Biology subjects

Hennighausen, L.

Publications and source records attributed to Hennighausen, L..

23 records · Page 2Linked to original sources

bioRxiv2020

Regulatory plasticity within a complex cytokine-sensing mammary enhancer during lactation

Enhancers are transcription factor platforms that synergize with promoters to activate gene expression up to several-thousand-fold. While genome-wide structural studies are used to predict enhancers, the in vivo significance is less clear. Specifically, the biological importance of individual transcription factors within enhancer complexes remains to be understood. Here we investigate the structural and biological importance of individual transcription factor binding sites and redundancy among transcription components within a complex enhancer in vivo. The Csn1s2b gene is expressed exclusively in mammary tissue and activated several thousand-fold during pregnancy and lactation. Using ChIP-seq we identified a complex lactation-specific candidate enhancer that binds multiple transcription factors and coincides with activating histone marks. Using experimental mouse genetics, we determined that deletion of canonical binding motifs for the transcription factors NFIB and STAT5, individually and combined, had a limited biological impact. Loss of these sites led to a shift of transcription factor binding to juxtaposed sites, suggesting exceptional plasticity that does not require direct protein-DNA interactions. Additional deletions revealed the critical importance of a non-canonical STAT5 binding site for enhancer activity. Our data also suggest that enhancer RNAs are not required for the activity of this specific enhancer. While ChIP-seq experiments predicted an additional candidate intronic enhancer, its deletion did not adversely affect gene expression, emphasizing the limited biological information provided by structural data. Our study provides comprehensive insight into the anatomy and biology of a composite mammary enhancer that activates its target gene several hundred-fold during lactation.

genomics↗

bioRxiv2020

Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers

ACE2, in concert with the protease TMPRSS2, binds the novel coronavirus SARS-CoV-2 and facilitates its cellular entry. The ACE2 gene is expressed in SARS-CoV-2 target cells, including Type II Pneumocytes (Ziegler, 2020), and is activated by interferons. Viral RNA was also detected in breast milk (Wu et al., 2020), raising the possibility that ACE2 expression is under the control of cytokines through the JAK-STAT pathway. Here we show that Ace2 expression in mammary tissue is induced during pregnancy and lactation, which coincides with the establishment of a candidate enhancer. The prolactin-activated transcription factor STAT5 binds to tandem sites that coincide with activating histone enhancer marks and additional transcription components. The presence of pan JAK-STAT components in mammary alveolar cells and in Type II Pneumocytes combined with the autoregulation of both STAT1 and STAT5 suggests a prominent role of cytokine signaling pathways in cells targeted by SARS-CoV-2.

genomics↗

bioRxiv2019

Cytosine but not adenine base editor generates mutations in mice

Deaminase base editing has emerged as a tool to install or correct point mutations in the genomes of living cells in a wide range of organisms and its ultimate success therapeutically depends on its accuracy. Here we have investigated the fidelity of cytosine base editor 4 (BE4) and adenine base editor (ABE) in mouse embryos using unbiased whole genome sequencing of a family-based trio cohort. We demonstrate that BE4-edited mice carry an excess of single-nucleotide variants and deletions compared to ABE-edited mice and controls.

genomics↗

bioRxiv2019

Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2

BackgroundSex differences in the incidence and progression of many liver diseases, including liver fibrosis and hepatocellular carcinoma, are associated with sex-biased expression of hundreds of genes in the liver. This sexual dimorphism is largely determined by the sex-specific pattern of pituitary growth hormone secretion, which controls a transcriptional regulatory network operative in the context of sex-biased chromatin states. Histone H3K27-trimethylation yields a major sex-biased repressive chromatin mark that is specifically deposited by polycomb repressive complex-2, via its homologous catalytic subunits Ezh1 and Ezh2, at many strongly female-biased genes in male mouse liver, but not at male-biased genes in female liver.\n\nResultsWe used Ezh1-knockout mice with a hepatocyte-specific knockout of Ezh2 to elucidate the sex bias of liver H3K27-trimethylation and its functional role in regulating sex-differences in the liver. Combined hepatic Ezh1/Ezh2 deficiency led to a significant loss of sex-biased gene expression, particularly in male liver, where many female-biased genes increased in expression while male-biased genes showed decreased expression. The associated loss of H3K27me3 marks, and increases in the active enhancer marks H3K27ac and H3K4me1, were also more pronounced in male liver. Many genes linked to liver fibrosis and hepatocellular carcinoma were induced in Ezh1/Ezh2-deficient livers, which may contribute to the increased sensitivity of these mice to hepatotoxin-induced liver pathology.\n\nConclusionsEzh1/Ezh2-catalyzed H3K27-trimethyation is thus essential for the sex-dependent epigenetic regulation of liver chromatin states controlling phenotypic sex differences in liver metabolism and liver fibrosis, and may be a critical determinant of the sex-bias in liver disease susceptibility.

genomics↗

bioRxiv2017

Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer

Enhancers are transcription factor platforms that also bind RNA polymerase II and generate enhancer RNAs (eRNA). Although eRNAs have been suggested as predictors of enhancer activities and possibly key components facilitating transcription, there is little genetic evidence to support this. We address the biology of eRNAs in vivo and investigate eRNA patterns, expression levels and possible functions within a mammary-specific super-enhancer that is composed of three units with distinct transcriptional capacities. We show that eRNA levels do not correspond with the activities of their respective enhancer units. However, changes in eRNA expression upon deletion of individual enhancer units reflect the change in overall super-enhancer activity. These data provide genetic evidence that eRNA levels are not a reliable readout of individual enhancers, but they predict super-enhancer activity in the absence of constituent elements.

genetics↗