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The evolution and mutational robustness of chromatin accessibility in Drosophila

https://doi.org/10.1101/2023.06.26.546587

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What this work says

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

inferredcites →https://doi.org/10.1002/0471142727.mb2129s109openalex-snapshot

ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide

inferredcites →https://doi.org/10.1016/j.ajhg.2018.04.002openalex-snapshot

The Post-GWAS Era: From Association to Function

inferredcites →https://doi.org/10.1016/j.bbagrm.2007.11.011openalex-snapshot

The DRE/DREF transcriptional regulatory system: a master key for cell proliferation

inferredcites →https://doi.org/10.1016/j.cell.2014.11.041openalex-snapshot

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

inferredcites →https://doi.org/10.1016/j.celrep.2020.107663openalex-snapshot

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

inferredcites →https://doi.org/10.1016/j.tig.2019.06.002openalex-snapshot

A New Portrait of Constitutive Heterochromatin: Lessons from Drosophila melanogaster

inferredcites →https://doi.org/10.1016/s0960-9822(02)01113-2openalex-snapshot

Evolution of yellow Gene Regulation and Pigmentation in Drosophila

inferredcites →https://doi.org/10.1038/371806a0openalex-snapshot

The Trithorax-like gene encodes the Drosophila GAGA factor

inferredcites →https://doi.org/10.1038/nature03235openalex-snapshot

Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila

inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot

Evolution of genes and genomes on the Drosophila phylogeny

inferredcites →https://doi.org/10.1038/nature09725openalex-snapshot

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

inferredcites →https://doi.org/10.1038/nature10002openalex-snapshot

Determinants of nucleosome organization in primary human cells

inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot

The accessible chromatin landscape of the human genome

inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot

An integrated encyclopedia of DNA elements in the human genome

inferredcites →https://doi.org/10.1038/nature13395openalex-snapshot

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

inferredcites →https://doi.org/10.1038/ng.3331openalex-snapshot

A method to predict the impact of regulatory variants from DNA sequence

inferredcites →https://doi.org/10.1038/ng.77openalex-snapshot

Regulatory changes underlying expression differences within and between Drosophila species

inferredcites →https://doi.org/10.1038/nmeth.1906openalex-snapshot

ChromHMM: automating chromatin-state discovery and characterization

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

inferredcites →https://doi.org/10.1038/nmeth.3547openalex-snapshot

Predicting effects of noncoding variants with deep learning–based sequence model

inferredcites →https://doi.org/10.1038/nprot.2017.124openalex-snapshot

Chromatin-state discovery and genome annotation with ChromHMM

inferredcites →https://doi.org/10.1038/nrg2063openalex-snapshot

The evolutionary significance of cis-regulatory mutations

inferredcites →https://doi.org/10.1038/s41576-018-0089-8openalex-snapshot

Chromatin accessibility and the regulatory epigenome

inferredcites →https://doi.org/10.1038/s41586-018-0692-zopenalex-snapshot

Improved reference genome of Aedes aegypti informs arbovirus vector control

inferredcites →https://doi.org/10.1038/s41586-020-2871-yopenalex-snapshot

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

inferredcites →https://doi.org/10.1038/s41586-021-04262-zopenalex-snapshot

Decoding gene regulation in the fly brain

inferredcites →https://doi.org/10.1038/s41586-022-04506-6openalex-snapshot

The evolution, evolvability and engineering of gene regulatory DNA

inferredcites →https://doi.org/10.1038/s41588-021-00782-6openalex-snapshot

Base-resolution models of transcription-factor binding reveal soft motif syntax

inferredcites →https://doi.org/10.1038/s41592-021-01252-xopenalex-snapshot

Effective gene expression prediction from sequence by integrating long-range interactions

inferredcites →https://doi.org/10.1093/bioinformatics/btt128openalex-snapshot

HAL: a hierarchical format for storing and analyzing multiple genome alignments

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btx105openalex-snapshot

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone

inferredcites →https://doi.org/10.1093/hmg/ddv259openalex-snapshot

Non-coding genetic variants in human disease: Figure 1.

inferredcites →https://doi.org/10.1093/molbev/msab011openalex-snapshot

Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads

inferredcites →https://doi.org/10.1093/molbev/msab048openalex-snapshot

Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii

inferredcites →https://doi.org/10.1093/molbev/msg077openalex-snapshot

Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites

inferredcites →https://doi.org/10.1093/molbev/msg096openalex-snapshot

The Effects of Selection Against Spurious Transcription Factor Binding Sites

inferredcites →https://doi.org/10.1093/molbev/msh026openalex-snapshot

Inference of Positive and Negative Selection on the 5′ Regulatory Regions of Drosophila Genes

inferredcites →https://doi.org/10.1093/nar/gkab1113openalex-snapshot

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

inferredcites →https://doi.org/10.1093/nar/gkf570openalex-snapshot

The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation

inferredcites →https://doi.org/10.1101/gad.341768.120openalex-snapshot

Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription

inferredcites →https://doi.org/10.1101/gr.112466.110openalex-snapshot

Genome-wide analysis of promoter architecture in Drosophila melanogaster

inferredcites →https://doi.org/10.1101/gr.200535.115openalex-snapshot

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

inferredcites →https://doi.org/10.1126/sciadv.abe2955openalex-snapshot

Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer

inferredcites →https://doi.org/10.1126/science.1257570openalex-snapshot

Phylogenomics resolves the timing and pattern of insect evolution

inferredcites →https://doi.org/10.1145/3292500.3330701openalex-snapshot

Optuna

inferredcites →https://doi.org/10.1186/gb-2007-8-2-r24openalex-snapshot

Quantifying similarity between motifs

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/gb-2011-12-4-r34openalex-snapshot

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

inferredcites →https://doi.org/10.1186/s13059-019-1721-4openalex-snapshot

Chromatin accessibility plays a key role in selective targeting of Hox proteins

inferredcites →https://doi.org/10.1186/s13072-017-0141-5openalex-snapshot

Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development

inferredcites →https://doi.org/10.1242/dev.178285openalex-snapshot

Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila

inferredcites →https://doi.org/10.1371/journal.pcbi.1006484openalex-snapshot

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

inferredcites →https://doi.org/10.1371/journal.pgen.1010439openalex-snapshot

Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster

inferredcites →https://doi.org/10.1371/journal.pone.0009129openalex-snapshot

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

inferredcites →https://doi.org/10.1534/g3.113.008185openalex-snapshot

Genome of Drosophila suzukii, the Spotted Wing Drosophila

inferredcites →https://doi.org/10.3389/fgene.2015.00322openalex-snapshot

Mechanisms of mutational robustness in transcriptional regulation

inferredcites →https://doi.org/10.48550/arxiv.1912.01703openalex-snapshot

PyTorch: An Imperative Style, High-Performance Deep Learning Library

inferredcites →https://doi.org/10.7554/elife.66668openalex-snapshot

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

What points at this work

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

inferred← citeshttps://doi.org/10.1186/s13059-023-03079-5openalex-snapshot

The evolution and mutational robustness of chromatin accessibility in Drosophila

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