Dana Wyman's research while affiliated with University of California, Irvine and other places

Publications (7)

Article
Full-text available
RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these stu...
Preprint
Full-text available
The steady state expression of each gene is the result of a dynamic transcription and degradation of that gene. While regular RNA-seq methods only measure steady state expression levels, RNA-seq of metabolically labeled RNA identifies transcripts that were transcribed during the window of metabolic labeling. Whereas short-read RNA sequencing can id...
Preprint
Full-text available
RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these stu...
Article
Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computat...
Preprint
Full-text available
Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computat...
Article
Full-text available
Motivation: Long-read, single-molecule sequencing platforms hold great potential for isoform discovery and characterization of multi-exon transcripts. However, their high error rates are an obstacle to distinguishing novel transcripts isoforms from sequencing artifacts. Therefore, we developed the package TranscriptClean to correct mismatches, mic...
Article
Full-text available
The reconstruction of gene regulatory networks underlying cell differentiation from high-throughput gene expression and chromatin data remains a challenge. Here, we derive dynamic gene regulatory networks for human myeloid differentiation using a 5-day time series of RNA-seq and ATAC-seq data. We profile HL-60 promyelocytes differentiating into mac...

Citations

... The method was further improved by using thermostable group II intron reverse transcriptase during the sequencing library preparation (DMS-MaPseq) [11]. Nicotinoyl-azide (NaZ) is another probe for RNA solvent accessibility introduced by Feng et al. [12] with subsequent development as LASER-Seq, LASER-Map [13], and icLASER [14]. However, commonly used reactivity readouts (reverse transcription (RT) stop or mutational profiling (MaP)) are not enriched based on their abundance during sample preparation. ...
... JEV replicon DNA templates for transcription were generated by XhoI linearization and transcribed in vitro using the mMESSAGE mMACHINE T7 Transcription Kit (Invitrogen). Transcribed RNAs were purified using the Quick-RNA Miniprep Kit (Zymo Research) and biotinylation was confirmed by streptavidin dot blot (Chan et al., 2020). ...
... However as these parameters are dependent on sequencing depth, the same threshold can generate vastly different results across multiple samples [21][22][23] . This can partially be addressed with additional thresholds such as a minimum relative isoform expression or transcripts-per-million. ...
... The ability of long read RNA-Seq to generate reads corresponding to full-length transcripts provides an opportunity to discover novel transcripts and thereby enable the quantification of isoform expression using context-specific annotations 16 . Tools such as FLAIR 17 , TALON 18 , or StringTie2 19 have been developed for transcript discovery from long read RNA-Seq and have been shown to identify novel transcripts even in well annotated genomes. However, RNA degradation, sequencing, and alignment artefacts can introduce false positive transcript candidates and impact quantification 20 . ...
... For the benchmarking of TALON (v5.0), we corrected aligned reads with TranscriptClean (v2.0.3) [68]. Next, we ran the talon_label_reads module to flagging reads for internal priming (params:-ar 20). ...
... However, and by contrast to a focus on changes to the epigenetic landscape guiding decision-making, the promyeloid cell line HL60 is able to differentiate into macrophages, neutrophils, monocytes, and monocyte-derived macrophages, and when HL60 cells differentiated along these pathways there were few differential changes in the chromatin landscape for up to 24 h. Instead, changes occurred during the middle to late stages of differentiation [77]. ...