/15592294.2018.1497387] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolving evidence links maternal stress exposure to changes in placental DNA methylation of specific genes regulating placental function that may have implications for the programming of a host of chronic disorders. Few studies have implemented an epigenome-wide approach. Using the Infinium HumanMethylation450 BeadChip (450K), we investigated epigenome-wide placental DNA methylation in relation to maternal experiences of traumatic and non-traumatic stressors over her lifetime assessed using the Life Stressor Checklist-Revised (LSC-R) survey (n = 207). We found differential DNA methylation at epigenome-wide statistical significance (FDR = 0.05) for 112 CpGs. Additionally, we observed three clusters that exhibited differential methylation in response to high maternal lifetime stress. Enrichment analyses, conducted at an FDR = 0.20, revealed lysine degradation to be the most significant pathway associated with maternal lifetimes stress exposure. Targeted enrichment analyses of the three largest clusters of probes, identified using the gap statistic, were enriched for genes associated with endocytosis (i.e., SMAP1, ANKFY1), tight junctions (i.e., EPB41L4B), and metabolic pathways (i.e., INPP5E, EEF1B2). These pathways, also identified in the top 10 KEGG pathways associated with maternal lifetime stress exposure, play important roles in multiple physiological functions necessary for proper fetal development. Further, two genes were identified to exhibit multiple probes associated with maternal lifetime stress (i.e., ANKFY1, TM6SF1). The methylation status of the probes belonging to each cluster and/or genes exhibiting multiple hits, may play a role in the pathogenesis of adverse health outcomes in children born to mothers with increased lifetime stress exposure.
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Affiliation(s)
- Kelly J Brunst
- a Department of Environmental Health , University of Cincinnati College of Medicine , Cincinnati , OH , USA
| | - Nicole Tignor
- b Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai One Gustave L. Levy Place , New York , NY , USA
| | - Allan Just
- c Department of Environmental Medicine and Public Health , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Zhonghua Liu
- d Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Xihong Lin
- d Department of Biostatistics , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Michele R Hacker
- e Department of Obstetrics and Gynecology , Beth Israel Deaconess Medical Center , Boston , MA , USA.,f Department of Obstetrics , Gynecology and Reproductive Biology, Harvard Medical School , Boston , MA , USA
| | - Michelle Bosquet Enlow
- g Department of Psychiatry, Program for Behavioral Science, Boston Children's Hospital and Department of Psychiatry , Harvard Medical School , Boston , MA , USA
| | - Robert O Wright
- c Department of Environmental Medicine and Public Health , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Pei Wang
- b Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai One Gustave L. Levy Place , New York , NY , USA
| | - Andrea A Baccarelli
- h Department of Environmental Health Sciences , Mailman School of Public Health, Columbia University , New York , NY , USA
| | - Rosalind J Wright
- c Department of Environmental Medicine and Public Health , Icahn School of Medicine at Mount Sinai , New York , NY , USA.,i Department of Pediatrics , Kravis Children's Hospital, Icahn School of Medicine at Mount Sinai , New York , NY , USA
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Marz M, Mosig A, Stadler BMR, Stadler PF. U7 snRNAs: a computational survey. GENOMICS PROTEOMICS & BIOINFORMATICS 2008; 5:187-95. [PMID: 18267300 PMCID: PMC5054213 DOI: 10.1016/s1672-0229(08)60006-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for functional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short sequence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.
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Affiliation(s)
- Manja Marz
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany
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Mostardini M, Appierto V, Pergolizzi R, Zucchi I, Mumm S, DeBellis G, Milanesi L, Rogozin IB, Biunno I. Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci. Gene 1997; 187:221-4. [PMID: 9099884 DOI: 10.1016/s0378-1119(96)00754-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To contribute to the identification and analysis of novel genes, we undertook the study of a cosmid clone in the Xq27 region of human DNA. The cloned fragment was previously observed to have a high number of evolutionarily conserved sequences. In this genomic stretch of DNA we have identified sequence homologous to the U7 RNA gene including its potential regulatory elements. This paper describes the genomic organisation of this gene and its mapping to the Xq27.1 genomic sub-interval between the DXS1232 and DXS119 loci.
