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Locus architecture affects mRNA expression levels in Drosophila embryos

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/dvdy.22535openalex-snapshot

cis‐regulatory mutations are a genetic cause of human limb malformations

inferredcites →https://doi.org/10.1002/j.1460-2075.1992.tb05498.xopenalex-snapshot

Regulation of even‐skipped stripe 2 in the Drosophila embryo.

inferredcites →https://doi.org/10.1006/dbio.1996.0117openalex-snapshot

Regulation of Two Pair-Rule Stripes by a Single Enhancer in theDrosophilaEmbryo

inferredcites →https://doi.org/10.1016/0092-8674(95)90136-1openalex-snapshot

Virus induction of human IFNβ gene expression requires the assembly of an enhanceosome

inferredcites →https://doi.org/10.1016/j.cell.2008.01.053openalex-snapshot

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

inferredcites →https://doi.org/10.1016/j.cell.2011.01.024openalex-snapshot

Functional and Mechanistic Diversity of Distal Transcription Enhancers

inferredcites →https://doi.org/10.1016/j.cell.2011.10.023openalex-snapshot

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

inferredcites →https://doi.org/10.1016/j.cell.2012.03.051openalex-snapshot

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

inferredcites →https://doi.org/10.1016/j.cell.2013.04.053openalex-snapshot

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

inferredcites →https://doi.org/10.1016/j.cell.2014.02.009openalex-snapshot

Looping Back to Leap Forward: Transcription Enters a New Era

inferredcites →https://doi.org/10.1016/j.celrep.2012.06.004openalex-snapshot

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria

inferredcites →https://doi.org/10.1016/j.cub.2010.06.070openalex-snapshot

Transcriptional Enhancers in Animal Development and Evolution

inferredcites →https://doi.org/10.1016/j.cub.2011.01.054openalex-snapshot

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

inferredcites →https://doi.org/10.1016/j.cub.2011.05.056openalex-snapshot

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

inferredcites →https://doi.org/10.1016/j.devcel.2009.12.026openalex-snapshot

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

inferredcites →https://doi.org/10.1016/j.gde.2011.01.021openalex-snapshot

Gene expression in time and space: additive vs hierarchical organization of cis-regulatory regions

inferredcites →https://doi.org/10.1016/j.tibs.2014.02.007openalex-snapshot

Enhancer RNAs and regulated transcriptional programs

inferredcites →https://doi.org/10.1016/j.tig.2009.08.003openalex-snapshot

Different gene regulation strategies revealed by analysis of binding motifs

inferredcites →https://doi.org/10.1016/j.ydbio.2009.11.035openalex-snapshot

Enhancers: The abundance and function of regulatory sequences beyond promoters

inferredcites →https://doi.org/10.1016/j.ymeth.2014.01.003openalex-snapshot

Comparing mRNA levels using in situ hybridization of a target gene and co-stain

inferredcites →https://doi.org/10.1038/msb.2009.97openalex-snapshot

Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo

inferredcites →https://doi.org/10.1038/msb.2012.48openalex-snapshot

A model of spatially restricted transcription in opposing gradients of activators and repressors

inferredcites →https://doi.org/10.1038/nature02189openalex-snapshot

A self-organizing system of repressor gradients establishes segmental complexity in Drosophila

