title: X-inactivation: quantitative predictions of protein interactions in the Xist network.
abstract: The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of epigenetic modifications. Little is known about the molecular machinery regulating initiation and maintenance of chromosomal silencing. Here, we introduce a new version of our algorithm catRAPID to investigate Xist associations with a number of proteins involved in epigenetic regulation, nuclear scaffolding, transcription and splicing processes. Our method correctly identifies binding regions and affinities of protein interactions, providing a powerful theoretical framework for the study of X-chromosome inactivation and other events mediated by ribonucleoprotein associations.
authors.affiliation: Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain.
authors.forename: Federico
authors.initials: F
authors.lastname: Agostini
authors.forename: Davide
authors.initials: D
authors.lastname: Cirillo
authors.forename: Benedetta
authors.initials: B
authors.lastname: Bolognesi
authors.forename: Gian Gaetano
authors.initials: GG
authors.lastname: Tartaglia
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D000071221:Enhancer of Zeste Homolog 2 Protein; D005260:Female; D034722:Heterogeneous-Nuclear Ribonucleoprotein U / Q000378:metabolism; D036961:Matrix Attachment Region Binding Proteins / Q000378:metabolism; D051379:Mice; D009687:Nuclear Proteins / Q000378:metabolism; D063151:Polycomb Repressive Complex 2 / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid; D000068103:Serine-Arginine Splicing Factors; D049951:X Chromosome Inactivation; D050986:YY1 Transcription Factor / Q000378:metabolism
chemical_list: D034722:Heterogeneous-Nuclear Ribonucleoprotein U; D036961:Matrix Attachment Region Binding Proteins; D009687:Nuclear Proteins; D062085:RNA, Long Noncoding; D016601:RNA-Binding Proteins; C558468:SAF-A protein, mouse; C469541:Satb1 protein, mouse; C494163:Suz12 protein, mouse; C077885:XIST non-coding RNA; D050986:YY1 Transcription Factor; D000068103:Serine-Arginine Splicing Factors; D000071221:Enhancer of Zeste Homolog 2 Protein; C498410:Ezh2 protein, mouse; D063151:Polycomb Repressive Complex 2