2,623 results match your criteria elongation chromatin


Retinoic acid induces NELFA-mediated 2C-like state of mouse embryonic stem cells associates with epigenetic modifications and metabolic processes in chemically defined media.

Cell Prolif 2021 May 7:e13049. Epub 2021 May 7.

The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.

Objectives: Mouse embryonic stem cells (ESCs) are derived from the inner cell mass of blastocyst-stage embryos and cultured in different culture media with varied pluripotency. Sporadically, a small population of ESCs exhibit 2-cell stage embryonic features in serum containing medium. However, whether ESCs can transit into 2-cell embryo-like (2C-like) cells in the chemically defined media remains largely unknown. Read More

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Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast.

Genetics 2019 Sep;213(1):161-172

Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada.

Histone H2B monoubiquitylation (H2Bub1) is tightly linked to RNA polymerase II transcription elongation, and is also directly implicated in DNA replication and repair. Loss of H2Bub1 is associated with defects in cell cycle progression, but how these are related to its various functions, and the underlying mechanisms involved, is not understood. Here we describe a role for H2Bub1 in the regulation of replication-dependent histone genes in the fission yeast Schizosaccharomyces pombe. Read More

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September 2019

Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast.

Genetics 2019 Sep;213(1):161-172

Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada.

Histone H2B monoubiquitylation (H2Bub1) is tightly linked to RNA polymerase II transcription elongation, and is also directly implicated in DNA replication and repair. Loss of H2Bub1 is associated with defects in cell cycle progression, but how these are related to its various functions, and the underlying mechanisms involved, is not understood. Here we describe a role for H2Bub1 in the regulation of replication-dependent histone genes in the fission yeast Schizosaccharomyces pombe. Read More

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September 2019

Two bHLH transcription factors, bHLH48 and bHLH60, associate with phytochrome interacting factor 7 to regulate hypocotyl elongation in Arabidopsis.

Cell Rep 2021 May;35(5):109054

State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China. Electronic address:

The basic helix-loop-helix (bHLH) transcription factor PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) is a central regulator that promotes stem growth by activating growth-related gene expression during shade-avoidance responses. Studying the co-factors of PIF7 can facilitate understanding of the mechanism of PIFs and light signal transduction. Here, we describe the identification of two bHLH transcription factors, bHLH48 and bHLH60 (bHLH48/bHLH60), as essential partners for PIF7-dependent modulation of hypocotyl elongation and function downstream of phytochrome B. Read More

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NF-YCs modulate histone variant H2A.Z deposition to regulate photomorphogenic growth in Arabidopsis.

J Integr Plant Biol 2021 May 4. Epub 2021 May 4.

Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.

In plants, light signals trigger a photomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2A.Z, which functions in transcriptional regulation, is deposited in chromatin by the SWI2/SNF2-RELATED 1 complex (SWR1c). Read More

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The lncRNA and the transcription factor WRKY42 target common cell wall EXTENSIN encoding genes to trigger root hair cell elongation.

Plant Signal Behav 2021 May 4:1920191. Epub 2021 May 4.

Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, CP, Argentina.

Plant long noncoding RNAs (lncRNAs) are key chromatin dynamics regulators, directing the transcriptional programs driving a wide variety of developmental outputs. Recently, we uncovered how the lncRNA () directly recognizes the locus encoding the root hair (RH) master regulator () modulating its transcriptional activation and leading to low temperature-induced RH elongation. We further demonstrated that interacts with the transcription factor WRKY42 in a novel ribonucleoprotein complex shaping epigenetic environment and integrating signals governing RH growth and development. Read More

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The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination.

Int J Mol Sci 2021 Apr 14;22(8). Epub 2021 Apr 14.

iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.

Histone chaperones regulate the flow and dynamics of histone variants and ensure their assembly into nucleosomal structures, thereby contributing to the repertoire of histone variants in specialized cells or tissues. To date, not much is known on the distribution of histone variants and their modifications in the dry seed embryo. Here, we bring evidence that genes encoding the replacement histone variant H3. Read More

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Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in .

Int J Mol Sci 2021 Apr 8;22(8). Epub 2021 Apr 8.

Department of Plant Physiology, Umeå Plant Science Center, Umeå University, S-901 87 Umeå, Sweden.

Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Read More

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The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis.

