scholarly journals Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Weipeng Mo ◽  
Bo Liu ◽  
Hong Zhang ◽  
Xianhao Jin ◽  
Dongdong Lu ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Transcription Initiation ◽  
Transcription Termination ◽  
Trna Genes ◽  
Genome Wide ◽  
Chimeric Transcripts ◽  
Wide Range ◽  
Wide Scale ◽  
Nascent Rna

Abstract Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5′ Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. Conclusions Our method is applicable to establish a comprehensive termination landscape in a broad range of species.

The Genetics and Genomics of Asthma

2018 ◽  
Vol 19 (1) ◽  
pp. 223-246 ◽  
Author(s):  
Saffron A.G. Willis-Owen ◽  
William O.C. Cookson ◽  
Miriam F. Moffatt
Keyword(s):  
Sequence Variation ◽  
Human Microbiome ◽  
Technological Advances ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Health And Disease ◽  
Wide Scale ◽  
Genetics And Genomics ◽  
The Individual

Asthma is a common, clinically heterogeneous disease with strong evidence of heritability. Progress in defining the genetic underpinnings of asthma, however, has been slow and hampered by issues of inconsistency. Recent advances in the tools available for analysis—assaying transcription, sequence variation, and epigenetic marks on a genome-wide scale—have substantially altered this landscape. Applications of such approaches are consistent with heterogeneity at the level of causation and specify patterns of commonality with a wide range of alternative disease traits. Looking beyond the individual as the unit of study, advances in technology have also fostered comprehensive analysis of the human microbiome and its varied roles in health and disease. In this article, we consider the implications of these technological advances for our current understanding of the genetics and genomics of asthma.

scholarly journals Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Jee Min Kim ◽  
Pat Visanpattanasin ◽  
Vivian Jou ◽  
Sheng Liu ◽  
Xiaona Tang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Dissociation Kinetics ◽  
Additional Function ◽  
Fast Kinetics ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Genome Wide ◽  
Regulatory Dna ◽  
Temporal Interactions

Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending ‘tug-of-war’ that controls a temporally shifting window of accessibility for the transcription initiation machinery.

scholarly journals Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anand Ranjan ◽  
Vu Q Nguyen ◽  
Sheng Liu ◽  
Jan Wisniewski ◽  
Jee Min Kim ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Transcription Initiation ◽  
General Mechanism ◽  
Pol Ii ◽  
Promoter Escape ◽  
Genome Wide ◽  
A Genome ◽  
Particle Imaging

The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit Rpb1. These findings link H2A.Z eviction to transcription initiation, promoter escape and early elongation activities of Pol II. Because passage of Pol II through +1 nucleosomes genome-wide would obligate H2A.Z turnover, we propose that global transcription at yeast promoters is responsible for eviction of H2A.Z. Such usage of yeast Pol II suggests a general mechanism coupling eukaryotic transcription to erasure of the H2A.Z epigenetic signal.

scholarly journals Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Katla Kristjánsdóttir ◽  
Alexis Dziubek ◽  
Hyun Min Kang ◽  
Hojoong Kwak
Keyword(s):  
Rna Sequencing ◽  
Transcription Initiation ◽  
High Sensitivity ◽  
Regulatory Sequences ◽  
Enhancer Activity ◽  
Human Lymphoblastoid Cell ◽  
Regulatory Variants ◽  
Transcription Sites ◽  
Nascent Rna ◽  
Human Lymphoblastoid Cell Lines

AbstractEnhancer RNAs (eRNA) are unstable non-coding RNAs, transcribed bidirectionally from active regulatory sequences, whose expression levels correlate with enhancer activity. We use capped-nascent-RNA sequencing to efficiently capture bidirectional transcription initiation across several human lymphoblastoid cell lines (Yoruba population) and detect ~75,000 eRNA transcription sites with high sensitivity and specificity. The use of nascent-RNA sequencing sidesteps the confounding effect of eRNA instability. We identify quantitative trait loci (QTLs) associated with the level and directionality of eRNA expression. High-resolution analyses of these two types of QTLs reveal distinct positions of enrichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation regions, both of which are associated with mRNA expression QTLs. These two regions—the central TF-binding footprint and the eRNA initiation cores—define a bipartite architecture of enhancers, inform enhancer function, and can be used as an indicator of the significance of non-coding regulatory variants.

