44 research outputs found
The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model
RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small \modifier RNAs' to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements [Meisner et al. (2004), Chem. Biochem. in press]. We discuss our model and recent experimental findings demonstrating the ffectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences
Intergenic Polycomb target sites are dynamically marked by non-coding transcription during lineage commitment
Non-coding (nc) RNAs are involved both in recruitment of vertebrate Polycomb (PcG) proteins to chromatin, and in activation of PcG target genes. Here we investigate dynamic changes in the relationship between ncRNA transcription and recruitment of PcG proteins to chromatin during differentiation. Profiling of purified cell populations from different stages of a defined murine in vitro neural differentiation system shows that over 50% of regulated intergenic non-coding transcripts precisely correspond to PcG target sites. We designate these PcG recruiting elements as Transcribed Intergenic Polycomb (TIP) sites. The relationship between TIP transcription and PcG recruitment switches dynamically during differentiation between different states, in which transcription and PcG recruitment exclude each other, or in which both are present. Reporter assays show that transcribed TIP sites can repress a flanking gene. Knockdown experiments demonstrate that TIP ncRNAs are themselves required for repression of target genes both in cis and in trans. We propose that TIP transcription may ensure coordinated regulation of gene networks via dynamic switching and recruitment of PcG proteins both in cis and in trans during lineage commitment
Activation-Induced Cytidine Deaminase (AID)-Associated Multigene Signature to Assess Impact of AID in Etiology of Diseases with Inflammatory Component
Activation-induced cytidine deaminase (AID) is expressed in B cells within germinal centers and is critically involved in class switch recombination and somatic hypermutation of immunoglobulin loci. Functionally active AID can additionally be detected within ectopic follicular structures developed at sites of chronic inflammation. Furthermore, AID may target non-Ig genes in B- and non-B-cell background. Therefore, AID-associated effects are of increasing interest in disease areas such as allergy, inflammation, autoimmunity, and cancer
An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs
Imprinted macro non-protein-coding (nc) RNAs are cis-repressor transcripts that silence multiple genes in at least three imprinted gene clusters in the mouse genome. Similar macro or long ncRNAs are abundant in the mammalian genome. Here we present the full coding and non-coding transcriptome of two mouse tissues: differentiated ES cells and fetal head using an optimized RNA-Seq strategy. The data produced is highly reproducible in different sequencing locations and is able to detect the full length of imprinted macro ncRNAs such as Airn and Kcnq1ot1, whose length ranges between 80–118 kb. Transcripts show a more uniform read coverage when RNA is fragmented with RNA hydrolysis compared with cDNA fragmentation by shearing. Irrespective of the fragmentation method, all coding and non-coding transcripts longer than 8 kb show a gradual loss of sequencing tags towards the 3′ end. Comparisons to published RNA-Seq datasets show that the strategy presented here is more efficient in detecting known functional imprinted macro ncRNAs and also indicate that standardization of RNA preparation protocols would increase the comparability of the transcriptome between different RNA-Seq datasets
AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer
Background Building up of pathway-/disease-relevant signatures provides a
persuasive tool for understanding the functional relevance of gene alterations
and gene network associations in multifactorial human diseases. Ovarian cancer
is a highly complex heterogeneous malignancy in respect of tumor anatomy,
tumor microenvironment including pro-/antitumor immunity and inflammation;
still, it is generally treated as single disease. Thus, further approaches to
investigate novel aspects of ovarian cancer pathogenesis aiming to provide a
personalized strategy to clinical decision making are of high priority. Herein
we assessed the contribution of the AID/APOBEC family and their associated
genes given the remarkable ability of AID and APOBECs to edit DNA/RNA, and as
such, providing tools for genetic and epigenetic alterations potentially
leading to reprogramming of tumor cells, stroma and immune cells. Results We
structured the study by three consecutive analytical modules, which include
the multigene-based expression profiling in a cohort of patients with primary
serous ovarian cancer using a self-created AID/APOBEC-associated gene
signature, building up of multivariable survival models with high predictive
accuracy and nomination of top-ranked candidate/target genes according to
their prognostic impact, and systems biology-based reconstruction of the AID
/APOBEC-driven disease-relevant mechanisms using transcriptomics data from
ovarian cancer samples. We demonstrated that inclusion of the AID/APOBEC
signature-based variables significantly improves the clinicopathological
variables-based survival prognostication allowing significant patient
stratification. Furthermore, several of the profiling-derived variables such
as ID3, PTPRC/CD45, AID, APOBEC3G, and ID2 exceed the prognostic impact of
some clinicopathological variables. We next extended the signature-/modeling-
based knowledge by extracting top genes co-regulated with target molecules in
ovarian cancer tissues and dissected potential networks/pathways/regulators
contributing to pathomechanisms. We thereby revealed that the AID/APOBEC-
related network in ovarian cancer is particularly associated with
remodeling/fibrotic pathways, altered immune response, and autoimmune
disorders with inflammatory background. Conclusions The herein study is, to
our knowledge, the first one linking expression of entire AID/APOBECs and
interacting genes with clinical outcome with respect to survival of cancer
patients. Overall, data propose a novel AID/APOBEC-derived survival model for
patient risk assessment and reconstitute mapping to molecular pathways. The
established study algorithm can be applied further for any biologically
relevant signature and any type of diseased tissue
Polycomb complexes act redundantly to repress genomic repeats and genes
Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb-repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. On the molecular level, the differentiation defect is caused by the derepression of a set of genes that is redundantly repressed by PRC1 and PRC2 in ES cells. Furthermore, we find that genomic repeats are Polycomb targets and show that, in the absence of Polycomb complexes, endogenous murine leukemia virus elements can mobilize. This indicates a contribution of the Polycomb group system to the defense against parasitic DNA, and a potential role of genomic repeats in Polycomb-mediated gene regulation
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.
RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small "modifier RNAs" to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements. We discuss our model and recent experimental findings demonstrating the effectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences
The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model
RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small \modifier RNAs' to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements [Meisner et al. (2004), Chem. Biochem. in press]. We discuss our model and recent experimental findings demonstrating the ffectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences