The function of chromatin in transcriptional control and chromosomal architecture is regulated by a diverse set of RNA components in all eukaryotes. Chief among them is the participation of small RNA (sRNA) generated by the RNA interference machineries (RNAi). The mechanisms that guide sRNA generation are diverse in different organisms, but they can be roughly divided in three steps. First, an initiation step generates an initial pool of primary sRNA, from a double stranded RNA (dsRNA) precursor processed by Dicer enzymes (plants and C elegans); degradation products of primary transcripts synthetized by RNA Pol II (S pombe); or processing of single stranded precursors by unknown nucleases, resulting in PIWI-interacting sRNA (piRNA; insects, mammals and C elegans). The sRNA can also be inherited from a previous generation or received from other cells (Plants). These primary sRNAs bind to Argonaute proteins, which find their cognate targets by sequence complementarity. This recognition can lead to cleavage of the target by the slicer capable Argonautes, and guides the second step that results in an amplification of the signal, with accumulation of secondary sRNA. Amplification can involve the generation of dsRNA by RNA dependent RNA polymerase (RdRP) activities on the Argonaute-targeted RNA, followed by Dicer processing (Plants and S pombe), by direct generation of secondary sRNA by RdRP (22G siRNA in C elegans), or by a series of cleavages in single stranded RNA precursors, carried out in alternating order by PIWI-clade Argonautes and other unknown nucleases (Ping-Pong cycle, insects and mammals). In the final step, Argonaute and PIWI-bound secondary sRNA can relocate to the homologous loci in the DNA, by base-pairing with nascent transcripts as they are synthetized by RNA Pol II (S pombe and C elegans) and specialized RNA polymerases (RNA Pol IV and V in plants), and mediate recruitment of Chromatin remodeling activities that can result in heterochromatin formation (methylation of Histone 3 Lysine 9 and binding of Heterochromatin protein 1 (HP1) homologs), DNA methylation (in Plants and Mammals), and establishment of other types of chromatin domains like centromeric chromatin (in C elegans). The RNAi machinery also directly protects genome integrity, by facilitating DNA replication and re-establishment of heterochromatin in the wake of the replication fork, and by Dicer processing of transcription products that arise in the vicinity of Double Strand Breaks in the DNA, that have a role in repair of the lesion (Plants and mammals). A similar phenomenon has been observed in the fungus Neurospora.
Conventions: RNA strand is represented in two different colours: red for sense and blue for antisense (or forward and reverse respectively in the case of non-coding RNAs). DNA is in light-blue double strand, and cytosine methylations are represented by “Me”. DNA dependent RNA polymerases are green ovals, and are identified where possible. Argonaute-type proteins are in shades of blue, RdRP proteins or complexes are in orange, and Dicer proteins are in magenta. Histone and DNA modification factors are in purple. When a particular residue in the sRNA is typical of a species (as in the 22/26-G RNAs in C elegans, and the 5′U and paired A signature of Ping-Pong amplified piRNA) it is represented as a letter in the sRNA.
Figure 1.
Abbreviations and definitions
S pombe
- Ago1
Argonaute
- Dcr1
Dicer
- RDRC
RNA-dependent RNA polymerase complex
- RITS
RNA-induced initiation of transcriptional silencing complex
- CLRC
Clr4 methyltransferase complex
- Swi6
HP1 homolog
C elegans
- RDE-1
AGO-clade Argonaute
- RdRP
RNA dependent RNA polymerase(s)
- PRG-1 and CSR-1
PIWI-clade Argonautes
- HRDE-1/WAGO9
Heritable RNAi defective/Worm-specific Argonaute
- NRDE
Nuclear RNA defective
- HPL-1
HP! homolog
Insects
- PIWI, Aub/Aubergine, Ago3
PIWI-clade Argonautes
- Rhino
HP1 homolog, needed for dual-strand piRNA cluster expression
Mice
- MILI/MIWI/MIWI2
PIWI-clade Argonautes
- DNMT3
DNA methyl transferase
Plants
- DCL2/3/4
Dicer-like homologs
- AGO2/AGO4
Ago-clade Argonautes
- RDR2/6
RNA dependent RNA polymerases
- DRM2,CMT3
DNA methyltransferases
- DRD1
SNF2 chromatin remodeler
- KYP
Kryptonite H3K9 methyltransferase
Contributor Information
Mikel Zaratiegui, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.
Robert A. Martienssen, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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