scholarly journals Genome-wide transcriptome profiling of the medicinal plant Zanthoxylum planispinum using a single-molecule direct RNA sequencing approach

Genomics ◽  
2019 ◽  
Vol 111 (4) ◽  
pp. 973-979 ◽  
Author(s):  
Jung-A Kim ◽  
Neha Samir Roy ◽  
Inn-hye Lee ◽  
Ah-Young Choi ◽  
Beom-Soon Choi ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Transcriptome Profiling ◽  
Genome Wide

scholarly journals Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin

2021 ◽  
Author(s):  
Jee Min Kim ◽  
Pat Visanpattanasin ◽  
Vivian Jou ◽  
Sheng Liu ◽  
Xiaona Tang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Dissociation Kinetics ◽  
Additional Function ◽  
Fast Kinetics ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Genome Wide ◽  
Regulatory Dna ◽  
Temporal Interactions

ABSTRACTConserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending ‘tug-of-war’ that controls a temporally shifting window of accessibility for the transcription initiation machinery.

scholarly journals Single-cell RNA Sequencing: In-depth Decoding of Heart Biology and Cardiovascular Diseases

2020 ◽  
Vol 21 (8) ◽  
pp. 585-601
Author(s):  
Zhongli Chen ◽  
Liang Wei ◽  
Firat Duru ◽  
Liang Chen
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Complex Structure ◽  
Cell Types ◽  
Genome Wide ◽  
Wide Range ◽  
Single Cell Rna Sequencing ◽  
Profiling Techniques ◽  
Developmental Dynamics ◽  
Phenotype Transition

Background: The cardiac system is a combination of a complex structure, various cells, and versatile specified functions and sophisticated regulatory mechanisms. Moreover, cardiac diseases that encompass a wide range of endogenous conditions, remain a serious health burden worldwide. Recent genome-wide profiling techniques have taken the lead in uncovering a new realm of cell types and molecular programs driving physiological and pathological processes in various organs and diseases. In particular, the emerging technique single-cell RNA sequencing dominates a breakthrough in decoding the cell heterogeneity, phenotype transition, and developmental dynamics in cardiovascular science. Conclusion: Herein, we review recent advances in single cellular studies of cardiovascular system and summarize new insights provided by single-cell RNA sequencing in heart developmental sciences, stem-cell researches as well as normal or disease-related working mechanisms.

scholarly journals ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

2021 ◽  
Author(s):  
Ramzan Umarov ◽  
Yu Li ◽  
Takahiro Arakawa ◽  
Satoshi Takizawa ◽  
Xin Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Accurate Identification ◽  
Regulatory Regions ◽  
Genome Wide ◽  
Wide Scale ◽  
Genome Level ◽  
Level Performance

Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understanding gene expression patterns. While there are many attempts to develop computational promoter and enhancer identification methods, reliable tools to analyze long genomic sequences are still lacking. Prediction methods often perform poorly on the genome-wide scale because the number of negatives is much higher than that in the training sets. To address this issue, we propose a dynamic negative set updating scheme with a two-model approach, using one model for scanning the genome and the other one for testing candidate positions. The developed method achieves good genome-level performance and maintains robust performance when applied to other species, without re-training. Moreover, the unannotated predicted regulatory regions made on the human genome are enriched for disease-associated variants, suggesting them to be potentially true regulatory elements rather than false positives. We validated high scoring "false positive" predictions using reporter assay and all tested candidates were successfully validated, demonstrating the ability of our method to discover novel human regulatory regions.

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