Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functions

Incorporation of CENP-A/CID into centromeres during early Drosophila embryogenesis does not require RNA polymerase II–mediated transcription

(2022) Samadri Ghosh et al.   CHROMOSOMA

Plasticity in centromere organization and kinetochore composition: Lessons from diversity

(2022) Midori Ishii et al.   CURRENT OPINION IN CELL BIOLOGY

DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide

(2022) Nicolas Altemose et al.   NATURE METHODS

A transcriptional roadblock protects yeast centromeres

(2022) Sabrine Hedouin et al.   NUCLEIC ACIDS RESEARCH

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario

(2022) Claire Vourc’h et al.   Genes

Repeat-based holocentromeres influence genome architecture and karyotype evolution

(2022) Paulo G. Hofstatter et al.   CELL

Human centromere repositioning activates transcription and opens chromatin fibre structure

(2022) Catherine Naughton et al.   Nature Communications

m 6 A modification of HSATIII lncRNAs regulates temperature‐dependent splicing

(2021) Kensuke Ninomiya et al.   EMBO JOURNAL

Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA

(2021) Ke Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Genome-wide mapping reveals R-loops associated with centromeric repeats in maize

(2021) Yang Liu et al.   GENOME RESEARCH

Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization

(2021) Zhongyang Lin et al.   NUCLEIC ACIDS RESEARCH

Activation of homologous recombination in G1 preserves centromeric integrity

(2021) Duygu Yilmaz et al.   NATURE

Mutation and selection explain why many eukaryotic centromeric DNA sequences are often A + T rich

(2021) Anne C Barbosa et al.   NUCLEIC ACIDS RESEARCH

BRCA1 prevents R-loop-associated centromeric instability

(2021) Carine Racca et al.   Cell Death & Disease

What makes a centromere?

(2020) Paul B. Talbert et al.   EXPERIMENTAL CELL RESEARCH

Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize

(2020) Yalin Liu et al.   PLOS BIOLOGY

“Lessons from the extremes: Epigenetic and genetic regulation in point monocentromere and holocentromere establishment on artificial chromosomes”

(2020) Charmaine Yan Yu Wong et al.   EXPERIMENTAL CELL RESEARCH

Super-Resolution Microscopy Reveals Diversity of Plant Centromere Architecture

(2020) Veit Schubert et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Centromeric RNA and Its Function at and Beyond Centromeric Chromatin

(2020) Samuel Corless et al.   JOURNAL OF MOLECULAR BIOLOGY

CENP-A nucleosome—a chromatin-embedded pedestal for the centromere: lessons learned from structural biology

(2020) Ahmad Ali-Ahmad et al.   Essays in Biochemistry

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

The centromere comes into focus: from CENP-A nucleosomes to kinetochore connections with the spindle

(2020) Kathryn Kixmoeller et al.   Open Biology

Centromeric Transcription: A Conserved Swiss-Army Knife

(2020) Ganesan Arunkumar et al.   Genes

Formation of the CenH3-Deficient Holocentromere in Lepidoptera Avoids Active Chromatin

(2020) Aruni P. Senaratne et al.   CURRENT BIOLOGY

R-loops at centromeric chromatin contribute to defects in kinetochore integrity and chromosomal instability in budding yeast

(2020) Prashant K. Mishra et al.   MOLECULAR BIOLOGY OF THE CELL

Massively multiplex single-molecule oligonucleosome footprinting

(2020) Nour J Abdulhay et al.   eLife

Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features

(2019) Drisya Vijayakumari et al.   RNA Biology

Interplay between DNA sequence and negative superhelicity drives R-loop structures

(2019) Robert Stolz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Point centromere activity requires an optimal level of centromeric noncoding RNA

(2019) Yick Hin Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2

(2019) Qi Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosomes Stabilize ssRNA-dsDNA Triple Helices in Human Cells

(2019) Rodrigo Maldonado et al.   MOLECULAR CELL

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

Identification of functional long non-coding RNAs in C. elegans

(2019) Alper Akay et al.   BMC BIOLOGY

R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation

(2019) Maiwen Caudron-Herger et al.   MOLECULAR CELL

Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

(2019) Feng Jiang et al.   RNA Biology

Islands of retroelements are major components of Drosophila centromeres

(2019) Ching-Ho Chang et al.   PLOS BIOLOGY

Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice

(2019) Yuan Fang et al.   GENOME RESEARCH

The histone variant H2A.Z in gene regulation

(2019) Benedetto Daniele Giaimo et al.   Epigenetics & Chromatin

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF

(2019) Anders S. Hansen et al.   MOLECULAR CELL

RNA Interactions Are Essential for CTCF-Mediated Genome Organization

(2019) Ricardo Saldaña-Meyer et al.   MOLECULAR CELL

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(2019) Daniel N. Weinberg et al.   NATURE

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

RNA Splicing by the Spliceosome

(2019) Max E. Wilkinson et al.   Annual Review of Biochemistry

Alpha satellite DNA biology: finding function in the recesses of the genome

(2018) Shannon M. McNulty et al.   CHROMOSOME RESEARCH

High‐resolution transcription maps reveal the widespread impact of roadblock termination in yeast

(2018) Tito Candelli et al.   EMBO JOURNAL

Unexpected conformational variations of the human centromeric chromatin complex

(2018) Jitendra Thakur et al.   GENES & DEVELOPMENT

Simple and Complex Centromeric Satellites inDrosophilaSibling Species

(2018) Paul B. Talbert et al.   GENETICS

Centromere transcription allows CENP-A to transit from chromatin association to stable incorporation

(2018) Georg O.M. Bobkov et al.   JOURNAL OF CELL BIOLOGY

Centromere Biology: transcription goes on stage.