inferredcites →https://doi.org/10.1038/nature02538openalex-snapshot

Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene

inferredcites →https://doi.org/10.1038/nature06929openalex-snapshot

Nucleosome organization in the Drosophila genome

inferredcites →https://doi.org/10.1038/nature09033openalex-snapshot

Widespread transcription at neuronal activity-regulated enhancers

inferredcites →https://doi.org/10.1038/nature09380openalex-snapshot

Mediator and cohesin connect gene expression and chromatin architecture

inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot

A map of human genome variation from population-scale sequencing

inferredcites →https://doi.org/10.1038/nature09692openalex-snapshot

A unique chromatin signature uncovers early developmental enhancers in humans

inferredcites →https://doi.org/10.1038/nature10200openalex-snapshot

Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

inferredcites →https://doi.org/10.1038/nature10811openalex-snapshot

The Drosophila melanogaster Genetic Reference Panel

inferredcites →https://doi.org/10.1038/nature10944openalex-snapshot

The genomic basis of adaptive evolution in threespine sticklebacks

inferredcites →https://doi.org/10.1038/nature12753openalex-snapshot

Topology of mammalian developmental enhancers and their regulatory landscapes

inferredcites →https://doi.org/10.1038/nbt.2137openalex-snapshot

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

inferredcites →https://doi.org/10.1038/nbt.2205openalex-snapshot

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

inferredcites →https://doi.org/10.1038/ng.101openalex-snapshot

Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes

inferredcites →https://doi.org/10.1038/ng.215openalex-snapshot

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease

inferredcites →https://doi.org/10.1038/ng.2305openalex-snapshot

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

inferredcites →https://doi.org/10.1038/ng.2713openalex-snapshot

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

inferredcites →https://doi.org/10.1038/nmeth.1318openalex-snapshot

Enzymatic assembly of DNA molecules up to several hundred kilobases

inferredcites →https://doi.org/10.1038/nprot.2007.328openalex-snapshot

Creating transgenic Drosophila by microinjecting the site-specific φC31 integrase mRNA and a transgene-containing donor plasmid

inferredcites →https://doi.org/10.1038/nrg3454openalex-snapshot

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

inferredcites →https://doi.org/10.1038/nsmb.1500openalex-snapshot

A quantitative model of transcription factor–activated gene expression

inferredcites →https://doi.org/10.1073/pnas.0902454106openalex-snapshot

Transcription factors mediate long-range enhancer–promoter interactions

inferredcites →https://doi.org/10.1073/pnas.0905754106openalex-snapshot

Conservation of enhancer location in divergent insects

inferredcites →https://doi.org/10.1073/pnas.1011480108openalex-snapshot

Two developmental modules establish 3D beak-shape variation in Darwin's finches

inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot

Histone H3K27ac separates active from poised enhancers and predicts developmental state

inferredcites →https://doi.org/10.1073/pnas.1102625108openalex-snapshot

Transcriptional repression via antilooping in the Drosophila embryo

inferredcites →https://doi.org/10.1073/pnas.1210678109openalex-snapshot

Complex effects of nucleotide variants in a mammalian cis -regulatory element

inferredcites →https://doi.org/10.1073/pnas.1219099110openalex-snapshot

Systematic functional regulatory assessment of disease-associated variants

inferredcites →https://doi.org/10.1073/pnas.1307449110openalex-snapshot

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis -regulatory function of ChIP-seq peaks

inferredcites →https://doi.org/10.1093/bfgp/elp022openalex-snapshot

Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease

inferredcites →https://doi.org/10.1093/bioinformatics/bti173openalex-snapshot

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster

inferredcites →https://doi.org/10.1093/hmg/ddl232openalex-snapshot

Conserved distances between vertebrate highly conserved elements

inferredcites →https://doi.org/10.1093/hmg/ddt559openalex-snapshot

Functional characterization ofSIM1-associated enhancers

inferredcites →https://doi.org/10.1093/nar/12.14.5589openalex-snapshot

Short and long range activation by the SV40 enhancer

inferredcites →https://doi.org/10.1093/nar/gkq999openalex-snapshot

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

inferredcites →https://doi.org/10.1093/nar/gkr342openalex-snapshot

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

inferredcites →https://doi.org/10.1101/gad.10.6.700openalex-snapshot

Short-range transcriptional repressors mediate both quenching and direct repression within complex loci in Drosophila.

inferredcites →https://doi.org/10.1101/gad.5.5.820openalex-snapshot

DNA looping between sites for transcriptional activation: self-association of DNA-bound Sp1.

