eLife · 2019 · 29 citations · 97 references
Life SciencesDevelopmental BiologyGeneticsEpigeneticsGene ExpressionTranscriptional RegulationCell Lineage SpecificationChromatinEpigenetic Control Of DifferentiationEpigenetic Regulation In DevelopmentLineage CommitmentPolycomb RegulationDifferentiationDifferentiation PotentialPolycomb Group ProteinsPolycomb Group RepressionPolycomb RepressionPolycomb-mediated Gene RepressionPolycomb-mediated RepressionRepressive Chromatin Marks
During development cells become restricted in their differentiation potential by repressing alternative cell fates, and the Polycomb complex plays a crucial role in this process. However, how alternative fate genes are lineage-specifically silenced is unclear. We studied Ultrabithorax (Ubx), a multi-lineage transcription factor of the Hox class, in two tissue lineages using sorted nuclei and interfered with Ubx in mesodermal cells. We find that depletion of Ubx leads to the de-repression of genes normally expressed in other lineages. Ubx silences expression of alternative fate genes by retaining the Polycomb Group protein Pleiohomeotic at Ubx targeted genomic regions, thereby stabilizing repressive chromatin marks in a lineage-dependent manner. Our study demonstrates that Ubx stabilizes lineage choice by suppressing the multipotency encoded in the genome via its interaction with Pho. This mechanism may explain why the Hox code is maintained throughout the lifecycle, since it could set a block to transdifferentiation in adult cells.
97
Fast gapped-read alignment with Bowtie 2
Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text
HTSeq—a Python framework to work with high-throughput sequencing data
Simon Anders, Paul Theodor Pyl, Wolfgang Huber · Bioinformatics · 2014 · 22.7K citations · Full text
Daehwan Kim, Geo Pertea, Cole Trapnell et al. · Genome biology · 2013 · 13.7K citations · Full text