(2018) Carlos Perea-Resa et al.   MOLECULAR AND CELLULAR BIOLOGY

Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer

(2018) Quan Zhu et al.   MOLECULAR CELL

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone H3K9 and H4 Acetylations and Transcription Facilitate the Initial CENP-AHCP−3 Deposition and De Novo Centromere Establishment in Caenorhabditis elegans Artificial Chromosomes

(2018) Jing Zhu et al.   Epigenetics & Chromatin

Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair

(2018) Wei-Ting Lu et al.   Nature Communications

Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells

(2018) Alexis Autour et al.   Nature Communications

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

Simple and Complex Centromeric Satellites inDrosophilaSibling Species

(2018) Paul B. Talbert et al.   GENETICS

The Biogenesis, Functions, and Challenges of Circular RNAs

(2018) Xiang Li et al.   MOLECULAR CELL

Centromere and Pericentromere Transcription: Roles and Regulation … in Sickness and in Health

(2018) Ksenia Smurova et al.   Frontiers in Genetics

Determinants of Histone H3K4 Methylation Patterns

(2017) Luis M. Soares et al.   MOLECULAR CELL

Is H3K4me1 at enhancers correlative or causative?

(2017) Alvaro Rada-Iglesias   NATURE GENETICS

Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize

(2017) Lu Chen et al.   NEW PHYTOLOGIST

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

Demethylated HSATII DNA and HSATII RNA Foci Sequester PRC1 and MeCP2 into Cancer-Specific Nuclear Bodies

(2017) Lisa L. Hall et al.   Cell Reports

Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

(2017) Oscar Velazquez Camacho et al.   eLife

RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin

(2017) Whitney L Johnson et al.   eLife

Mitotic noncoding RNA processing promotes kinetochore and spindle assembly inXenopus

(2016) Andrew W. Grenfell et al.   JOURNAL OF CELL BIOLOGY

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

The Phylogenetic Origins and Evolutionary History of Holocentric Chromosomes

(2016) Marcial Escudero et al.   SYSTEMATIC BOTANY

A Centromere-Signaling Network Underlies the Coordination among Mitotic Events

(2016) Prasad Trivedi et al.   TRENDS IN BIOCHEMICAL SCIENCES

Acetylation of histone H4 lysine 5 and 12 is required for CENP-A deposition into centromeres

(2016) Wei-Hao Shang et al.   Nature Communications

Epigenetic engineering reveals a balance between histone modifications and transcription in kinetochore maintenance

(2016) Oscar Molina et al.   Nature Communications

Centromeric Transcription Regulates Aurora-B Localization and Activation

(2016) Michael D. Blower   Cell Reports

The Chromatin of Candida albicans Pericentromeres Bears Features of Both Euchromatin and Heterochromatin

(2016) Verónica Freire-Benéitez et al.   Frontiers in Microbiology

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

(2015) Jakub Kochan et al.   BIOTECHNIQUES

Transcription of tandemly repetitive DNA: functional roles

(2015) Maria Assunta Biscotti et al.   CHROMOSOME RESEARCH

Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription

(2015) Chin-Chi Chen et al.   DEVELOPMENTAL CELL

Mitotic Transcription Installs Sgo1 at Centromeres to Coordinate Chromosome Segregation

(2015) Hong Liu et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Short- and long-term effects of chromosome mis-segregation and aneuploidy

(2015) Stefano Santaguida et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Holocentromeres inRhynchosporaare associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

(2015) André Marques et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

Sequence Features and Transcriptional Stalling within Centromere DNA Promote Establishment of CENP-A Chromatin

(2015) Sandra Catania et al.   PLoS Genetics

Centromeric Heterochromatin: The Primordial Segregation Machine

(2014) Kerry S. Bloom   Annual Review of Genetics

Histone H4 Lys 20 Monomethylation of the CENP-A Nucleosome Is Essential for Kinetochore Assembly

(2014) Tetsuya Hori et al.   DEVELOPMENTAL CELL

The FACT complex interacts with the E3 ubiquitin ligase Psh1 to prevent ectopic localization of CENP-A

(2014) Gary M.R. Deyter et al.   GENES & DEVELOPMENT

Centromeric histone variant CENP-A represses acetylation-dependent chromatin transcription that is relieved by histone chaperone NPM1

(2014) Jayasha Shandilya et al.   JOURNAL OF BIOCHEMISTRY

Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division

(2014) Silvana Rošić et al.   JOURNAL OF CELL BIOLOGY

Identification of novelDrosophilacentromere-associated proteins

(2014) Teresa K. Barth et al.   PROTEOMICS

Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation

(2014) Jakub O. Westholm et al.   Cell Reports

A long non-coding RNA is required for targeting centromeric protein A to the human centromere

