New layer of control in gene expression

In an NIEHS-funded study, researchers uncovered a previously unknown way that genes code for proteins. Rather than directions going one way from DNA, through messenger RNA (mRNA), to proteins, the study showed that RNA can modify how DNA is transcribed into mRNA and translated to produce proteins.

The researchers studied mice stem cells to explore the mechanisms of gene expression. They found that mRNA modifies how DNA is transcribed using a reversible chemical reaction called methylation, which can change the activity of a DNA segment without changing the sequence. The researchers identified and characterized a number of proteins that recognized the methylated mRNA.

They also discovered that a group of RNAs called chromosome-associated regulatory RNAs (carRNAs) used the same methylation process. However, the carRNAs did not code proteins and were not directly involved in protein translation. Instead, they controlled how DNA was stored and transcribed. The researchers determined that a specific methylation modification known as N6-methyladenosine (m6A) served as a switch to control carRNA levels, which regulated DNA transcription. When they disrupted m6A in mouse stem cells, the abundance of carRNAs increased, as did gene expression.

According to the authors, the findings have major implications in basic biology because they provide a new role for m6A and carRNAs in how DNA becomes proteins, affecting our understanding of mechanisms involved in human disease and drug design.

Citation: Liu J, Dou X, Chen C, Chen C, Liu C, Xu MM, Zhao S, Shen B, Gao Y, Han D, He C. 2020. N 6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science 367(6477):580–586.

BPA substitute disrupts mouse placenta, may affect developing brain

NIEHS grantees reported that bisphenol S (BPS), a replacement for bisphenol A (BPA), disrupted the mouse placenta during pregnancy. According to the authors, the findings show that BPS exposure may be just as hazardous to the placenta as BPA and may lead to effects on a fetus’s developing brain.

Concerns about the safety of BPA, a chemical in plastics and other products, has led to production of BPA-free goods, which often use closely related chemicals such as BPS. To compare the effects of BPA and BPS, the researchers exposed pregnant mice to one or the other chemical, then collected placental samples and compared them with placental samples from unexposed pregnant mice.

They found that BPA and BPS led to almost identical changes in placental gene expression. The team observed defects in the junctional zone of the placenta, which is a main compartment that produces hormones, growth factors, and immune cells important for the normal progression of pregnancy. They also found that BPA and BPS led to lower levels of placental serotonin, which is essential for fetal brain development in both mice and humans.

The researchers concluded that these observations in mice imply potential associated effects on the placenta and developing brain in humans. Further studies are warranted to ensure the safety of BPA alternatives, such as BPS.

Citation: Mao J, Jain A, Denslow ND, Nouri MZ, Chen S, Wang T, Zhu N, Koh J, Sarma SJ, Sumner BW, Lei Z, Sumner LW, Bivens NJ, Roberts RM, Tuteja G, Rosenfeld CS. 2020. Bisphenol A and bisphenol S disruptions of the mouse placenta and potential effects on the placenta−brain axis. Proc Natl Acad Sci U S A 17(9):4642–4652.

Unanticipated response to estrogen at the single cell level

NIEHS grantees found that individual cells in a population respond differently to estrogen stimulation at both the level of single cells and alleles, which are other possible forms of a gene. These differences were not explained by estrogen receptor levels in the cells or its activation status.

The researchers treated human breast cancer cells with estrogen in the lab and looked at expression of two well-characterized genes, GREB1 and MYC, whose activities are regulated by estrogen. As expected, they found that estrogen activated GREB1 and MYC genes within 15 minutes. Unexpectedly, individual cells exhibited large differences in the level of gene activation. These differences occurred even between alleles within the same cell.

To determine whether estrogen receptor regulators were involved in modifying the response to estrogen, the scientists used automated high-throughput technologies to test a collection of small molecule inhibitors of the estrogen receptor regulators. One inhibitor, called MS049, markedly increased the response of individual alleles to estrogen.

The researchers altered estrogenic response by inhibiting estrogen receptor regulators, establishing a previously unrecognized regulation path for estrogen to activate genes at the single cell level. According to the authors, the findings provide novel insights into the complex ways that cells maintain variability in response to stimuli, an important adaptation strategy for cell populations.

Citation: Stossi F, Dandekar RD, Mancini MG, Gu G, Fuqua SAW, Nardone A, De Angelis C, Fu X, Schiff R, Bedford MT, Xu W, Johansson HE, Stephan CC, Mancini MA. 2020. Estrogen-induced transcription at individual alleles is independent of receptor level and active conformation but can be modulated by coactivators activity. Nucleic Acids Res 48(4):1800–1810.

Ambient air pollution associated with breast cancer risk

Using several modeling approaches, NIEHS grantees found links between air pollutants near major roadways and increased breast cancer risk. Previous studies of air pollution and breast cancer have generally used one method of assessing exposure and have focused on white women, with inconsistent results. In this study, the researchers used three exposure assessment methods to investigate associations between long-term air pollution exposure and breast cancer risk for 57,589 women in the Southern California Multiethnic Cohort.

Using methods known as kriging, land use regression (LUR), and the California Line Source Dispersion model (CALINE4), the team estimated air pollution exposures of particulate matter and nitrogen oxides. Among all women, breast cancer risk was positively, but not significantly, associated with nitrogen oxides determined by kriging and LUR, as well as with particulate matter using kriging. However, among women who lived within 500 meters of major roads, the scientists observed significantly increased risks associated with nitrogen oxides and particulate matter as determined by kriging, as well as nitrogen oxides using LUR. No overall associations were observed using CALINE4.

When they analyzed subgroups within the population, stronger associations between nitrogen oxides and breast cancer risk among African Americans and Japanese Americans became apparent. According to the authors, further studies of multiethnic populations are needed using different modeling methods to confirm the effects of air pollution, particularly with near‐roadway exposures.

Citation: Cheng I, Tseng C, Wu J, Yang J, Conroy SM, Shariff-Marco S, Li L, Hertz A, Gomez SL, Le Marchand L, Whittemore AS, Stram DO, Ritz B, Wu AH. 2020. Association between ambient air pollution and breast cancer risk: The Multiethnic Cohort Study. Int J Cancer 146(3):699–711.