Papers of the Month
By Robin Arnette, Carol Kelly, Rajneesh Pathania, and Andrew Trexler
NIEHS and NTP report life experiences may alter DNA methylation
Scientists at NIEHS and the National Toxicology Program (NTP), along with collaborators, reported that DNA sequence may determine where methylation events occur, and that life events such as pregnancy could alter DNA methylation patterns. The researchers used inbred mice to examine methylation, which is the addition of methyl groups onto DNA, in regions where the nucleotide cytosine is followed by a phosphate and the nucleotide guanine. Methylation of these areas, known as CpG sites, may serve as an epigenetic record of life events in body cells.
Researchers intercrossed two inbred mouse strains, C57BL/6N and C3H/HeN, and measured DNA methylation patterns in the livers of parents and offspring using whole-genome bisulfite sequencing. They found that DNA methylation patterns were closely linked to the genetic makeup of the animal, which is known as genotype. These patterns were unchanged when passed to male and female offspring. However, in female animals that had experienced pregnancy, hundreds of DNA sites showed decreased methylation compared with virgin females.
These findings suggest that genetics influences DNA methylation patterns and that major life events may leave a distinct methylation signature. Although the team has not determined exactly how these female mice had a loss of DNA methylation, the work bolsters the importance of epigenetics in influencing gene regulation. (RA)
Citation: Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li J, Merrick BA, Tice RR, Wang T, Xu X, NISC Comparative Sequencing Program, Buchel PR, Fargo DC, Mullikin JC, Wade PA. 2019. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nat Commun 10(1):305.
Sleep, sex hormones, and irregular menstruation
According to NIEHS researchers and their collaborators, the increase in progesterone levels that occurs during late puberty in girls may be responsible for the switch to slower luteinizing hormone (LH) pulses during sleep in the follicular phase (FP). These findings have important implications for the normal development of the female reproductive system in late puberty.
In girls going through puberty, LH pulse frequency is faster during sleep than when awake, whereas in adult women, LH pulses are slower during sleep compared with awake during the FP of the menstrual cycle. This sleep-specific slowing is thought to be important for follicle growth.
The research team studied a cohort of 23 healthy, racially diverse adolescent girls from the greater Boston area. Hormone levels in blood and urine were monitored during two consecutive menstrual cycles and during an overnight sleep study conducted during the FP.
The researchers found a strong inverse association between progesterone levels in the first menstrual cycle and LH pulse frequency during sleep in the FP of the following menstrual cycle. Follicle growth, however, was not disrupted in girls who lacked the adult pattern of sleep-specific slowing of LH pulses. These data suggest that immature sleep and wake patterning of LH secretion is unlikely to contribute to menstrual irregularity in adolescent girls. (AT)
Citation: Sun BZ, Kangarloo T, Adams JM, Sluss P, Chandler DW, Zava DT, McGrath JA, Umbach DM, Shaw ND. 2019. The relationship between progesterone, sleep, and LH and FSH secretory dynamics in early post-menarchal girls. J Clin Endocrinol Metab; doi:10.1210/jc.2018-02400 [Online 15 January 2019].
Pol beta side chain residue prevents insertion of Fapy-dGTP damage
In DNA polymerase (Pol) beta, an enzyme mainly involved in DNA repair, the side chain of amino acid aspartate 276 prevents Pol beta from incorporating the oxidatively-induced damaged nucleotide 4,6-Diamino-5-formamidopyrimidine (Fapy-dGTP) into DNA. The discovery, made by NIEHS scientists and their collaborators, sheds more light on how Pol beta has evolved to prevent Fapy-dGTP insertion, a process that potentially results in adverse health outcomes, such as cancer. The finding may also lead to advances in certain cancer therapies.
