The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes DOI Creative Commons
Tetsuya Hisanaga, Facundo Romani, Shuangyang Wu

et al.

Current Biology, Journal Year: 2023, Volume and Issue: 33(20), P. 4367 - 4380.e9

Published: Sept. 21, 2023

The mobility of transposable elements (TEs) contributes to evolution genomes. Their uncontrolled activity causes genomic instability; therefore, expression TEs is silenced by host are marked with DNA and H3K9 methylation, which associated silencing in flowering plants, animals, fungi. However, distantly related groups eukaryotes, H3K27me3 deposited the Polycomb repressive complex 2 (PRC2), an epigenetic mark gene plants animals. direct PRC2 has so far only been shown one species ciliates. To test if silences a broader range we generated mutants reduced analyzed role extant along lineage Archaeplastida diatom P. tricornutum. In this red alga C. merolae, greater proportion than genes were repressed PRC2, whereas bryophytes. contained potential cis-elements recognized transcription factors neighbor as transcriptional units PRC2. Thus, observed not but also diatoms ciliates, suggesting that silence last common ancestor eukaryotes. We hypothesize during Archaeplastida, TE fragments selected shape regulation, controlling networks regulated

Language: Английский

Long non-coding RNAs: definitions, functions, challenges and recommendations DOI Open Access
John S. Mattick, Paulo Amaral, Piero Carninci

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(6), P. 430 - 447

Published: Jan. 3, 2023

Language: Английский

Citations

1235

Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development DOI Creative Commons
Ariane Lismer, Sarah Kimmins

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: April 14, 2023

Abstract Although more studies are demonstrating that a father’s environment can influence child health and disease, the molecular mechanisms underlying non-genetic inheritance remain unclear. It was previously thought sperm exclusively contributed its genome to egg. More recently, association have shown various environmental exposures including poor diet, toxicants, stress, perturbed epigenetic marks in at important reproductive developmental loci were associated with offspring phenotypes. The cellular routes underlie how transmitted fertilization, resist reprogramming embryo, drive phenotypic changes only now beginning be unraveled. Here, we provide an overview of state field intergenerational paternal mammals present new insights into relationship between embryo development three pillars inheritance: chromatin, DNA methylation, non-coding RNAs. We evaluate compelling evidence sperm-mediated transmission retention embryo. Using landmark examples, discuss sperm-inherited regions may escape impact via implicate transcription factors, chromatin organization, transposable elements. Finally, link paternally functional pre- post-implantation Understanding factors will permit greater understanding related origins disease.

Language: Английский

Citations

82

Repetitive DNA sequence detection and its role in the human genome DOI Creative Commons
Xingyu Liao,

Wufei Zhu,

Juexiao Zhou

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Sept. 19, 2023

Abstract Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, structural characteristics of repeats. Besides, introduced diverse biological functions repeats reviewed existing methods for automatic repeat detection, classification, masking. Finally, analyzed type, structure, regulation human genome their role induction complex diseases. We believe that review will facilitate a comprehensive understanding provide guidance annotation in-depth exploration its association with

Language: Английский

Citations

69

Transposable elements as essential elements in the control of gene expression DOI Creative Commons
Alemu Gebrie

Mobile DNA, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 18, 2023

Abstract Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes higher animals. TEs contribute in controlling expression genes locally and even far away at transcriptional post-transcriptional levels, which is one their functional effects on gene function genome evolution. There are different mechanisms through control genes. First, offer cis-regulatory regions with inherent regulatory features for own expression, making them potential factors host Promoter enhancer contain sites generated from TE, binding variety trans-acting factors. Second, miRNAs long non-coding RNAs (lncRNAs) have been shown that encode RNAs, revealing TE origin these RNAs. Furthermore, it was sequences essential RNAs' actions, include target mRNA. By being member RNA sequences, therefore play roles. Additionally, has suggested TE-derived both evolutionary novelty regulation. systems arising frequently tissue-specific functions. The objective this review discuss TE-mediated regulation, particular emphasis processes, contributions various types, differential roles tissue based mostly recent studies humans.

Language: Английский

Citations

64

Transposable elements in mammalian chromatin organization DOI
Heather A. Lawson, Yonghao Liang, Ting Wang

et al.

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(10), P. 712 - 723

Published: June 7, 2023

Language: Английский

Citations

58

Activation of human endogenous retroviruses and its physiological consequences DOI
Nicholas Dopkins, Douglas F. Nixon

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 25(3), P. 212 - 222

Published: Oct. 23, 2023

Language: Английский

Citations

57

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements DOI Creative Commons
Ashlyn G. Anderson, Brianne B. Rogers, Jacob M. Loupe

et al.

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(3), P. 100263 - 100263

Published: Feb. 2, 2023

Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated cortical 7 AD 8 to identify candidate

Language: Английский

Citations

54

Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity DOI Creative Commons
Alice Wenger, Alva Biran, Nicolás Alcaraz

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(9), P. 1567 - 1578

Published: Sept. 1, 2023

Modified parental histones are segregated symmetrically to daughter DNA strands during replication and can be inherited through mitosis. How this may sustain the epigenome cell identity remains unknown. Here we show that transmission of histone-based information maintains fidelity embryonic stem plasticity. Asymmetric segregation H3-H4 in MCM2-2A mutants compromised mitotic inheritance histone modifications globally altered epigenome. This included widespread spurious deposition repressive modifications, suggesting elevated epigenetic noise. Moreover, H3K9me3 loss at repeats caused derepression H3K27me3 redistribution across bivalent promoters correlated with misexpression developmental genes. mutation challenged dynamic transitions cellular states cycle, enhancing naïve pluripotency reducing lineage priming G1. Furthermore, competence was diminished, correlating impaired exit from pluripotency. Collectively, argues a correctly balanced chromatin landscape able support mammalian differentiation.

Language: Английский

Citations

48

Single-cell analysis of chromatin accessibility in the adult mouse brain DOI Creative Commons
Songpeng Zu, Yang Eric Li, Kangli Wang

et al.

Nature, Journal Year: 2023, Volume and Issue: 624(7991), P. 378 - 389

Published: Dec. 13, 2023

Abstract Recent advances in single-cell technologies have led to the discovery of thousands brain cell types; however, our understanding gene regulatory programs these types is far from complete 1–4 . Here we report a comprehensive atlas candidate cis -regulatory DNA elements (cCREs) adult mouse brain, generated by analysing chromatin accessibility 2.3 million individual cells 117 anatomical dissections. The includes approximately 1 cCREs and their across 1,482 distinct populations, adding over 446,000 most recent such annotation genome. are moderately conserved human brain. mouse-specific cCREs—specifically, those identified subset cortical excitatory neurons—are strongly enriched for transposable elements, suggesting potential role emergence new neuronal diversity. Finally, infer networks 260 subclasses develop deep-learning models predict activities different sequence alone. Our results provide resource analysis cell-type-specific regulation both brains.

Language: Английский

Citations

46

Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells DOI

Tongyu Sun,

Yueyuan Xu,

Yu Xiang

et al.

Nature Genetics, Journal Year: 2023, Volume and Issue: 55(8), P. 1324 - 1335

Published: July 20, 2023

Language: Английский

Citations

45