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Constrained Transcriptional Polarity in the Organization of Mammalian Hox Gene Clusters

https://doi.org/10.1101/572875
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/j.1460-2075.1989.tb03534.xopenalex-snapshot
The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes.
inferredcites →https://doi.org/10.1002/j.1460-2075.1991.tb07764.xopenalex-snapshot
Murine genes related to the Drosophila AbdB homeotic genes are sequentially expressed during development of the posterior part of the body.
inferredcites →https://doi.org/10.1007/978-3-642-86659-3openalex-snapshot
Evolution by Gene Duplication
inferredcites →https://doi.org/10.1016/0092-8674(89)90909-4openalex-snapshot
Hox and HOM: Homologous gene clusters in insects and vertebrates
inferredcites →https://doi.org/10.1016/0092-8674(89)90912-4openalex-snapshot
The murine and Drosophila homeobox gene complexes have common features of organization and expression
inferredcites →https://doi.org/10.1016/0168-9525(94)90132-5openalex-snapshot
Colinearity and functional hierarchy among genes of the homeotic complexes
inferredcites →https://doi.org/10.1016/bs.ctdb.2015.11.022openalex-snapshot
Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci
inferredcites →https://doi.org/10.1016/j.cell.2005.04.010openalex-snapshot
Multiple Mechanisms Confining RNA Polymerase II Ubiquitylation to Polymerases Undergoing Transcriptional Arrest
inferredcites →https://doi.org/10.1016/j.celrep.2013.09.002openalex-snapshot
Multiple Enhancers Regulate Hoxd Genes and the Hotdog LncRNA during Cecum Budding
inferredcites →https://doi.org/10.1016/j.devcel.2009.08.010openalex-snapshot
Cdx and Hox Genes Differentially Regulate Posterior Axial Growth in Mammalian Embryos
inferredcites →https://doi.org/10.1016/j.devcel.2010.11.009openalex-snapshot
Functional Analysis of CTCF During Mammalian Limb Development
inferredcites →https://doi.org/10.1016/j.devcel.2018.12.004openalex-snapshot
Tail Bud Progenitor Activity Relies on a Network Comprising Gdf11, Lin28, and Hox13 Genes
inferredcites →https://doi.org/10.1016/j.molcel.2012.08.027openalex-snapshot
RNA Polymerase II Collision Interrupts Convergent Transcription
inferredcites →https://doi.org/10.1016/j.molcel.2013.11.012openalex-snapshot
Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin
inferredcites →https://doi.org/10.1016/j.molcel.2014.05.009openalex-snapshot
Regulatory Interactions between RNA and Polycomb Repressive Complex 2
inferredcites →https://doi.org/10.1016/j.molcel.2016.03.034openalex-snapshot
RNA Polymerase Collision versus DNA Structural Distortion: Twists and Turns Can Cause Break Failure
inferredcites →https://doi.org/10.1016/j.tig.2006.12.001openalex-snapshot
HOM-C evolution in Drosophila: is there a need for Hox gene clustering?
inferredcites →https://doi.org/10.1016/j.ydbio.2009.04.031openalex-snapshot
Axial patterning in snakes and caecilians: Evidence for an alternative interpretation of the Hox code
inferredcites →https://doi.org/10.1016/j.ydbio.2010.12.034openalex-snapshot
A regulatory ‘landscape effect’ over the HoxD cluster
inferredcites →https://doi.org/10.1016/s0012-1606(02)00137-9openalex-snapshot
Hoxb13 mutations cause overgrowth of caudal spinal cordand tail vertebrae
inferredcites →https://doi.org/10.1016/s0092-8674(00)81303-3openalex-snapshot
Gene Transpositions in the HoxD Complex Reveal a Hierarchy of Regulatory Controls
inferredcites →https://doi.org/10.1016/s0092-8674(01)00436-6openalex-snapshot
Localized and Transient Transcription of Hox Genes Suggests a Link between Patterning and the Segmentation Clock
inferredcites →https://doi.org/10.1038/276565a0openalex-snapshot
A gene complex controlling segmentation in Drosophila
inferredcites →https://doi.org/10.1038/82593openalex-snapshot
Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing
inferredcites →https://doi.org/10.1038/nature06967openalex-snapshot
The amphioxus genome and the evolution of the chordate karyotype
inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
inferredcites →https://doi.org/10.1038/ng.3058openalex-snapshot
A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3542openalex-snapshot
ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
inferredcites →https://doi.org/10.1038/nrg3663openalex-snapshot
CTCF: an architectural protein bridging genome topology and function
inferredcites →https://doi.org/10.1038/nsmb.2679openalex-snapshot
Promiscuous RNA binding by Polycomb repressive complex 2
