RESUMEN
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
Asunto(s)
Drosophila melanogaster/genética , Complejo Represivo Polycomb 1/genética , Complejo Represivo Polycomb 2/genética , Proteínas del Grupo Polycomb/genética , Elementos de Respuesta/genética , Animales , Proteínas Cromosómicas no Histona/genética , Islas de CpG/genética , Proteínas de Unión al ADN/genética , Proteínas de Drosophila/genética , Genes Homeobox/genética , Histonas/metabolismo , Humanos , Ratones , Procesamiento Proteico-Postraduccional , Factores de Transcripción/metabolismoRESUMEN
Polycomb/Trithorax response elements (PRE/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE/TREs that switch function by switching the direction of noncoding RNA transcription.
Asunto(s)
Proteínas Cromosómicas no Histona/genética , Proteínas de Drosophila/genética , Genes de Cambio , Proteínas del Grupo Polycomb/genética , ARN no Traducido , Elementos de Respuesta , Transcripción Genética , Animales , Secuencia de Bases , Sitios de Unión , Cromatina/genética , Proteínas de Unión al ADN/genética , Drosophila melanogaster , Genoma de los Insectos , N-Metiltransferasa de Histona-Lisina/genética , Datos de Secuencia Molecular , Factores de Transcripción/genéticaRESUMEN
Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cis-regulatory elements defined by mapping DNase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B-cell identity and function by regulating distinct target genes in early and late B lymphopoiesis.
