New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary tertiary structures essential their function. Thus there is a growing need develop technologies that enable rapid characterization structural features within complex RNA populations. We developed high-throughput technique, SHAPE-Seq, can simultaneously measure quantitative, single nucleotide-resolution information hundreds molecules arbitrary sequence. SHAPE-Seq...

Sequence census methods reduce molecular measurements such as transcript abundance and protein-nucleic acid interactions to counting problems via DNA sequencing. We focus on a novel assay utilizing this approach, called s elective 2′- h ydroxyl cylation analyzed by p rimer e xtension sequencing (SHAPE-Seq), that can be used characterize RNA secondary tertiary structure. describe fully automated data analysis pipeline for SHAPE-Seq includes read processing, mapping, structural inference based...

Knowledge of RNA structure is critical to understanding both the important functional roles in biology and engineering control biological systems. This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) that, through combination structure-dependent chemical probing next-generation technologies, achieves structural characterization hundreds RNAs single experiment. applicable variety conditions, represents an tool biology. The...

RNA plays key regulatory roles in diverse cellular processes, where its functionality often derives from folding into and converting between structures. Many RNAs further rely on co-existence of alternative structures, which govern their response to signals. However, characterizing heterogeneous landscapes is difficult, both experimentally computationally. Recently, structure profiling experiments have emerged as powerful affordable characterization methods, improve computational prediction....

Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure at transcriptome scale and living cells, creating unprecedented opportunities for biology. Propelled by these experimental advances, massive data ever-increasing diversity complexity been generated, which give rise to new challenges interpreting analyzing data.

Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations alleviated by integration probing data into prediction algorithms. However, existing algorithms optimized for a specific type data. Recently, new chemistries combined with advances in sequencing have facilitated at unprecedented scale sensitivity. novel technologies anticipated wealth...

Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification strategy", which involves application of chemicals that are sensitive and result modifications can be assayed via sequencing technologies. One approach reveal paired nucleotides chemical followed by SHAPE, has been used conjunction with capillary...

Abstract RNA helicases are a class of enzymes that unwind duplexes in vitro but whose cellular functions largely enigmatic. Here, we provide evidence the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination transcription Saccharomyces cerevisiae via Nrd1-Nab3-Sen1 (NNS) complex. First, find loss DBP2 results polymerase II accumulation at 3′ ends small nucleolar RNAs and subset mRNAs. In addition, associates with sequence motifs regions bound...

RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal tRNAs. Three proteins found both complexes, Pop1, Pop6, Pop7 also telomerase-associated. Here, we determine how temperature sensitive POP1 POP6 alleles affect yeast telomerase. At permissive temperatures, mutant Pop1/6 have little or no effect on cell growth, global protein levels, the abundance of Est1 Est2 (telomerase proteins), TLC1 RNA). However, pop mutants, is more abundant,...

Structure mapping is a classic experimental approach for determining nucleic acid structure that has gained renewed interest in recent years following advances chemistry, genomics, and informatics. The encompasses numerous techniques use different means to introduce nucleotide-level modifications structure-dependent manner. Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). advent of NGS dramatically increased the throughput,...

In single stranded (+)-sense RNA viruses, structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore features of third genome segment cucumber mosaic virus (CMV), RNA3 (2216 nt), both vitro plant cell lysates. Comparing SHAPE-Seq analysis results revealed multiple SEs coat protein open reading frame 3′ untranslated...

Establishing a link between RNA structure and function remains great challenge in biology. The emergence of high-throughput profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines motifs data. demonstrate PATTERNA detects with accuracy comparable commonly used...

RNA biology is revolutionized by recent developments of diverse high-throughput technologies for transcriptome-wide profiling molecular structures. structurome data can be used to identify differentially structured regions between groups samples. Existing methods are limited in scope specific and/or do not account biological variation. Here, we present dStruct which the first broadly applicable method differential analysis accounting variation data. compatible with technologies, validated...

Abstract Summary Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated be functionally significant. High-throughput structure chemical probing methods generate millions sequencing reads provide structural constraints for prediction. At present, processed data from experiments are difficult access without computational expertise. Here we present FoldAtlas, web interface accessing raw and across thousands...

The diverse functionalities of RNA can be attributed to its capacity form complex and varied structures. recent proliferation new structure probing techniques coupled with high-throughput sequencing has helped studies expand in both scope depth. Despite differences techniques, most experiments face similar challenges reproducibility due the stochastic nature chemical sequencing. As these protocols transcriptome-wide studies, quality control becomes a more daunting task. General efficient...

Gene therapy is an emerging alternative to conventional anti-HIV-1 drugs, and can potentially control the virus while alleviating major limitations of current approaches. Yet, HIV-1's ability rapidly acquire mutations escape presents a critical challenge any novel treatment paradigm. Viral thus key consideration in design gene-based technique. We develop computational model HIV's evolutionary dynamics vivo presence genetic explore impact parameters strategies on development resistance. Our...

Motivation: An important property of a valid method for testing differential expression is that the false positive rate should at least roughly correspond to p-value cutoff, so if 10,000 genes are tested cutoff 10−4, and all null hypotheses true, then there be only about 1 gene declared significantly differentially expressed. We this by resampling from existing RNA-Seq data sets also matched negative binomial simulations. Results: Methods we examined, which rely strongly on model, such as...

ABSTRACT The underrepresentation of women in science, technology, engineering, and mathematics (STEM) fields, including biomedical remains a persistent challenge emphasizes the need for initiatives that attract retain more field. Such should address this gender imbalance aim to harness diverse perspectives talents all genders. Women engineering face unique challenges due field’s male-dominated nature. Gender bias, stereotypes, family-unfriendly expectations can significantly affect women’s...

High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest elements whose underlying structures necessary for their biological functions. We previously introduced patteRNA, an algorithm rapidly mining SP data patterns characteristic of such motifs. This work provided a proof-of-concept the detection motifs and capability distinguishing displaying pronounced...

To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent high-throughput sequencing-based structure profiling experiments has provided important insights and widened the scope studies. However, as a broad range approaches continues to emerge, universal framework needed quantitatively ensure consistent high-quality data. We present SEQualyzer, visual interactive application that makes it easy...

The bit stuffing algorithm is a technique for coding constrained sequences by the insertion of bits into an arbitrary data sequence. This approach was previously introduced and applied to (d,k) codes. Results show that maximum average rate code achieves capacity when k=d+1 or k=/spl infin/, while it suboptimal all other pairs. Furthermore, this generalized produce codes with However, extension results in more complicated scheme. correspondence proposes modification maintains its simplicity....

We study coding schemes which encode unconstrained sequences into run-length-limited (d, k)-constrained sequences. present a general framework for the construction of such k)-codes from variable-length source codes. This is an extension previously suggested bit stuffing, flipping, and symbol sliding algorithms. show that it gives rise to new code constructions achieve improved performance over three aforementioned Therefore, we are interested in finding optimal codes under this framework,...