RESEARCH HIGHLIGHTS
Nature Reviews Genetics | AOP, published online 22 November 2012; doi:10.1038/nrg3136

G E N E R E G U L AT I O NRNAi gets stuck into transcription

UP THE RESOLUTION

RNAi is best known for its various
roles in post-transcriptional genesilencing in the cytoplasm. It is also
known to have nuclear functions
associated with repressive chromatin
or gene silencing, such as the formation of heterochromatin in somespecies. Researchers have now uncovered a rather different nuclear role forsome key RNAi proteins: interaction
with the core transcriptional machinery at transcriptionally active loci.
Through a series of cellular andchromatin fractionation experiments
in Drosophila melanogaster cells,
Cernilogar et al. showed that theRNAi components Dicer 2 (DCR2)
and Argonaute 2 (AGO2) are mainly
nuclear and associated with chromatin. In vivo staining with antibodies
against these proteins revealed
that they localize to euchromatic,transcriptionally active regions ofD. melanogaster polytene chromosomes, including loci containing
copies of the heat-shock gene Hsp70.
The authors found that depletionof AGO2 or DCR2 resulted inincreased expression of heat-shock
genes under non-heat-shockconditions. A key mode of transcriptional regulation of the heatshock genes is RNA polymerase II(RNAPII) pausing; prior to heatshock, RNAPII stops a short distancedownstream of the transcriptional
start site and heat shock triggers
transcriptional elongation. Throughfurther experiments, including
chromatin immunoprecipitation tolook at the distribution of RNAPII,
Cernilogar et al. showed that these
RNAi proteins are involved in maintaining RNAPII pausing. This influence on pausing also occurs at lociother than heat-shock genes: in particular, AGO2 and DCR2 seem to be
involved in the global transcriptional
repression of non-heat-shock genesthat occurs after heat shock, andtheir influence on RNAPII dynamics
requires their enzymatic activity.
The authors examined therelationship between these RNAi
proteins and the core transcriptional
machinery in more detail. They
found that DCR2 and AGO2 interact
with RNAPII and negative elongation factor E (NELFE) and that theyalso influence the association ofNATURE REVIEWS | GENETICSRNAPII with NELFE; this might bea mechanism by which the RNAi
proteins influence RNAPII dynamics.
However, small RNAs also seemto be involved in the activity of theRNAi proteins at active loci: highthroughput sequencing of RNAs thatare associated with AGO2 produced
small RNA tags that map across thetranscription unit of active genes.
This distribution suggests a possible
influence of AGO2 on RNAPII
processivity as well as pausing. TheAGO2‑associated RNAs were derived
from the antisense strand, and sothey might target AGO2 to sensetranscripts.
This work reveals a novel sphereof influence of RNAi. It will beinteresting to explore whether thisinvolvement in RNAPII activity
occurs in other species and also tofurther dissect the mechanisms andthe types of genes that it acts on.
Mary Muers
ORIGINAL RESEARCH PAPER
Cernilogar, F. M. et al. Chromatin-associatedRNA interference components contribute totranscriptional regulation in Drosophila. Nature
6 Nov 2011 (doi: 10.1038/nature10492)

VOLUME 13 | JANUARY 2012
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