Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Vierstra, Jeff; Rynes, Eric; Sandstrom, Richard; Zhang, Miaohua; Canfield, Theresa K.; Hansen, R. Scott; Stehling-Sun, Sandra; Sabo, Peter J.; Byron, Rachel; Humbert, Richard; Thurman, Robert E.; Johnson, Audra; Vong, Shinny; Lee, Kristen; Bates, Daniel; Neri, Fidencio; Diegel, Morgan; Giste, Erika; Haugen, Eric; Dunn, Douglas; Wilken, Matthew S.; Josefowicz, Steven Z.; Samstein, Robert M.; Chang, Kai Hsin; Eichler, Evan E.; Bruijn, Marella de; Reh, Thomas A.; Skoultchi, Arthur I.; Rudensky, Alexander Y.; Orkin, Stuart H.; Papayannopoulou, Thalia; Treuting, Piper M.; Selleri, Licia; Kaul, Rajinder; Groudine, Mark; Bender, Michael A.; Stamatoyannopoulos, J

doi:10.1126/science.1246426

Cited by 257 publications

(356 citation statements)

References 52 publications

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“…An ongoing debate in the field of genomics is the degree to which phylogenetic conservation at the DNA sequence level is an accurate predictor of functional CREs, given that there is rapid turnover of individual TF binding sites in the course of evolution (Dermitzakis and Clark 2002;Vierstra et al 2014). We observed significantly higher vertebrate conservation (as measured by PhastCons scores) (Siepel et al 2005) for the most strongly expressed retinal and brain DHSs in the retina and cortex, respectively.…”

Section: Parameters That Predict Cis-regulatory Activitymentioning

confidence: 99%

Massively parallel cis-regulatory analysis in the mammalian central nervous system

et al. 2015

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Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell-derived organoids.

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Section: Parameters That Predict Cis-regulatory Activitymentioning

confidence: 99%

Massively parallel cis-regulatory analysis in the mammalian central nervous system

et al. 2015

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“…Among these, we identified three non-coding DNA segments (E1, E2, E3) within the 5′ end of the Pdgfrb locus with the highest cross-species sequence conservation and/or displaying DNaseI hypersensitive sites (HS) indicative of open chromatin (Fig. 5C) (Vierstra et al, 2014). Chromatin immunoprecipitation (ChIP) assays were performed to determine whether Pbx1 binds to these regions in vivo.…”

Section: Pbx1 Ablation In Vmcs Perturbs Renal Arterial Patterningmentioning

confidence: 99%

Pbx1 dependent control of VMC differentiation kinetics underlies gross renal vascular patterning

et al. 2015

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The architecture of an organ's vascular bed subserves its physiological function and metabolic demands. However, the mechanisms underlying gross vascular patterning remain elusive. Using intravital dye labeling and 3D imaging, we discovered that systems-level vascular patterning in the kidney is dependent on the kinetics of vascular mural cell (VMC) differentiation. Conditional ablation of the TALE transcription factor Pbx1 in renal VMC progenitors in the mouse led to the premature upregulation of PDGFRβ, a master initiator of VMC-blood vessel association. This precocious VMC differentiation resulted in nonproductive angiogenesis, abnormal renal arterial tree patterning and neonatal death consistent with kidney dysfunction. Notably, we establish that Pbx1 directly represses Pdgfrb, and demonstrate that decreased Pdgfrb dosage in conditional Pbx1 mutants substantially rescues vascular patterning defects and neonatal survival. These findings identify, for the first time, an in vivo transcriptional regulator of PDGFRβ, and reveal a previously unappreciated role for VMCs in systems-level vascular patterning.

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“…10 Recent analysis of DNase I hypersensitive sites and occupancy profiles of transcription-factor binding in humans and mice suggests the preservation of similar regulatory mechanisms for adipose gene expression in both species, and this preservation could be leveraged to inform disease pathways. 23,24 We describe here the analysis of gene expression in 770 subcutaneous adipose samples from Metabolic Syndrome in Men (METSIM), a study of 10,197 men, 45-73 years of age, living in the Kuopio area of Finland. Study data include dense genotypes and extensive metabolic and cardiovascular traits, such as plasma lipids, inflammatory markers, glycemic traits, and anthropometric traits.…”

Section: Introductionmentioning

confidence: 99%

Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits

Civelek

Pan

et al. 2017

The American Journal of Human Genetics

154

211

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Subcutaneous adipose tissue stores excess lipids and maintains energy balance. We performed expression quantitative trait locus (eQTL) analyses by using abdominal subcutaneous adipose tissue of 770 extensively phenotyped participants of the METSIM study. We identified cis-eQTLs for 12,400 genes at a 1% false-discovery rate. Among an approximately 680 known genome-wide association study (GWAS) loci for cardio-metabolic traits, we identified 140 coincident cis-eQTLs at 109 GWAS loci, including 93 eQTLs not previously described. At 49 of these 140 eQTLs, gene expression was nominally associated (p < 0.05) with levels of the GWAS trait. The size of our dataset enabled identification of five loci associated (p < 5 3 10 À8 ) with at least five genes located >5 Mb away. These trans-eQTL signals confirmed and extended the previously reported KLF14-mediated network to 55 target genes, validated the CIITA regulation of class II MHC genes, and identified ZNF800 as a candidate master regulator. Finally, we observed similar expression-clinical trait correlations of genes associated with GWAS loci in both humans and a panel of genetically diverse mice. These results provide candidate genes for further investigation of their potential roles in adipose biology and in regulating cardio-metabolic traits.

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Cited by 257 publications

References 52 publications

Massively parallel cis-regulatory analysis in the mammalian central nervous system

Massively parallel cis-regulatory analysis in the mammalian central nervous system

Pbx1 dependent control of VMC differentiation kinetics underlies gross renal vascular patterning

Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits

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