Non-coding RNAs in Polycomb/Trithorax regulation

Hekimoglu, Betül; Ringrose, Leonie

doi:10.4161/rna.6.2.8178

Cited by 63 publications

(56 citation statements)

References 69 publications

(171 reference statements)

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“…Moreover, ;20% of the 3300 lincRNAs in human cells are associated with polycomb repressor complex 2 (Hekimoglu and Ringrose, 2009). Emerging evidence supports the view that lincRNAs play important roles in many fundamental biological processes (Hekimoglu and Ringrose, 2009;Chen and Carmichael, 2010;Tsai et al, 2010; K.C. Cabianca et al, 2012).…”

Section: Introductionmentioning

confidence: 68%

“…lincRNAs are expressed in a tissue-specific manner, and many lincRNA genes are regulated by stress (Dinger et al, 2008;Cabili et al, 2011). Moreover, ;20% of the 3300 lincRNAs in human cells are associated with polycomb repressor complex 2 (Hekimoglu and Ringrose, 2009). Emerging evidence supports the view that lincRNAs play important roles in many fundamental biological processes (Hekimoglu and Ringrose, 2009;Chen and Carmichael, 2010;Tsai et al, 2010; K.C.…”

Section: Introductionmentioning

confidence: 69%

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of introncontaining lincRNAs.

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Section: Introductionmentioning

confidence: 68%

Section: Introductionmentioning

confidence: 69%

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

et al. 2012

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“…As in flies, the role of ncRNAs in PcG protein recruitment is not yet fully established, but it is possible that RNA species contribute to PcG protein recruitment at least for a subset of their targets (Rinn et al, 2007;Zhao et al, 2008) (reviewed by Hekimoglu and Ringrose, 2009). …”

Section: The Quest For Mammalian Presmentioning

confidence: 99%

“…2C). Small interfering RNAs and the RNAi machinery might also contribute to PcG protein complex recruitment (for a review, see Hekimoglu and Ringrose, 2009). Finally, PcG protein complex binding might be actively blocked by the presence of transcription factors or co-activators at K4-recruiter sites that are not bound at PREs (Fig.…”

Section: Reviewmentioning

confidence: 99%

Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice

2009

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Polycomb group (PcG) protein complexes dynamically define cellular identity through the regulation of key developmental genes. Important advances in the PcG field have come from genome-wide mapping studies in a variety of tissues and cell types that have analyzed PcG protein complexes, their associated histone marks and putative mechanisms of PcG protein recruitment. We review how these analyses have contributed to our understanding of PcG protein complex targeting to chromatin and consider the importance of diverse PcG protein complex composition for gene regulation. Finally, we focus on the dynamics of PcG protein complex action during cell fate transitions and on the implications of histone modifications for cell lineage commitment.

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“…Recently mlncRNAs have been identified as crucial components in the polycomb/trithorax regulation system. The interaction of PcG and TrxG proteins with their target 10 m a n u s c r i p t sites, the PRE/TREs (polycomb/trithorax responsive elements) can be achieved by several distinct mechanisms [71] that are also employed by other modification enzymes. The modifier complex may bind directly to a nascent complex, also proposed e.g.…”

Section: Guiding Chromatin-modification To Dna Locimentioning

confidence: 99%

Innovation in gene regulation: The case of chromatin computation

Prohaska

Stadler

Krakauer

2010

Journal of Theoretical Biology

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Chromatin regulation is understood to be one of the fundamental modes of gene regulation in eukaryotic cells. We argue that the basic proteins that determine the chromatin architecture constitute an evolutionary ancient layer of transcriptional regulation common to all three domains of life. We explore phylogenetically, sources of innovation in chromatin regulation, focusing on protein domains related to chromatin structure and function, demonstrating a step-wise increase of complexity in chromatin regulation. Building upon the highly conserved use of variants of chromosomal architectural proteins to distinguish chromosomal states, Eukarya secondarily acquired mechanisms for "writing" chemical modifications onto chromatin that constitute persistent signals. The acquisition of reader domains enabled decoding of these complex, signal combinations and a decoupling of the signal from immediate biochemical effects. We show how the coupling of reading and writing, which is most prevalent in crown-group Eukarya, could have converted chromatin into a powerful computational device capable of storing and processing more information than pure cis-regulatory networks.Key words: Chromatin, gene regulation, evolution Summary of Findings and Evolutionary HypothesisGene regulation in extant organisms is a complex adaptive system making use of a diversity of mechanisms to ensure that proteins and complementary macromolecular components are produced and maintained at functional levels in variable environments.In this contribution we focus on one key regulatory subsystem of the cell: chromatin regulation. We argue that chromatin functioned as general regulator of transcription in the primordial nucleus, and that a series of key molecular innovations has significantly expanded the regulatory scope of the cell. In this section we summarize the key empirical results of the paper. Sections 2 through 6 provide the empirical support for these claims. In section 7, we formulate an evolutionary Email addresses: sonja@bioinf.uni-leipzig.de (Sonja J. Prohaska), studla@bioinf.uni-leipzig.de (Peter F. Stadler), krakauer@santafe.edu (David C. Krakauer) hypothesis that seeks to explain our findings in terms of the evolution of proto-genetic regulation. We then interpret this evolutionary sequence in terms of increasing computational power by locating key stages of the evolutionary sequence within a formal model of computation. Since sections 2-6 are primarily concerned with presenting evidence, those interested in the conceptual development of the argument can focus on sections 7 and 8.Two variants of Chromosomal Architectural Proteins (ChAPs) are sufficient to define binary genomic, and potentially phenotypic, states. We show how extensions to this binary system lead to potential distinctions among an increasing number of genomic states, culminating in forms of control localized to specific sites in the genome, as illustrated for example by extant mammalian histone variants capable of differential expression and/or localization to r...

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Non-coding RNAs in Polycomb/Trithorax regulation

Cited by 63 publications

References 69 publications

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice

Innovation in gene regulation: The case of chromatin computation

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