Abstract
On the basis of available data of ChIP-seq and ChIPchip experiments performed using antibodies against GAGA and CNC transcription factors, genome-wide binding mapping of these factors at hours 0–12 and 16–24 of Drosophila embryogenesis, as well as on white pre-pupae stage, was conducted. It was shown that the bulk of GAGA and CNC binding falls into promoter regions and introns, with the maximal density of peaks in the vicinity of the transcription start site. Moreover, in both 0–12 and 16–24 hour old embryos GAGA and CNC are frequently co-localized, while on white pre-pupae stage there is no co-localization of these factors on a genome–wide scale. In order to select a set of genes potentially co-regulated by GAGA and CNC, the study of their co-binding in annotated regulatory regions (promoter areas and segments corresponding to the 5’-UTR and 3’-UTR of mRNA) was performed. The results obtained clearly demonstrated that the sets of genes characterized by co-binding of both factors vary greatly at different stages. Thus from 353 genes with overlapped GAGA and CNC binding loci on the 0–12 hour old embryos and 611 genes on the 0–12 hour old embryos only 61 genes “belong” to both stages. For an explanation it is proposed that different sets of target genes are regulated by combinations of various GAGA and CNC isoforms, which are characterized by distinct expression patterns during drosophila embryogenesis. Functional annotation analysis of genes, in whose regulatory regions both GAGA and CNC were found at all investigated stages, demonstrates enrichment by genes controlling embryogenesis, neurogenesis and wing development. The data obtained suggest the interaction of GAGA and CNC during D. melanogaster embryogenesis.
Highlights
На основании доступных данных ChIP-seq и ChIP-chip эксперимен тов, выполненных с использованием антител к транскрипционным факторам GAGA и CNC, проведен анализ распределения по геному участков связывания этих факторов в эмбриогенезе, а также на стадии белой предкуколки дрозофилы
It was shown that the bulk of GAGA and CNC binding falls into promoter regions and introns, with the maximal density of peaks in the vicinity of the transcription start site
In order to select a set of genes potentially co-regulated by GAGA and CNC, the study of their co-binding in annotated regulatory regions was performed
Summary
На основании доступных данных ChIP-seq и ChIP-chip эксперимен тов, выполненных с использованием антител к транскрипционным факторам GAGA и CNC, проведен анализ распределения по геному участков связывания этих факторов в эмбриогенезе (возраст эмбрионов 0–12 и 16–24 ч), а также на стадии белой предкуколки дрозофилы. Предполагается, что различные подгруппы генов-мишеней этих факторов регулируются разными сочетаниями изоформ GAGA и CNC, паттерны экспрессии которых изменяются в ходе эмбриоге неза дрозофилы. Org; Roy et al, 2010) были получены профили связывания для более чем 80 ТФ на разных стадиях развития дрозофилы. Однако в настоящее время только для очень небольшого количества этих факторов получены профили связывания для нескольких следующих друг за другом стадий развития, что дает возможность проследить динамику колокализации районов связывания разных ТФ и сделать предположения об их возможном взаимодействии в течение развития. Поскольку ChIP-chip для 0–12-часовых эмбрионов проводили в рамках одного эксперимента, данные о про-
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