DNA-directed termination of mammalian RNA polymerase II.

The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage of the nascent RNA. The RNAPII-associated cleavage product is then degraded by XRN2, dislodging RNAPII from the DNA template. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly at T-tracts in the coding DNA strand.

The prevalence of chronic pain in children and adolescents: a systematic review update and meta-analysis.

Chronic pain, defined as persistent or recurring pain or pain lasting longer than 3 months, is a common childhood problem. The objective of this study was to conduct an updated systematic review and meta-analysis on the prevalence of chronic pain (ie, overall, headache, abdominal pain, back pain, musculoskeletal pain, multisite/general pain, and other) in children and adolescents. EMBASE, PubMed, CINAHL, and PsycINFO were searched for publications between January 1, 2009, and June 30, 2023.

Elongation roadblocks mediated by dCas9 across human genes modulate transcription and nascent RNA processing.

Non-cleaving Cas9 (dCas9) is widely employed to manipulate specific gene loci, often with scant regard for unintended transcriptional effects. We demonstrate here that dCas9 mediates precise RNA polymerase II transcriptional pausing followed by transcription termination and potential alternative polyadenylation. By contrast, alternative splicing is unaffected, likely requiring more sustained alteration to elongation speed.

Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages.

Introduction: Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, particularly in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells affect 3'UTR-APA and IPA in primary human macrophages was unclear.

Physical Activity Trajectories in Early Childhood: Investigating Personal, Environmental, and Participation Factors.

Introduction/purpose: To determine personal, environmental, and participation factors that predict children's physical activity (PA) trajectories from preschool through to school years.

Methods: Two hundred seventy-nine children (4.5 ± 0.

Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy.

Spinal muscular atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped, cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide (ASO) that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7.

Preschool to School-Age Physical Activity Trajectories and School-Age Physical Literacy: A Longitudinal Analysis.

Purpose: The associations between longitudinal physical activity (PA) patterns across childhood and physical literacy have not been studied. The purpose of this study was to identify PA trajectories from preschool to school-age, and to determine if trajectory group membership was associated with school-age physical literacy.

Methods: Participants (n = 279, 4.

Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics.

Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some lncRNA synthesis may reflect transcriptional 'noise', recent studies define unique functions for either specific lncRNAs or for the process of lncRNA synthesis.

POINT technology illuminates the processing of polymerase-associated intact nascent transcripts.

Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly because of technical limitations in purifying authentic nascent transcripts. We present a new approach to characterize nascent RNA, called polymerase intact nascent transcript (POINT) technology.

Enhancers predominantly regulate gene expression during differentiation via transcription initiation.

Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide.

Dual RNA 3'-end processing of H2A.X messenger RNA maintains DNA damage repair throughout the cell cycle.

Phosphorylated H2A.X is a critical chromatin marker of DNA damage repair (DDR) in higher eukaryotes. However, H2A.

Motor Competence, Physical Activity, and Fitness across Early Childhood.

Objectives: To examine if the associations between motor competence and physical activity and musculoskeletal fitness change over time, whether motor competence is associated with longitudinal trajectories of physical activity and fitness, and mediating pathways among these constructs across early childhood.

Methods: Four hundred and eighteen children 3 to 5 yr of age (210 boys; age, 4.5 ± 1.

R-Loops Promote Antisense Transcription across the Mammalian Genome.

Widespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II).

Retrograde shift in carotid artery longitudinal wall motion after one-year follow-up in children.

Background And Aims: Cross-sectional studies suggest that arterial stiffness increases during childhood; however, this evidence stems from pressure-dependent arterial distension, while longitudinal movement of the arterial wall has not been explored. Carotid artery longitudinal wall motion (CALM) has been identified as a novel biomarker of vascular health in adults and may provide complementary biaxial wall information to vascular changes during childhood development. Accordingly, the purpose of this study was to assess how CALM changes and tracks over a one-year period in young children.

Associations between carotid artery longitudinal wall motion and arterial stiffness indicators in young children.

Background And Aims: Carotid artery longitudinal wall motion (CALM) is associated with established indicators of arterial stiffness in healthy adults and in adults with cardiovascular disease risk factors. CALM assessment may be more feasible for incorporation into routine clinical examination than traditional assessments of arterial stiffness; however, the relationship between CALM and arterial stiffness in children has not been established.

Methods: Data were collected from a subset of children participating in the Health Outcomes and Physical activity in Preschoolers study.

Transcriptional Control by Premature Termination: A Forgotten Mechanism.

The concept of early termination as an important means of transcriptional control has long been established. Even so, its role in metazoan gene expression is underappreciated. Recent technological advances provide novel insights into premature transcription termination (PTT).

Physical Activity and Trajectories of Cardiovascular Health Indicators During Early Childhood.

Objectives: Cardiovascular disease prevention should begin in childhood. However, the influence of physical activity on cardiovascular health in early childhood is unknown. Our purpose in this study was to determine the effect of physical activity on trajectories of cardiovascular health indicators during early childhood.

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins.

Accurate regulation of mRNA termination is required for correct gene expression. Here, we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation (polyA) sites. The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) phosphorylated on both Ser2 and Ser5 and are detected at early, alternative polyA sites.

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development.

Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease.

Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle.

R-loop formation during S phase is restricted by PrimPol-mediated repriming.

During DNA replication, conflicts with ongoing transcription are frequent and require careful management to avoid genetic instability. R-loops, three-stranded nucleic acid structures comprising a DNA:RNA hybrid and displaced single-stranded DNA, are important drivers of damage arising from such conflicts. How R-loops stall replication and the mechanisms that restrain their formation during S phase are incompletely understood.

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence.

Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNAs are generally short lived, length restricted, and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly, depletion of the ubiquitous Pol-II-associated transcription elongation factor SPT6 promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes, which correlates with increased lncRNA transcription.

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.

The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in footprints of approximately 60 nucleotides.