inferredcites →https://doi.org/10.1038/srep03355openalex-snapshot
Generation of mutant mice by pronuclear injection of circular plasmid expressing Cas9 and single guided RNA
inferredcites →https://doi.org/10.1038/srep11315openalex-snapshot
Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing
inferredcites →https://doi.org/10.1038/srep12658openalex-snapshot
Erratum: Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing
inferredcites →https://doi.org/10.1073/pnas.0401389101openalex-snapshot
Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development
inferredcites →https://doi.org/10.1073/pnas.132270899openalex-snapshot
Transcriptional collision between convergent genes in budding yeast
inferredcites →https://doi.org/10.1080/21541264.2017.1285851openalex-snapshot
Directing traffic on DNA—How transcription factors relieve or induce transcriptional interference
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/genetics/94.1.115openalex-snapshot
CYTOGENETIC ANALYSIS OF CHROMOSOME 3 IN DROSOPHILA MELANOGASTER: THE HOMOEOTIC GENE COMPLEX IN POLYTENE CHROMOSOME INTERVAL 84A-B
inferredcites →https://doi.org/10.1093/nar/gku410openalex-snapshot
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
inferredcites →https://doi.org/10.1093/nar/gkw343openalex-snapshot
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
inferredcites →https://doi.org/10.1101/gad.10.18.2326openalex-snapshot
In vivo targeted mutagenesis of a regulatory element required for positioning the Hoxd-11 and Hoxd-10 expression boundaries.
inferredcites →https://doi.org/10.1101/gad.288324.116openalex-snapshot
CTCF-mediated topological boundaries during development foster appropriate gene regulation
inferredcites →https://doi.org/10.1101/gad.307769.117openalex-snapshot
The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes
inferredcites →https://doi.org/10.1101/gad.5.10.1767openalex-snapshot
HOX-4 genes and the morphogenesis of mammalian genitalia.
inferredcites →https://doi.org/10.1101/gad.993302openalex-snapshot
Hox11 paralogous genes are essential for metanephric kidney induction
inferredcites →https://doi.org/10.1126/science.1207194openalex-snapshot
The Dynamic Architecture of Hox Gene Clusters
inferredcites →https://doi.org/10.1126/science.1231143openalex-snapshot
Multiplex Genome Engineering Using CRISPR/Cas Systems
inferredcites →https://doi.org/10.1126/science.1234167openalex-snapshot
A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs
inferredcites →https://doi.org/10.1146/annurev-genom-083115-022339openalex-snapshot
CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1242/dev.001065openalex-snapshot
The rise and fall of Hox gene clusters
inferredcites →https://doi.org/10.1242/dev.104.supplement.169openalex-snapshot
Spatially restricted domains of homeo-gene transcripts in mouse embryos: relation to a segmented body plan
inferredcites →https://doi.org/10.1242/dev.122.4.1175openalex-snapshot
A mutational analysis of the 5′ HoxD genes: dissection of genetic interactions during limb development in the mouse
inferredcites →https://doi.org/10.1242/dev.122.9.2651openalex-snapshot
Function of posterior HoxD genes in the morphogenesis of the anal sphincter
inferredcites →https://doi.org/10.1242/dev.124.18.3493openalex-snapshot
Ulnaless (Ul), a regulatory mutation inducing both loss-of-function and gain- of-function of posterior Hoxd genes
inferredcites →https://doi.org/10.1242/dev.1994.supplement.125openalex-snapshot
Gene duplications and the origins of vertebrate development
inferredcites →https://doi.org/10.1371/journal.pgen.0030232openalex-snapshot
Distinct Roles and Regulations for Hoxd Genes in Metanephric Kidney Development
inferredcites →https://doi.org/10.1371/journal.pgen.1006232openalex-snapshot
Hotair Is Dispensible for Mouse Development
inferredcites →https://doi.org/10.1371/journal.pone.0085879openalex-snapshot
HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis
inferredcites →https://doi.org/10.1371/journal.pone.0124633openalex-snapshot
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1534/genetics.106.069484openalex-snapshot
Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice
inferredcites →https://doi.org/10.3389/fgene.2012.00122openalex-snapshot
Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci
inferredcites →https://doi.org/10.4161/trns.2.1.13511openalex-snapshot
Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors
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