J Genet Genomics 2021 Mar 4. Epub 2021 Mar 4.

State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China. Electronic address:

Plant reproduction requires the coordinated development of both male and female reproductive organs. Jasmonic acid (JA) plays an essential role in stamen filament elongation. However, the mechanism by which the JA biosynthesis genes are regulated to promote stamen elongation remains unclear. Read More

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Crystallin gene expression: Insights from studies of transcriptional bursting.

Exp Eye Res 2021 Apr 21;207:108564. Epub 2021 Apr 21.

Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.

Cellular differentiation is marked by temporally and spatially regulated gene expression. The ocular lens is one of the most powerful mammalian model system since it is composed from only two cell subtypes, called lens epithelial and fiber cells. Lens epithelial cells differentiate into fiber cells through a series of spatially and temporally orchestrated processes, including massive production of crystallins, cellular elongation and the coordinated degradation of nuclei and other organelles. Read More

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HsfA1d promotes hypocotyl elongation under chilling via enhancing expression of ribosomal protein genes in Arabidopsis.

New Phytol 2021 Apr 23. Epub 2021 Apr 23.

The State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.

How plants maintain growth under non-freezing low temperatures (chilling) is not well understood. Here we use hypocotyl elongation under dark to investigate molecular mechanisms for chilling growth in Arabidopsis thaliana. The function of HsfA1d (Heat shock transcription factor A1d) in chilling growth is investigated by physiological and molecular characterization of its mutants. Read More

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controls plant architecture by locally restricting environmental responses.

Proc Natl Acad Sci U S A 2021 Apr;118(17)

Cell and Developmental Biology Department, John Innes Centre, NR4 7UH Norwich, United Kingdom

The diversity and environmental plasticity of plant growth results from variations of repetitive modules, such as the basic shoot units made of a leaf, axillary bud, and internode. Internode elongation is regulated both developmentally and in response to environmental conditions, such as light quality, but the integration of internal and environmental signals is poorly understood. Here, we show that the compressed rosette growth habit of is maintained by the convergent activities of the organ boundary gene () and of the gibberellin-signaling genes. Read More

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Histone sumoylation and chromatin dynamics.

Nucleic Acids Res 2021 Apr 22. Epub 2021 Apr 22.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially thought that histone sumoylation exclusively suppressed gene transcription, but recent advances in proteomics and genomics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodeling, transcript elongation, and blocking cryptic initiation. Histone sumoylation is integral to complex signaling codes that prime additional histone PTMs as well as modifications of the RNA polymerase II carboxy-terminal domain (RNAPII-CTD) during transcription. Read More

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COMMD4 functions with the histone H2A-H2B dimer for the timely repair of DNA double-strand breaks.

Commun Biol 2021 Apr 19;4(1):484. Epub 2021 Apr 19.

Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba, QLD, Australia.

Genomic stability is critical for normal cellular function and its deregulation is a universal hallmark of cancer. Here we outline a previously undescribed role of COMMD4 in maintaining genomic stability, by regulation of chromatin remodelling at sites of DNA double-strand breaks. At break-sites, COMMD4 binds to and protects histone H2B from monoubiquitination by RNF20/RNF40. Read More

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The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae.

Genetics 2021 Apr;217(4)

Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA.

RSC (Remodels the Structure of Chromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that RSC contributes in generating accessible nucleosomes in transcribed coding sequences (CDSs). RSC MNase ChIP-seq data revealed that RSC-bound nucleosome fragments were very heterogenous (∼80 bp to 180 bp) compared to a sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC promotes accessibility of nucleosomal DNA. Read More

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Structural basis of nucleosome transcription mediated by Chd1 and FACT.

Nat Struct Mol Biol 2021 Apr 12;28(4):382-387. Epub 2021 Apr 12.

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.

Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. Read More

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FRIZZY PANICLE defines a regulatory hub for simultaneously controlling spikelet formation and awn elongation in bread wheat.

New Phytol 2021 Apr 10. Epub 2021 Apr 10.

State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, PR China.

Grain yield in bread wheat (Triticum aestivum) is largely determined by inflorescence architecture. Zang734 is an endemic Tibetan wheat variety that exhibited rare triple-spikelet (TRS) phenotype with significantly increased spikelet/floret number per spike. However, the molecular basis underlying this specific spike morphology is completely unknown. Read More

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The Paf1 Complex: A Keystone of Nuclear Regulation Operating at the Interface of Transcription and Chromatin.