Because Fapy-dGTP was difficult to isolate, the researchers produced a version that was similar in structure, called Beta-C-Fapy-dGTP. They used insertion kinetic studies and crystal structures of Beta-C-Fapy-dGTP and Pol beta to determine that the side chain of aspartate 276, which is positioned in the active site of Pol beta, distorts critical catalytic atoms and thus prevents the binding of Beta-C-Fapy-dGTP. Once the side chain was removed, Beta-C-Fapy-dGTP could bind to Pol beta, and therefore, be included in a DNA strand.
The results highlight the precise conditions necessary for Pol beta to do its job of including nucleotides, as well as how it has developed as a gatekeeper to avoid inserting the damaged nucleotide Fapy-dGTP during DNA repair. The researchers theorize that this same protective strategy may be replicated in other DNA polymerases. (CK)
Citation: Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH. 2019. A guardian residue hinders insertion of a Fapy-dGTP analog by modulating the open-closed DNA polymerase transition. Nucleic Acids Res; doi:10.1093/nar/gkz002 [Online 16 January 2019].
DNA methylation pattern may indicate childhood asthma risk
Novel epigenetic markers, which are chemical tags that attach to DNA, may indicate a newborn’s risk of asthma, according to an international team of scientists led by NIEHS. The data were generated by the Pregnancy and Childhood Epigenetics Consortium and may help researchers identify at birth which children will eventually develop asthma and to determine biomarkers of this disease.
The scientists examined DNA methylation patterns in blood taken from newborns and followed the children until they reached school age, to see who developed asthma. The team also looked at DNA methylation patterns during childhood in different groups of children with and without asthma. The study revealed the children followed from birth who developed asthma had nine areas, or loci, in their DNA with different levels of methylation compared with children who did not develop asthma. The children with a previous asthma diagnosis had 173 DNA differentially methylated loci in relation to asthma. Many of these loci were also differentially methylated in relation to asthma in a separate study of cells taken from the nose, which reflect processes in the lower respiratory system. Several of the implicated genes are targets for either approved or potential asthma drugs.
The newly identified DNA methylation loci in newborns are potential biomarkers of later asthma risk. The differentially methylated loci in older children may reflect both risks and effects of asthma. (RP)
Citation: Reese SE, Xu CJ, den Dekker HT, Lee MK, Sikdar S, Ruiz-Arenas C, Merid SK, Rezwan FI, Page CM, Ullemar V, Melton PE, Oh SS, Yang IV, Burrows K, Soderhall C, Jima DD, Gao L, Arathimos R, Kuppers LK, Wielscher M, Rzehak P, Lahti J, Laprise C, Madore AM, Ward J, Bennett BD, Wang T, Bell DA, BIOS consortium, Vonk JM, Haberg SE, Zhao S, Karlsson R, Hollams E, Hu D, Richards AJ, Bergstrom A, Sharp GC, Felix JF, Bustamante M, Gruzieva O, Maguire RL, Gilliland F, Baiz N, Nohr EA, Corpeleijn E, Sebert S, Karmaus W, Grote V, Kajantie E, Magnus MC, Ortqvist AK, Eng C, Liu AH, Kull I, Jaddoe VWV, Sunyer J, Kere J, Hoyo C, Annesi-Maesano I, Arshad SH, Koletzko B, Brunekreef B, Binder EB, Raikkonen K, Reischl E, Holloway JW, Jarvelin MR, Snieder H, Kazmi N, Breton CV, Murphy SK, Pershagen G, Anto JM, Relton CL, Schwartz DA, Burchard EG, Huang RC, Nystad W, Almqvist C, Henderson AJ, Melen E, Duijts L, Koppelman GH, London SJ. 2018. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J Allergy Clin Immunol; doi:10.1016/j.jaci.2018.11.043 [Online 21 December 2018]. (Story)
(Carol Kelly is a technical writer and editor for the NIEHS Office of Communications and Public Liaison. Rajneesh Pathania, Ph.D., is a research fellow in the NIEHS Systems Biology Group. Andrew Trexler is a postbaccalaureate research fellow in the National Cancer Institute Center for Cancer Research Laboratory of Toxicology and Toxicokinetics, housed at NIEHS.)