heterochromatin formation

[ DETAILS ]
In the context of the genome, topology is discussed at two interconnected and overlapping levels. The first (DNA topology )focuses the DNA double helix itself, and includes alterations such as those triggered by DNA interacting proteins, processes which require the separation of the two DNA strands and DNA knotting. The second level (chromosome topology) is centered on the higher order organization of DNA into chromosomes, as well as dynamic conformational changes that occur on a chromosomal scale.
Structural maintenance of chromosomes (SMC) protein complexes are central to the interplay between DNA and chromosome topology have accumulated. The SMC complexes regulate replication, segregation, repair and transcription, all processes which influence, and are influenced by, DNA and chromosome topology.

Heterochromatin plays an important role in the regulation of transcriptional repression, recombination and chromosome segregation. Heterochromatin formation at these loci involves conserved pathways of histone modifications, including deacetylation and methylation on key histone residues. For example, S. pombe Clr4, a mammalian Suv39 homolog, specifically methylates histone H3 on lysine 9 (H3-K9) at loci targeted for heterochromatin formation. H3-K9 methyl marks have been shown to act as binding sites for chromodomain proteins such as Swi6 (an HP1 homolog). 

RNA interference (RNAi) is a gene silencing mechanism that utilizes siRNAs generated from the cleavage of dsRNAs to target the destruction or translational inhibition of mRNAs. Genetic and biochemical studies from diverse species have revealed that an RNase III-type endonuclease, Dicer, processes dsRNAs into siRNAs, which in turn associate with RNA-induced silencing complex (RISC) to direct degradation of cognate mRNAs. RNAi factors have also been implicated in transposon suppression, programmed genome rearrangements, virus resistance, germ line development, and stem cell maintenance.
The RNAi pathway also plays an important and conserved role in heterochromatin assembly and proper segregation of chromosomes. Deletions of RNAi components including Argonaute (Ago1), Dicer (Dcr1), or RNA-dependent RNA polymerase (Rdp1) in S. pombe impair epigenetic silencing at centromeres and the initiation of heterochromatin assembly at the mat locus, resulting in a loss of H3-K9 methylation and Swi6 localization from these loci. An RNAi effector complex (RITS) consisted of a chromodomain protein Chp1, Tas3, Ago1, and small interfering RNAs (siRNAs) was recently shown to be necessary for heterochromatin assembly. RITS localizes to all known heterochromatic loci and acts primarily in cis to promote transcriptional and posttranscriptional silencing. Importantly, a mutation in the Chp1 chromodomain that has been shown to bind methylated H3-K9, or deletion of H3-K9 methyltransferase clr4, not only prevents RITS from binding to chromatin but also leads to the loss of siRNAs copurifying with RITS. These analyses imply a self-enforcing loop mechanism in which siRNAs generated by the RNAi pathway help target heterochromatin proteins such as Clr4 to homologous sequences. Clr4-mediated H3-K9 methylation anchors RITS to chromatin, allowing the RNAi machinery to act in cis to process nascent transcripts and efficiently generate siRNAs for the targeting of heterochromatin complexes. As per this model, RITS may be a component of a larger RNAi complex assembled on chromatin, along with Rdp1 and Dcr1, which directly couples siRNA generation with heterochromatin assembly.
RNA-dependent RNA polymerases (RdRPs), which are believed to play an important role in the RNAi process, have been identified in several species including plants, fungi, and Caenorhabditis elegans, and are required for a variety of different cellular functions. For example, in Arabidopsis SDE1/SGS2/RDR6 is necessary for posttranscriptional gene silencing (PTGS) and virus resistance, and RDR2 is required for the production of siRNAs from endogenous transcripts. In C. elegans, RRF-1 and EGO-1 are essential for secondary siRNA production from RNAi-targeted transcripts in somatic cells and germ-line development, respectively, and Sad1 in Neurospora crassa is required for silencing unpaired DNA during meiosis. It is believed that RdRPs generate dsRNAs from single-stranded transcripts either by de novo second-strand synthesis or by relying on siRNAs to prime transcription. Thus, RdRP activity may initiate RNAi/PTGS and/or dramatically enhance RNAi response. However, no RdRP homologs have been identified in Drosophila and mammals, leading to the suggestion that RNAi can occur in the absence of RdRP activity.

In S. pombe, rdp1 deletion results in loss of pericentric heterochromatin. However, it is not known whether the RdRP activity of Rdp1 is essential for heterochromatin formation. In this study, we demonstrated that Rdp1 possesses RdRP activity that is indispensable for centromeric silencing, heterochromatin assembly, chromosome segregation, and telomere clustering during mitosis. In addition, we found that components of RITS and heterochromatin machinery cooperate to recruit Rdp1 to centromeres. Our analyses suggest that Rdp1 is an essential component of a self-enforcing RNAi loop that couples the generation of siRNAs with heterochromatin assembly.

