4.8 Article

HIRA-dependent boundaries between H3 variants shape early replication in mammals

Related references

Note: Only part of the references are listed.
Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Biochemistry & Molecular Biology

H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

Bobbie Pelham-Webb et al.

Summary: This study elucidates the principles and mediators of molecular resetting in mouse pluripotent stem cells during self-renewal, including the asynchronous transcriptional and architectural resetting upon mitotic exit, and the potential bookmarking function of H3K27 acetylation.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

Replication timing maintains the global epigenetic state in human cells

Kyle N. Klein et al.

Summary: Loss of RIF1 disrupts the temporal order of DNA replication, leading to changes in chromatin modifications and genome architecture. Depletion of RIF1 causes increased heterogeneity between individual cells, resulting in replication-dependent disruption of histone modifications and alterations in genome architecture. These effects are magnified with successive cycles of altered replication timing.

SCIENCE (2021)

Article Biochemistry & Molecular Biology

Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication

Weitao Wang et al.

Summary: The study successfully mapped early-replication initiation events in human cells using the ORM method, revealing a consistent distribution of replication initiation with accessible chromatin enrichment. The results indicate that stochastic regulation of replication kinetics is a fundamental feature of eukaryotic replication.

MOLECULAR CELL (2021)

Article Multidisciplinary Sciences

H2A.Z facilitates licensing and activation of early replication origins

Haizhen Long et al.

NATURE (2020)

Article Biochemical Research Methods

SciPy 1.0: fundamental algorithms for scientific computing in Python

Pauli Virtanen et al.

NATURE METHODS (2020)

Article Multidisciplinary Sciences

Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway

David Sitbon et al.

NATURE COMMUNICATIONS (2020)

Review Cell Biology

Chromatin replication and epigenetic cell memory

Kathleen R. Stewart-Morgan et al.

NATURE CELL BIOLOGY (2020)

Review Cell Biology

The roles of histone variants in fine-tuning chromatin organization and function

Sara Martire et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2020)

Article Multidisciplinary Sciences

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

Alexy Promonet et al.

NATURE COMMUNICATIONS (2020)

Review Multidisciplinary Sciences

Array programming with NumPy

Charles R. Harris et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Two HIRA-dependent pathways mediate H3.3 de novo deposition and recycling during transcription

Julia Torne et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Developmental differences in genome replication program and origin activation

Cathia Rausch et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans

Maude Strobino et al.

GENOME RESEARCH (2020)

Article Multidisciplinary Sciences

The expanding landscape of 'oncohistone' mutations in human cancers

Benjamin A. Nacev et al.

NATURE (2019)

Article Biotechnology & Applied Microbiology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim et al.

NATURE BIOTECHNOLOGY (2019)

Review Cell Biology

Control of DNA replication timing in the 3D genome

Claire Marchal et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Jiao Sima et al.

Article Biochemistry & Molecular Biology

Transcription shapes DNA replication initiation and termination in human cells

Yu-Hung Chen et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

The Encyclopedia of DNA elements (ENCODE): data portal update

Carrie A. Davis et al.

NUCLEIC ACIDS RESEARCH (2018)

Editorial Material Multidisciplinary Sciences

Chromatin domains rich in inheritance

Danny Reinberg et al.

SCIENCE (2018)

Article Multidisciplinary Sciences

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

Morgane Macheret et al.

NATURE (2018)

Article Multidisciplinary Sciences

High-resolution visualization of H3 variants during replication reveals their controlled recycling

Camille Clement et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit

Dominique Ray-Gallet et al.

NATURE COMMUNICATIONS (2018)

Review Multidisciplinary Sciences

Chromatin plasticity: A versatile landscape that underlies cell fate and identity

Tejas Yadav et al.

SCIENCE (2018)

Article Biochemistry & Molecular Biology

H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication

Rentian Wu et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

Joseph C. Siefert et al.

GENOME RESEARCH (2017)

Review Cell Biology

Variants of core histones and their roles in cell fate decisions, development and cancer

Marcus Buschbeck et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Review Cell Biology

DNA replication origins-where do we begin?

Marie-Noelle Prioleau et al.

GENES & DEVELOPMENT (2016)

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers

Benoit Miotto et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Cell Biology

Maintenance of Epigenetic Information

Genevieve Almouzni et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2016)

Article Multidisciplinary Sciences

Replication landscape of the human genome

Nataliya Petryk et al.

NATURE COMMUNICATIONS (2016)

Article Genetics & Heredity

The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation

Neha P. Paranjape et al.

G3-GENES GENOMES GENETICS (2016)

Article Biochemistry & Molecular Biology

The chromatin environment shapes DNA replication origin organization and defines origin classes

Christelle Cayrou et al.

GENOME RESEARCH (2015)

Article Biochemistry & Molecular Biology

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

Juan Carlos Rivera-Mulia et al.

GENOME RESEARCH (2015)

Editorial Material Multidisciplinary Sciences

Epigenomics Roadmap for regulation

Casey E. Romanoski et al.

NATURE (2015)

Article Multidisciplinary Sciences

The histone chaperone CAF-1 safeguards somatic cell identity

Sihem Cheloufi et al.

NATURE (2015)

Review Cell Biology

DNA replication origin activation in space and time

Michalis Fragkos et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Review Cell Biology

Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control

Dan Filipescu et al.

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30 (2014)

Article Biochemistry & Molecular Biology

Evolution of histone H3: emergence of variants and conservation of post-translational modification sites

Jakob H. Waterborg

BIOCHEMISTRY AND CELL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Interference Between DNA Replication and Transcription as a Cause of Genomic Instability

Yea-Lih Lin et al.

CURRENT GENOMICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

Emilie Besnard et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

Article Biochemical Research Methods

Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing

Julien N. Bianco et al.

METHODS (2012)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Aaron D. Goldberg et al.

Article Biochemistry & Molecular Biology

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

Ichiro Hiratani et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

R. Scott Hansen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Editorial Material Multidisciplinary Sciences

Mixing or Not Mixing

Dominique Ray-Gallet et al.

SCIENCE (2010)

Article Multidisciplinary Sciences

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

Roger B. Deal et al.

SCIENCE (2010)

Review Cell Biology

Epigenetic inheritance during the cell cycle

Aline V. Probst et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

Ichiro Hiratani et al.

PLOS BIOLOGY (2008)