(2014) Delphine Quénet et al.   eLife

Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans

(2013) J. Thakur et al.   GENOME RESEARCH

Histone Variant H2A.Z Functions in Sister Chromatid Cohesion in Saccharomyces cerevisiae

(2013) Upasna Sharma et al.   MOLECULAR AND CELLULAR BIOLOGY

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

A two-step mechanism for epigenetic specification of centromere identity and function

(2013) Daniele Fachinetti et al.   NATURE CELL BIOLOGY

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neocentromeres: a place for everything and everything in its place

(2013) Kristin C. Scott et al.   TRENDS IN GENETICS

Structural basis of transcription elongation

(2012) Fuensanta W. Martinez-Rucobo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

(2012) Krishanpal Karmodiya et al.   BMC GENOMICS

High-resolution mapping and transcriptional activity analysis of chicken centromere sequences on giant lampbrush chromosomes

(2012) Alla Krasikova et al.   CHROMOSOME RESEARCH

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis

(2012) Daniël P. Melters et al.   CHROMOSOME RESEARCH

Breaking the HAC Barrier: Histone H3K9 acetyl/methyl balance regulates CENP-A assembly

(2012) Jun-ichirou Ohzeki et al.   EMBO JOURNAL

DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation

(2012) Mina Nakama et al.   GENES TO CELLS

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam et al.   GENOME RESEARCH

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

(2012) J. H. Bergmann et al.   JOURNAL OF CELL SCIENCE

An inverse relationship to germline transcription defines centromeric chromatin in C. elegans

(2012) Reto Gassmann et al.   NATURE

Transcription in the maintenance of centromere chromatin identity

(2012) F. L. Chan et al.   NUCLEIC ACIDS RESEARCH

Repeatless and Repeat-Based Centromeres in Potato: Implications for Centromere Evolution

(2012) Z. Gong et al.   PLANT CELL

Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

(2012) Julia Salzman et al.   PLoS One

Active transcription and essential role of RNA polymerase II at the centromere during mitosis

(2012) F. L. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of FACT in making and breaking nucleosomes

(2011) Tim Formosa   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin

(2011) S. Chantalat et al.   GENOME RESEARCH

Identification of Noncoding Transcripts from within CENP-A Chromatin at Fission Yeast Centromeres

(2011) Eun Shik Choi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BRCA1 tumour suppression occurs via heterochromatin-mediated silencing

(2011) Quan Zhu et al.   NATURE

Assembly of Drosophila Centromeric Chromatin Proteins during Mitosis

(2011) Barbara G. Mellone et al.   PLoS Genetics

Epigenetic engineering shows H3K4me2 is required for HJURP targeting and CENP-A assembly on a synthetic human kinetochore

(2010) Jan H Bergmann et al.   EMBO JOURNAL

TERRA biogenesis, turnover and implications for function

(2010) Sascha Feuerhahn et al.   FEBS LETTERS

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

(2010) W.-H. Shang et al.   GENOME RESEARCH

A super-resolution map of the vertebrate kinetochore

(2010) S. A. Ribeiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA

(2010) Yaqing Du et al.   PLoS Genetics

Histone modification patterns and epigenetic codes

(2009) Andreas Lennartsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Centromeric Nucleosomes Induce Positive DNA Supercoils

(2009) Takehito Furuyama et al.   CELL

The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation

(2009) Julie M. Claycomb et al.   CELL

DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions

(2009) Suhasni Gopalakrishnan et al.   HUMAN MOLECULAR GENETICS

Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription

(2009) Bing Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CENP-H–containing Complex Facilitates Centromere Deposition of CENP-A in Cooperation with FACT and CHD1

(2009) Masahiro Okada et al.   MOLECULAR BIOLOGY OF THE CELL

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase

(2009) Federica Ferri et al.   NUCLEIC ACIDS RESEARCH

Histone Modifications within the Human X Centromere Region

(2009) Brankica Mravinac et al.   PLoS One

Synthetic Heterochromatin Bypasses RNAi and Centromeric Repeats to Establish Functional Centromeres

(2009) A. Kagansky et al.   SCIENCE

Neocentromeres Form Efficiently at Multiple Possible Loci in Candida albicans

(2009) Carrie Ketel et al.   PLoS Genetics

A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

(2008) Dawn M. Carone et al.   CHROMOSOMA

Reversal of RNA Polymerase II Ubiquitylation by the Ubiquitin Protease Ubp3

(2008) Kristian Kvint et al.   MOLECULAR CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Epigenetic regulation of centromeric chromatin: old dogs, new tricks?

(2008) Robin C. Allshire et al.   NATURE REVIEWS GENETICS

Heterochromatin and RNAi Are Required to Establish CENP-A Chromatin at Centromeres

(2008) H. D. Folco et al.   SCIENCE

Heterochromatin Integrity Affects Chromosome Reorganization After Centromere Dysfunction

(2008) K. Ishii et al.   SCIENCE