A major role of the RNAi pathway in S. pombe is to nucleate heterochromatin, but it remains unclear whether this mechanism is conserved. To address this question in Drosophila, we performed genome-wide localization of Argonaute2 (AGO2) by ChIP-seq in two different embryonic cell lines and found that AGO2 localizes to euchromatin but not heterochromatin. This localization pattern is further supported by immunofluorescence staining of polytene chromosomes and cell lines, and these studies also indicate that a substantial fraction of AGO2 resides in the nucleus. Intriguingly, AGO2 colocalizes extensively with CTCF/CP190 chromatin insulators but not with genomic regions corresponding to endogenous siRNA production. Moreover, AGO2, but not its catalytic activity or Dicer-2, is required for CTCF/CP190-dependent Fab-8 insulator function. Fab-8 insulator activity is critical for proper spatial homeotic gene expression and abdominal development. AGO2 interacts physically with CTCF and CP190, and depletion of either CTCF or CP190 results in genome-wide loss of AGO2 chromatin association. Finally, mutation of CTCF, CP190, or AGO2 leads to reduction of chromosomal looping interactions, thereby altering gene expression. We propose that RNAi-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome.

Project Start
Project End
Budget Start
Budget End
Support Year
5
Fiscal Year
2011
Total Cost
$1,310,934
Indirect Cost
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State
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Chen, Dahong; Dale, Ryan K; Lei, Elissa P (2018) Shep regulates Drosophila neuronal remodeling by controlling transcription of its chromatin targets. Development 145:
Nazer, Ezequiel; Dale, Ryan K; Chinen, Madoka et al. (2018) Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PLoS Genet 14:e1007276
Chinen, Madoka; Lei, Elissa P (2017) Drosophila Argonaute2 turnover is regulated by the ubiquitin proteasome pathway. Biochem Biophys Res Commun 483:951-957
Cubeñas-Potts, Caelin; Rowley, M Jordan; Lyu, Xiaowen et al. (2017) Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res 45:1714-1730
Caravaca, Juan Manuel; Lei, Elissa P (2016) Maintenance of a Drosophila melanogaster Population Cage. J Vis Exp :
Li, Li; Lyu, Xiaowen; Hou, Chunhui et al. (2015) Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell 58:216-31
Názer, Ezequiel; Lei, Elissa P (2014) Modulation of chromatin modifying complexes by noncoding RNAs in trans. Curr Opin Genet Dev 25:68-73
Dale, Ryan K; Matzat, Leah H; Lei, Elissa P (2014) metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res 42:9158-70
Lei, Elissa P (2014) The regulation of gene expression is fundamental to development and disease. Introduction. Biochim Biophys Acta 1839:117
King, Matthew R; Matzat, Leah H; Dale, Ryan K et al. (2014) The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. J Cell Sci 127:2956-66

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