A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix DOI Open Access
Charlotte N. Kunkler, Grace E. Schiefelbein, Nathan J. O'Leary

et al.

RNA, Journal Year: 2022, Volume and Issue: 28(9), P. 1172 - 1184

Published: July 12, 2022

Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could the formation of these helices is through RNA modifications. With over 140 naturally occurring modifications, we hypothesize that some modifications stabilize while others destabilize them. Here, focus on pyrimidine-motif helix composed canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays microscale thermophoresis examine how 11 different at single position in an affect stability: 5-methylcytidine (m 5 C), 5-methyluridine U or rT), 3-methyluridine 3 U), pseudouridine (Ψ), 4-thiouridine (s 4 N 6 -methyladenosine A), inosine (I), each nucleobase 2′- O -methylation (Nm). Compared unmodified triple, have no significant change stability (Um•A-T), ∼2.5-fold decreases U•A-T, Ψ•A-T, s U•A-T), completely disrupt U•A-T). To identify potential biological examples controlled by modification, searched RMVar, database for mapped single-nucleotide resolution, lncRNAs containing modification within pyrimidine-rich sequence. Using assays, binding DNA-DNA 22-mer segment human lncRNA Al157886.1 was destabilized ∼1.7-fold substitution m C known sites. Therefore, cellular be influenced

Language: Английский

Long-read RNA sequencing can probe organelle genome pervasive transcription DOI
Matheus Sanitá Lima, Douglas Silva Domingues, Alexandre Rossi Paschoal

et al.

Briefings in Functional Genomics, Journal Year: 2024, Volume and Issue: 23(6), P. 695 - 701

Published: June 17, 2024

Abstract 40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field genomics has exposed an unparallel diversity in genome architecture (i.e. size, structure, and content). The transcription these eccentric can just as elaborate – are pervasively transcribed into a plethora RNA types. while protein-coding genes known produce polycistronic transcripts that undergo heavy posttranscriptional processing, nature noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments second-generation sequencing data short reads) have been useful determine certain types RNAs, particularly RNAs. We then explain third-generation (long-read) RNA-Seq represent new frontier transcriptomics. show public repositories (e.g. NCBI SRA) already contain enough for inter-phyla comparative studies argue biologists benefit from such data. discuss prospects using publicly available organelle-focused examine challenges approach. highlight lack comprehensive database dedicated genomics/transcriptomics major impediment development with implications basic applied science.

Language: Английский

Citations

2
Out of the dark: the emerging roles of lncRNAs in pain DOI Creative Commons
Abdella M. Habib, James J. Cox, Andrei L. Okorokov

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(8), P. 694 - 705

Published: June 25, 2024

Language: Английский

Citations

2
N6-Methyladenosine-Modified LEAWBIH Drives Hepatocellular Carcinoma Progression through Epigenetically Activating Wnt/β-Catenin Signaling DOI Creative Commons
Huamei Wei,

Lizheng Huang,

Qi Lu

et al.

Journal of Hepatocellular Carcinoma, Journal Year: 2023, Volume and Issue: Volume 10, P. 1991 - 2007

Published: Nov. 1, 2023

N6-methyladenosine (m6A) modification plays an important role in regulating RNA maturation, stability, and translation. Thus, m6A is involved various pathophysiological processes including hepatocellular carcinoma (HCC). However, the direct contribution of modifications to function HCC remains unclear. Here, we identified LEAWBIH (long non-coding epigenetically activating Wnt/β-catenin signalling HCC) as m6A-modified long (lncRNA) investigated effects on HCC.Quantitative polymerase chain reaction was performed measure gene expression tissues cells. The level detected using a methylated immunoprecipitation assay single-base elongation- ligation-based qPCR amplification method. Cell proliferation evaluated Glo cell viability CCK-8 assays. migration invasion were Transwell mechanisms modified chromatin isolation by purification, immunoprecipitation, dual-luciferase reporter assays.LEAWBIH highly expressed correlated with poor survival patients. transcript. increased transcript stability. HCC, high predicted survival. promotes proliferation, migration, modification-dependent manner. Mechanistic investigations revealed that activated signaling. binds reader YTHDC1, which further interacts recruits H3K9me2 demethylase KDM3B CTNNB1 promoter, leading demethylation transcription activation. Functional rescue assays showed blocking signaling abolished HCC.m6A-modified exerts oncogenic signaling, highlighting promising therapeutic target for HCC.

Language: Английский

Citations

6
Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes DOI Creative Commons

Steven Ingersoll,

Abby Trouth,

Xinlong Luo

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 5, 2024

SUMMARY Facultative heterochromatinization of genomic regulators by Polycomb repressive complex (PRC) 1 and 2 is essential in development differentiation; however, the underlying molecular mechanisms remain obscure. Using genetic engineering, approaches, live-cell single-molecule imaging, we quantify number proteins within condensates formed through liquid-liquid phase separation (LLPS) find that mouse embryonic stem cells (mESCs), approximately 3 CBX2 nucleate many PRC1 PRC2 subunits to form one non-stoichiometric condensate. We demonstrate sparse prevents from migrating constitutive heterochromatin, demarcates spatial boundaries facultative controls deposition H3K27me3, regulates transcription, impacts cellular differentiation. Furthermore, show LLPS required for demarcation H3K27me3 Our findings uncover new functional roles formation heterochromatin unravel a mechanism which low-abundant other compartments enable them execute their functions.

Language: Английский

Citations

2
A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix DOI Open Access
Charlotte N. Kunkler, Grace E. Schiefelbein, Nathan J. O'Leary

et al.

RNA, Journal Year: 2022, Volume and Issue: 28(9), P. 1172 - 1184

Published: July 12, 2022

Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could the formation of these helices is through RNA modifications. With over 140 naturally occurring modifications, we hypothesize that some modifications stabilize while others destabilize them. Here, focus on pyrimidine-motif helix composed canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays microscale thermophoresis examine how 11 different at single position in an affect stability: 5-methylcytidine (m 5 C), 5-methyluridine U or rT), 3-methyluridine 3 U), pseudouridine (Ψ), 4-thiouridine (s 4 N 6 -methyladenosine A), inosine (I), each nucleobase 2′- O -methylation (Nm). Compared unmodified triple, have no significant change stability (Um•A-T), ∼2.5-fold decreases U•A-T, Ψ•A-T, s U•A-T), completely disrupt U•A-T). To identify potential biological examples controlled by modification, searched RMVar, database for mapped single-nucleotide resolution, lncRNAs containing modification within pyrimidine-rich sequence. Using assays, binding DNA-DNA 22-mer segment human lncRNA Al157886.1 was destabilized ∼1.7-fold substitution m C known sites. Therefore, cellular be influenced

Language: Английский

Citations

8