Coding RNAs with a non-coding function: Maintenance of open chromatin structure

Caudron-Herger, Maïwen; Müller-Ott, Katharina; Mallm, Jan‐Philipp; Marth, Caroline; Schmidt, Ute; Fejes-Tóth, Katalin; Rippe, Karsten

doi:10.4161/nucl.2.5.17736

Cited by 48 publications

(50 citation statements)

References 58 publications

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“…However, also coding RNAs seem to regulate gene activity as ciRNAs were detected to be part of transcription factories in human and mouse. 18,31 Our recent study amplified the set of RNAs influencing gene activity by the snoRNAs and add an additional mechanism in that RNP-complexes directly alter the compaction state of higher order structures of chromatin. 19…”

Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 98%

“…16,18 In addition, several protein components of C/D snoRNPs were linked with chromatin remodeling and with transcription. The yeast homologs of the human snoRNP proteins p55 and p50, called Rvb1 and Rvb2, have been shown to form a dimer with ATPase activity in vitro and to possess chromatin-remodeling activity in vivo.…”

Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 99%

“…Furthermore, initial functional characterizations indicated roles for caR-NAs in chromatin organization and in the regulation of genomic activity. [16][17][18] We recently addressed the potential function of chromatin-associated RNA in Drosophila SL2 cells. 19 The packaging of chromatin into the different levels of higher order structures can be partially assessed by its sensitivity to endonucleases.…”

Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 99%

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Changes in higher order structures of chromatin by RNP complexes

Schubert

Längst

2013

RNA Biology

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More than four decades ago, it was shown that RNA stably associates with chromatin. These studies indicated that chromatin-associated RNAs (caRNA) might be involved in the organization of chromatin structure. However, it is only recently that pools of chromatin-associated RNAs were characterized and functional studies were initiated. In Drosophila cells, an RNP complex consisting of snoRNAs and Decondensation factor 31 (Df31) is stably tethered to chromatin, mediated by the RNA- and histone-binding activities of Df31. Biochemical and functional characterizations suggest a structural role of this complex in chromatin organization. The binding of the Df31-snoRNA complex to chromatin results in the opening and the maintenance of accessible higher order structures of chromatin. We suggest that different classes of chromatin-associated RNPs are required for the targeted opening of higher order structures of chromatin, enabling the activation of DNA-dependent processes such as transcription.

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Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 98%

Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 99%

Section: Novel Snornp Complexes and Their Chromatin-specific Functionsmentioning

confidence: 99%

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Changes in higher order structures of chromatin by RNP complexes

Schubert

Längst

2013

RNA Biology

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“…1a). Because RNase A treatment destabilizes open chromatin structures that contain RNAPIIdependent RNAs and active transcription factories 22 , the majority of the RNAPIIo elongation complexes, but not the inactive RNAPIIa, were found in the CB:RNA þ fraction (Fig. 1b, centre lane; Fig.…”

Section: Top1 Is Sumoylated At K391 and K436 During Transcriptionmentioning

confidence: 99%

RECQ5-dependent SUMOylation of DNA topoisomerase I prevents transcription-associated genome instability

Pokharel

Wang

et al. 2015

Nat Commun

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DNA topoisomerase I (TOP1) has an important role in maintaining DNA topology by relaxing supercoiled DNA. Here we show that the K391 and K436 residues of TOP1 are SUMOylated by the PIAS1-SRSF1 E3 ligase complex in the chromatin fraction containing active RNA polymerase II (RNAPIIo). This modification is necessary for the binding of TOP1 to RNAPIIo and for the recruitment of RNA splicing factors to the actively transcribed chromatin, thereby reducing the formation of R-loops that lead to genome instability. RECQ5 helicase promotes TOP1 SUMOylation by facilitating the interaction between PIAS1, SRSF1 and TOP1. Unexpectedly, the topoisomerase activity is compromised by K391/K436 SUMOylation, and this provides the first in vivo evidence that TOP1 activity is negatively regulated at transcriptionally active chromatin to prevent TOP1-induced DNA damage. Therefore, our data provide mechanistic insight into how TOP1 SUMOylation contributes to genome maintenance during transcription.

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“…For example, DNA methyltransferases, DNMT3A, DNMT3A, and co-factor DNMT3L, all contain an ADD (ATRX-DNMT3-DNMT3L) domain, which binds to H3K9 methylated and unmodified histones via their PHD domain within ADD. H3K4me3 prevents the binding of the ADD domain and these DNA methyltransferases to the H3 tail(Rose and Klose, 2014).RNA and epigenetic modifiersNuclear RNA, coding or non-coding (ncRNA), regulates the structure and function of chromatin(Gardini and Shiekhattar, 2015, Caudron-Herger et al, 2011, Caudron-Herger and Rippe, 2012, Natoli and Andrau, 2012, Rodriguez-Campos and Azorin, 2007, Orom and Shiekhattar, 2011, Ansari and Morse, 2013, Lai et al, 2013. There is mounting evidence that RNA-bound chromatin modifiers and remodelers play key roles in determining histone PTM positions along chromatin.…”

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confidence: 99%

Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing

Davie

Delcuve

2016

Biochem. Cell Biol.

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Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5' splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.

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Coding RNAs with a non-coding function: Maintenance of open chromatin structure

Cited by 48 publications

References 58 publications

Changes in higher order structures of chromatin by RNP complexes

Changes in higher order structures of chromatin by RNP complexes

RECQ5-dependent SUMOylation of DNA topoisomerase I prevents transcription-associated genome instability

Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing

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