4.6 Article

Sex-specific variation in R-loop formation in Drosophila melanogaster

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

FlyBase: updates to the Drosophila melanogaster knowledge base

Aoife Larkin et al.

Summary: FlyBase is an essential online database for researchers using Drosophila melanogaster, offering a wide range of genetic, molecular, genomic resources. New features include Pathway Reports, paralog information, disease models based on orthology, customizable tables, and expression and disease data overview displays. Recent updates include developmental proteome incorporation, GAL4 search tab upgrades, additional Experimental Tool Reports, migration to JBrowse for genome browsing, and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

NUCLEIC ACIDS RESEARCH (2021)

Article Genetics & Heredity

Association analysis of repetitive elements and R-loop formation across species

Chao Zeng et al.

Summary: Repetitive elements such as satellite DNA, LINEs, and DNA transposons are specifically enriched for R-loop formation in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops tend to arise in regions of low-complexity or simple repeats across species and the repetitive elements associated with R-loop formation differ according to developmental stage. This research advances understanding of the regulatory effects of repetitive elements on R-loop biology, which may vary by species or developmental stage.

MOBILE DNA (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Multidisciplinary Sciences

Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome

Sara Lago et al.

Summary: G-quadruplex structures play complex roles linked to transcription regulation. Here the authors, by comparing G4 location and transcript levels in liposarcoma and keratinocyte cells, reveal that G4s cooperate with transcription factors to determine cell-specific transcriptional programs.

NATURE COMMUNICATIONS (2021)

Review Biochemistry & Molecular Biology

Emerging roles for R-loop structures in the management of topological stress

Frederic Chedin et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

Review Cell Biology

Regulatory R-loops as facilitators of gene expression and genome stability

Christof Niehrs et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2

Celia Alecki et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

The evolution of sex-biased gene expression in the Drosophila brain

Samuel Khodursky et al.

GENOME RESEARCH (2020)

Article Biochemistry & Molecular Biology

CircRNA inhibits DNA damage repair by interacting with host gene

Xiaolong Xu et al.

MOLECULAR CANCER (2020)

Review Biochemistry & Molecular Biology

R-Loops as Cellular Regulators and Genomic Threats

Madzia P. Crossley et al.

MOLECULAR CELL (2019)

Article Biochemistry & Molecular Biology

R-Loops Enhance Polycomb Repression at a Subset of Developmental Regulator Genes

Konstantina Skourti-Stathaki et al.

MOLECULAR CELL (2019)

Article Multidisciplinary Sciences

Interplay between DNA sequence and negative superhelicity drives R-loop structures

Robert Stolz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

FlyBase 2.0: the next generation

Jim Thurmond et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Lin An et al.

GENOME BIOLOGY (2019)

Review Biochemistry & Molecular Biology

Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs

Maria Samata et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 87 (2018)

Article Multidisciplinary Sciences

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramirez et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

Sarah Cohen et al.

NATURE COMMUNICATIONS (2018)

Review Genetics & Heredity

The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats

Nicole C. Riddle et al.

GENETICS (2018)

Article Multidisciplinary Sciences

BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment

Giuseppina D'Alessandro et al.

NATURE COMMUNICATIONS (2018)

Article Immunology

Divergent IncRNA GATA3-AS1 Regulates GATA3 Transcription in T-Helper 2 Cells

Hunter R. Gibbons et al.

FRONTIERS IN IMMUNOLOGY (2018)

Article Biochemistry & Molecular Biology

RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

Laszlo Halasz et al.

GENOME RESEARCH (2017)

Article Biochemistry & Molecular Biology

A sequence-specific core promoter-binding transcription factor recruits TRF2 to coordinately transcribe ribosomal protein genes

Douglas G. Baumann et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids

Shira Sagie et al.

NATURE COMMUNICATIONS (2017)

Article Plant Sciences

The R-loop is a common chromatin feature of the Arabidopsis genome

Wei Xu et al.

NATURE PLANTS (2017)

Review Genetics & Heredity

Sex-Biased Gene Expression

Sonja Grath et al.

ANNUAL REVIEW OF GENETICS, VOL 50 (2016)

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Chemistry, Multidisciplinary

The Reverse Transcriptase Encoded by LINE-1 Retrotransposons in the Genesis, Progression, and Therapy of Cancer

Ilaria Sciamanna et al.

FRONTIERS IN CHEMISTRY (2016)

Article Biochemistry & Molecular Biology

The Release 6 reference sequence of the Drosophila melanogaster genome

Roger A. Hoskins et al.

GENOME RESEARCH (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

Poshen B. Chen et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)

Article Multidisciplinary Sciences

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Raquel Boque-Sastre et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

Francesca Bersani et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Cell Biology

Dosage Compensation in Drosophila

John C. Lucchesi et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Biochemistry & Molecular Biology

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

Poshen B. Chen et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2015)

Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Multidisciplinary Sciences

R-loops induce repressive chromatin marks over mammalian gene terminators

Konstantina Skourti-Stathaki et al.

NATURE (2014)

Article Multidisciplinary Sciences

RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells

Rajika Arora et al.

NATURE COMMUNICATIONS (2014)

Article Genetics & Heredity

Genome-Wide Profiling of Yeast DNA: RNA Hybrid Prone Sites with DRIP-Chip

Yujia A. Chan et al.

PLOS GENETICS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Topoisomerase II plays a role in dosage compensation in Drosophila

Simona Cugusi et al.

TRANSCRIPTION-AUSTIN (2013)

Article Biochemistry & Molecular Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

Paul A. Ginno et al.

MOLECULAR CELL (2012)

Review Biochemistry & Molecular Biology

R Loops: From Transcription Byproducts to Threats to Genome Stability

Andres Aguilera et al.

MOLECULAR CELL (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Genetics & Heredity

The NSL Complex Regulates Housekeeping Genes in Drosophila

Kin Chung Lam et al.

PLOS GENETICS (2012)

Article Biochemical Research Methods

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

Simon J. van Heeringen et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

FIMO: scanning for occurrences of a given motif

Charles E. Grant et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

Konstantina Skourti-Stathaki et al.

MOLECULAR CELL (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Guillaume J. Filion et al.

Article Biochemistry & Molecular Biology

Thermodynamic prediction of RNA-DNA duplex-forming regions in the human genome

Julian L. Huppert

MOLECULAR BIOSYSTEMS (2008)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Biotechnology & Applied Microbiology

Global patterns of sequence evolution in Drosophila

Miguel Gallach et al.

BMC GENOMICS (2007)

Article Genetics & Heredity

Using FlyAtlas to identify better Drosophila melanogaster models of human disease

Venkateswara R. Chintapalli et al.

NATURE GENETICS (2007)