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Affiliation(s)
- M Mostardini
- Istituto Tecnologie Biomediche Avanzate, CNR, Milano, Italy
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Abstract
A subclone containing a single Xenopus borealis U7 snRNA-encoding gene has been microinjected into X. laevis oocyte nuclei to examine its expression using [32P]GTP as an in vivo label. Only two U7 snRNA bands were detected after incubation, and subsequent fractionation of the oocyte showed that only the larger transcript is present in the nucleus. The sequence of this functional U7 gene shows that, in addition to the coding region, it contains, in the appropriate locations, the 3'-box and proximal sequence element (PSE) which are typical of Pol II-transcribed snRNA genes. Surprisingly, the Xenopus U7 gene contains two adjacent octamer-binding motifs located only 12 and 24 bp upstream from the PSE, instead of the usual location around 150-200 bp upstream. No other cis-acting elements appear to be present. A 5' deletion analysis shows that the transcription level of this U7 gene remains constant if sequences upstream of the two octamer motifs are removed, yet is undetectable when an additional 34 bp containing both octamers and the PSE are removed. This confirms that the Xenopus U7 gene is the most compact snRNA-encoding gene isolated to date. A comparison of U7 sequences shows there is a much greater conservation in the 5' half of the molecule, which contains sequences that base-pair with target pre-mRNA, than in the 3' half which can form a single stem-loop structure that varies in size.
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Affiliation(s)
- N J Watkins
- Department of Biochemistry, University of Liverpool, UK
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Abstract
The rodent 4.5 S RNA is an RNA polymerase III product with a sequence related to the Alu family of interspersed repeated DNA. A previous study identified a tandem array of 4.2-kb repeating units that contain the 4.5 S RNA coding sequence as well as many short repetitive sequences. To understand the genomic organization of this gene family, we have isolated and characterized 4.5 S RNA sequences that are part of the tandem array as well as identified members that are not part of the array. One variant 4.5 S RNA gene family member exhibits length polymorphisms in its minisatellite sites relative to the single previously reported gene. The 4.5 S RNA sequences that are not part of the tandem array possess many of the features of processed pseudogenes and are found adjacent to other interspersed repeated elements. These findings suggest that the mouse 4.5 S RNA can behave as a retroposon, resulting in the accumulation of 4.5 S RNA-like elements at many sites in the genome.
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Affiliation(s)
- R Kraft
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
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Bond UM, Yario TA, Steitz JA. Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro. Genes Dev 1991; 5:1709-22. [PMID: 1885007 DOI: 10.1101/gad.5.9.1709] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To study the role of base-pairing between the mammalian U7 snRNA and the highly variable histone downstream element (HDE) during the 3'-end maturation of mammalian histone pre-mRNAs, we mutated the HDE of the mouse H2A-614 gene and assayed processing in HeLa cells both in vivo and in vitro. Either a 9-nucleotide deletion or a block substitution of pyrimidines for 6 purines within the HDE abolished all 3'-end processing. Compensatory changes were introduced into a synthetic human U7 gene, whose transcripts assemble into Sm snRNPs in vivo. Suppression of the 6-purine substitution as well as a 3-purine substitution within the HDE was obtained in vivo by coexpressing the corresponding U7 suppressor RNAs and in vitro by using nuclear extracts prepared from HeLa cells containing U7 suppressor genes. Our results not only provide genetic evidence for base-pairing between the U7 snRNP and the HDE of mammalian histone pre-mRNAs but reveal an unexpected tolerance to drastic changes in the nature of the base-paired region.
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Affiliation(s)
- U M Bond
- Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
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