inferredcites →https://doi.org/10.1101/gad.939601openalex-snapshot

Transcriptional repression: the long and the short of it

inferredcites →https://doi.org/10.1101/gr.142646.112openalex-snapshot

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

inferredcites →https://doi.org/10.1101/gr.6669607openalex-snapshot

Genomic regulatory blocks underlie extensive microsynteny conservation in insects

inferredcites →https://doi.org/10.1126/science.1176980openalex-snapshot

Intraspecific Polymorphism to Interspecific Divergence: Genetics of Pigmentation in Drosophila

inferredcites →https://doi.org/10.1126/science.1182213openalex-snapshot

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

inferredcites →https://doi.org/10.1126/science.1197005openalex-snapshot

Diversity of Human Copy Number Variation and Multicopy Genes

inferredcites →https://doi.org/10.1126/science.1200684openalex-snapshot

The Developmental Role of Agouti in Color Pattern Evolution

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1128/mcb.14.5.3364openalex-snapshot

Specific DNA Recognition and Intersite Spacing Are Critical for Action of the Bicoid Morphogen

inferredcites →https://doi.org/10.1128/mcb.15.12.7059openalex-snapshot

Mechanism of Differential Utilization of the his3 T R and T C TATA Elements

inferredcites →https://doi.org/10.1128/mcb.8.11.4608openalex-snapshot

Genetic evidence for promoter competition in Saccharomyces cerevisiae.

inferredcites →https://doi.org/10.1136/jmg.2007.055699openalex-snapshot

A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome

inferredcites →https://doi.org/10.1146/annurev.genom.7.080505.115623openalex-snapshot

Transcriptional Regulatory Elements in the Human Genome

inferredcites →https://doi.org/10.1186/gb-2006-7-12-r123openalex-snapshot

Three-dimensional morphology and gene expression in the Drosophilablastoderm at cellular resolution I: data acquisition pipeline

inferredcites →https://doi.org/10.1186/gb-2010-11-5-r52openalex-snapshot

Towards a comprehensive structural variation map of an individual human genome

inferredcites →https://doi.org/10.1242/dev.00611openalex-snapshot

Conservation ofEndo16expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

inferredcites →https://doi.org/10.1242/dev.065987openalex-snapshot

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

inferredcites →https://doi.org/10.1242/dev.069146openalex-snapshot

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

inferredcites →https://doi.org/10.1242/dev.119.3.767openalex-snapshot

Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter

inferredcites →https://doi.org/10.1242/dev.122.1.205openalex-snapshot

The eve stripe 2 enhancer employs multiple modes of transcriptional synergy

inferredcites →https://doi.org/10.1242/dev.126.11.2527openalex-snapshot

Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients*

inferredcites →https://doi.org/10.1371/journal.pbio.0030093openalex-snapshot

Functional Evolution of a cis-Regulatory Module

inferredcites →https://doi.org/10.1371/journal.pbio.0060263openalex-snapshot

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

inferredcites →https://doi.org/10.1371/journal.pcbi.1003467openalex-snapshot

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

inferredcites →https://doi.org/10.1371/journal.pgen.1000106openalex-snapshot

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

inferredcites →https://doi.org/10.1371/journal.pgen.1000308openalex-snapshot

Shaping Skeletal Growth by Modular Regulatory Elements in the Bmp5 Gene

inferredcites →https://doi.org/10.1371/journal.pgen.1003243openalex-snapshot

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

inferredcites →https://doi.org/10.1371/journal.pgen.1004060openalex-snapshot

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

inferredcites →https://doi.org/10.1534/genetics.166.4.1775openalex-snapshot

Construction of Transgenic Drosophila by Using the Site-Specific Integrase From Phage C31

inferredcites →https://doi.org/10.5483/bmbrep.2012.45.10.105openalex-snapshot

Mesodermal repression of single-minded in Drosophila embryo is mediated by a cluster of Snail-binding sites proximal to the early promoter

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s42003-020-01375-5openalex-snapshot

A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development

inferred← citeshttps://doi.org/10.70675/375b5b81z3e0dz42f1z8c46z6f2263bd048bopenalex-snapshot

Discovery and analysis of silencers in Drosophila acting as enhancers in other cellular contexts

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