This study reveals how prime editing guide RNA (pegRNA) secondary structure and reverse transcriptase template length affect prime editing efficiency in correcting the phospholamban R14del cardiomyopathy‐associated mutation. Insights support the design of structurally optimized enhanced pegRNAs for precise gene therapy.
Bing Yao+7 more
wiley +1 more source
The elemental mechanism of transcriptional pausing. [PDF]
Transcriptional pausing underlies regulation of cellular RNA biogenesis. A consensus pause sequence that acts on RNA polymerases (RNAPs) from bacteria to mammals halts RNAP in an elemental paused state from which longer-lived pauses can arise.
Chua, Xien Yu+6 more
core +1 more source
Single‐cell insights into the role of T cells in B‐cell malignancies
Single‐cell technologies have transformed our understanding of T cell–tumor cell interactions in B‐cell malignancies, revealing new T‐cell subsets, functional states, and immune evasion mechanisms. This Review synthesizes these findings, highlighting the roles of T cells in pathogenesis, progression, and therapy response, and underscoring their ...
Laura Llaó‐Cid
wiley +1 more source
Flexible RNA design under structure and sequence constraints using formal languages [PDF]
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure.
Denise, Alain+5 more
core +5 more sources
Use of RNA secondary structure for evolutionary relationships : investigating RNase P and RNase MRP : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand [PDF]
Bioinformatics is applied here to examine whether RNA secondary structure data can reflect distant evolutionary relationships. This is important when there is little confidence in sequence data such as when looking at the evolution of RNase MRP (MRP ...
Collins, Lesley Joan
core
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs [PDF]
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped ...
A Derti+52 more
core +4 more sources
The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1)
The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins ...
E Meng+8 more
doaj +1 more source
RCARE: RNA Sequence Comparison and Annotation for RNA Editing [PDF]
The post-transcriptional sequence modification of transcripts through RNA editing is an important mechanism for regulating protein function and is associated with human disease phenotypes. The identification of RNA editing or RNA-DNA difference (RDD) sites is a fundamental step in the study of RNA editing.
Chan Hee Park+4 more
openaire +3 more sources
In the adult T‐cell leukemia/lymphoma (ATL) cell line ED, the human T‐cell leukemia virus type 1 (HTLV‐1) provirus was integrated into the intron of the ift81 gene in the antisense orientation. Despite this integration, both the intact ift81 and the viral oncogene hbz were simultaneously expressed, likely due to the functional insufficiency of viral ...
Mayuko Yagi+5 more
wiley +1 more source
Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks
RNA inverse design is an essential part of many RNA therapeutic strategies. To date, there have been great advances in computationally driven RNA design.
Amirhossein Manzourolajdad+1 more
doaj +1 more source