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R Loops: From Transcription Byproducts to Threats to Genome Stability

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DNA sequence required for efficient transcription termination in yeast

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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

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The C-terminal domain of RNA polymerase II couples mRNA processing to transcription

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Insights Into the Role of CircRNAs: Biogenesis, Characterization, Functional, and Clinical Impact in Human Malignancies

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Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration

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Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

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TET‐catalyzed oxidation of intragenic 5‐methylcytosine regulates CTCF‐dependent alternative splicing

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Stochastic Kinetics of Nascent RNA

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Alternative splicing in cancers: From aberrant regulation to new therapeutics

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CDK9 keeps RNA polymerase II on track

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RNA Binding Proteins RZ-1B and RZ-1C Play Critical Roles in Regulating Pre-mRNA Splicing and Gene Expression during Development in Arabidopsis

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Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

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Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIRPreprint

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Sites of Transcription Initiation Drive mRNA Isoform Selection

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Structure-mediated modulation of mRNA abundance by A-to-I editing

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Efficient RNA polymerase II pause release requires U2 snRNP function

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Diversification of the muscle proteome through alternative splicing

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Repair of Rhodopsin mRNA by Spliceosome-Mediated RNA Trans -Splicing: A New Approach for Autosomal Dominant Retinitis Pigmentosa

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Quantitative regulation of FLC via coordinated transcriptional initiation and elongation

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Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

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The RNA exosome promotes transcription termination of backtracked RNA polymerase II

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The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

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Controlling translation via modulation of tRNA levels

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The competitive landscape of the dsRNA world

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Best practices for the visualization, mapping, and manipulation of R‐loops

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R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants

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Transcription and splicing: A two‐way street

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Pre-mRNA splicing and its cotranscriptional connections

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Selective inhibition of CDK7 reveals high-confidence targets and new models for TFIIH function in transcriptionPreprint

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Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies

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From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond

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The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processingPreprint

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Non-Coding RNAs in Response to Drought Stress

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Remodeling oncogenic transcriptomes by small molecules targeting NONO

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Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate

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Cajal body function in genome organization and transcriptome diversity

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Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast

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Constitutive splicing and economies of scale in gene expression

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Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A

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Global donor and acceptor splicing site kinetics in human cells

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Transcription preinitiation complex structure and dynamics provide insight into genetic diseases

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Regulated Intron Retention and Nuclear Pre-mRNA Decay Contribute to PABPN1 Autoregulation

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RNA Targets Ribogenesis Factor WDR43 to Chromatin for Transcription and Pluripotency Control

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Transcription: Insights From the HIV-1 Promoter

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TEFM regulates both transcription elongation and RNA processing in mitochondria

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U1 snRNP Telescripting: Suppression of Premature Transcription Termination in Introns as a New Layer of Gene RegulationPreprint

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A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination

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The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model

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Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation

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Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry

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Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC

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Precision Medicine through Antisense Oligonucleotide-Mediated Exon Skipping

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Multiple Export Mechanisms for mRNAs

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Intron retention and its impact on gene expression and protein diversity: A review and a practical guide

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mRNA – A game changer in regenerative medicine, cell-based therapy and reprogramming strategies

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RBP–RNA interactions in the control of autoimmunity and autoinflammation

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Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs

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ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

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A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

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Nonstructural Protein NP1 of Human Bocavirus 1 Plays a Critical Role in the Expression of Viral Capsid Proteins

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WDR82/PNUTS-PP1 Prevents Transcription-Replication Conflicts by Promoting RNA Polymerase II Degradation on Chromatin

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Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A

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Splicing in immune cells—mechanistic insights and emerging topics

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Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch

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Recent research progress on circular RNAs: Biogenesis, properties, functions, and therapeutic potential

Sharma, A. R., Bhattacharya, M., Bhakta, S., Saha, A., Lee, S., & Chakraborty, C. (2021) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2021.05.022 · Cited by 66

Genetic effects on promoter usage are highly context-specific and contribute to complex traits

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A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

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A generative model for the behavior of RNA polymerase

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The dark side of RNA:DNA hybrids

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Alternative polyadenylation by sequential activation of distal and proximal PolyA sites

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Cyclin-Dependent Kinase 12 Increases 3′ End Processing of Growth Factor-Induced c-FOS Transcripts

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NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia

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How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing?

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Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis

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Circular RNA: New Regulatory Molecules

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Widespread intra-dependencies in the removal of introns from human transcripts

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What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans

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Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

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Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions

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Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm

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The Promise and Current Status of CDK12/13 Inhibition for the Treatment of Cancer

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Calcium-mediated histone modifications regulate alternative splicing in cardiomyocytes

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Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions

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