nucleosome assembly factors - histones
The nascent transcript model for small interfering RNA-mediated heterochromatin formation in fission yeast. The RITS complex mediates heterochromatin formation by associating with nascent transcripts, through its interaction with an siRNA and its association with methylated nucleosomes. These interactions result in the recruitment of the RDRC and Dicer, which produce more siRNAs, thereby enforcing a feedback loop. Chromatin silencing requires HP1 proteins (Swi6 and Chp2), which promote the RITS/nascent transcript interaction and recruit deacetylase complexes. Modified from Moazed (2009) with permission from the author and publisher. Ago1, argonaute 1; ARC, argonaute siRNA chaperone; cenRNA, centromeric RNA; CLRC, Clr4 methyltransferase complex; dsRNA, double-stranded RNA; H3K9, lysine 9 of histone 3; Pol II, polymerase II; RDRC, RNA-dependent RNA polymerase complex; RITS, RNA-induced transcriptional silencing; SHREC, a histone deacetylase complex; siRNA, small-interfering RNA; Tas3, adapter protein that links Ago1 and Chp1; TRAMP, a polyadenylation complex that stimulates exosome activity.
Filter

Click on a column header name to sort

ORTHOLOGY CLASS Homo sapiens L. (human) [HSA] Mus musculus L. (mouse) [MMU] Caenorhabditis elegans Maupas (nematode) [CEL] Drosophila melanogaster Meigen (fruit fly) [DME] Saccharomyces cerevisiae Meyen ex E.C. Hansen (budding yeast) [SCE] Schizo-saccharomyces pombe Lindner (fission yeast) [SPO] Escherichia coli Migula (bacterium) K-12 MG1655 [ECO] Arabidopsis thaliana (L.) Heynh. (mouse-ear cress) [ATH]
ko:K11419 (histone-lysine N-methyltransferase SUV39H [EC:2.1.1.43]) SUV39H1
SUV39H2
Suv39h1
Suv39h2
Su(var)3-9 clr4
ko:K11644 (paired amphipathic helix protein Sin3a) SIN3A Sin3a sin-3 Sin3A SIN3 pst1 SNL4
SNL3
ko:K11421 (histone-lysine N-methyltransferase SETDB [EC:2.1.1.43]) SETDB1
SETDB2
Setdb2
Setdb1
met-2 egg
ko:K10752 (histone-binding protein RBBP4) RBBP4 Rbbp4 rba-1
lin-53
Caf1 HAT2 pcf3
prw1
mis16
MSI2
FVE
NFC5
MSI3
MSI1
ko:K11643 (chromodomain-helicase-DNA-binding protein 4 [EC:3.6.4.12]) CHD4 Chd4 let-418 Mi-2 PKL
ko:K11642 (chromodomain-helicase-DNA-binding protein 3 [EC:3.6.4.12]) CHD3 Chd3
ko:K06067 (histone deacetylase 1/2 [EC:3.5.1.98]) HDAC1
HDAC2
Hdac1
Hdac2
hda-2
hda-1
hda-3
Rpd3 RPD3 clr6 hda17
HDA9
HD1
HDA7
HDA6
ko:K00558 (DNA (cytosine-5-)-methyltransferase [EC:2.1.1.37]) DNMT3L
DNMT3B
DNMT1
DNMT3A
Dnmt1
Dnmt3b
Dnmt3l
Dnmt3a
Dcm CMT3
CMT1
AT4G08990
MEE57
DMT2
CMT2
MET1
ko:K11701 (helicase required for RNAi-mediated heterochromatin assembly 1 [EC:3.6.4.13]) hrr1
ko:K11700 (poly(A) RNA polymerase Cid12 [EC:2.7.7.19]) cid12
ko:K11699 (RNA-dependent RNA polymerase 1 [EC:2.7.7.48]) rdp1
ko:K11597 (RNA-induced transcriptional silencing complex protein Tas3) tas3
ko:K11596 (argonaute) ago1 ZLL
AGO5
AGO1
ko:K11595 (chromo domain-containing protein 1) chp1
ko:K11594 (ATP-dependent RNA helicase [EC:3.6.4.13]) DDX3Y
DDX3X
D1Pas1
Ddx3x
Ddx3y
vbh-1
gi:71995718
bel DED1
DBP1
sum3 gi:15227951
gi:79315530
gi:15231074
ko:K02156 (aubergine) gi:310132318
PIWIL3
PIWIL1
PIWIL4
PIWIL2
Piwil2
Piwil1
Piwil4
prg-2
prg-1
AGO3
piwi
aub
ko:K11593 (eukaryotic translation initiation factor 2C) EIF2C3
EIF2C4
EIF2C1
EIF2C2
Eif2c3
Eif2c1
Eif2c2
Eif2c4
alg-2
alg-1
AGO1
ko:K11592 (endoribonuclease Dicer [EC:3.1.26.-]) DICER1 Dicer1 dcr-1 Dcr-1 dcr1 DCL1
DCL4
ko:K10507 (zinc finger and BTB domain-containing protein 33) ZBTB33 Zbtb33
ko:K10801 (methyl-CpG-binding domain protein 4 [EC:3.2.2.-]) MBD4 (MED1) Mbd4 ATMBD4
ko:K11591 (methyl-CpG-binding domain protein 3) MBD3 Mbd3
ko:K11590 (methyl-CpG-binding domain protein 2) MBD2 Mbd2 MBD-like
ko:K11589 (methyl-CpG-binding domain protein 1) MBD1 Mbd1
ko:K11588 (methyl CpG binding protein 2) MECP2 Mecp2
ko:K11587 (chromobox protein 5) CBX5 Cbx5 Su(var)205
ko:K11586 (chromobox protein 3) CBX3 Cbx3
gi:309267436
Gm6901
HP1c
ko:K11585 (chromobox protein 1) CBX1 Cbx1 hpl-2 HP1b
HP1e

Last modification date: Oct. 4, 2011