J Mol Biol 2021 Apr 1:166979. Epub 2021 Apr 1.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States. Electronic address:

The regulation of transcription by RNA polymerase II is closely intertwined with the regulation of chromatin structure. A host of proteins required for the disassembly, reassembly, and modification of nucleosomes interacts with Pol II to aid its movement and counteract its disruptive effects on chromatin. The highly conserved Polymerase Associated Factor 1 Complex, Paf1C, travels with Pol II and exerts control over transcription elongation and chromatin structure, while broadly impacting the transcriptome in both single cell and multicellular eukaryotes. Read More

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The Telomeric Protein TRF2 Regulates Replication Origin Activity within Pericentromeric Heterochromatin.

Life (Basel) 2021 Mar 24;11(4). Epub 2021 Mar 24.

Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d'Azur, 06107 Nice, France.

Heterochromatic regions render the replication process particularly difficult due to the high level of chromatin compaction and the presence of repeated DNA sequences. In humans, replication through pericentromeric heterochromatin requires the binding of a complex formed by the telomeric factor TRF2 and the helicase RTEL1 in order to relieve topological barriers blocking fork progression. Since TRF2 is known to bind the Origin Replication Complex (ORC), we hypothesized that this factor could also play a role at the replication origins (ORI) of these heterochromatin regions. Read More

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Dynamic extrinsic pacing of the HOX clock in human axial progenitors controls motor neuron subtype specification.

Development 2021 Mar 29;148(6). Epub 2021 Mar 29.

Institut du Fer à Moulin, 75005 Paris, France

Rostro-caudal patterning of vertebrates depends on the temporally progressive activation of HOX genes within axial stem cells that fuel axial embryo elongation. Whether the pace of sequential activation of HOX genes, the 'HOX clock', is controlled by intrinsic chromatin-based timing mechanisms or by temporal changes in extrinsic cues remains unclear. Here, we studied HOX clock pacing in human pluripotent stem cell-derived axial progenitors differentiating into diverse spinal cord motor neuron subtypes. Read More

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Is Subdivision of Atypia of Undetermined Significance AUS/Follicular Lesion of Undetermined Significance Cases According to Detailed Nuclear Features Vital for Assessing the Risk of Malignancy?

J Cytol 2020 Oct-Dec;37(4):204-209. Epub 2020 Nov 6.

Department of Medical Statistics, Faculty of Medicine, Zonguldak Bulent Ecevit Universtiy, Kozlu, Zonguldak, Turkey.

Background: It has been known that the "atypia of undetermined significance (AUS)/follicular lesion of undetermined significance (FLUS)" category is the most problematic category in Bethesda system due to its highly heterogeneous morphological features. Recently, it has been reported that aspirates including nuclear atypia in the AUS/FLUS category have a higher risk of malignancy.

Aims: This study aimed to assess each nuclear property in aspirates with cytological atypia and also to determine the relationship with the risk of malignancy. Read More

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November 2020

Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA polymerase II transcription.

Cell Death Differ 2021 Mar 17. Epub 2021 Mar 17.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.

Co-activator complexes dynamically deposit post-translational modifications (PTMs) on histones, or remove them, to regulate chromatin accessibility and/or to create/erase docking surfaces for proteins that recognize histone PTMs. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The deubiquitylation module (DUB) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and three adaptor proteins, ATXN7, ATXN7L3 and ENY2, which are all needed for the full activity of the USP22 enzyme to remove monoubiquitin (ub1) from histone H2B. Read More

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Genome stability is guarded by yeast Rtt105 through multiple mechanisms.

Genetics 2021 Feb;217(2)

CNRS UMR7258, INSERM U1068, Aix-Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France.

Ty1 mobile DNA element is the most abundant and mutagenic retrotransposon present in the genome of the budding yeast Saccharomyces cerevisiae. Protein regulator of Ty1 transposition 105 (Rtt105) associates with large subunit of RPA and facilitates its loading onto a single-stranded DNA at replication forks. Here, we dissect the role of RTT105 in the maintenance of genome stability under normal conditions and upon various replication stresses through multiple genetic analyses. Read More

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February 2021

Promoter-specific changes in initiation, elongation, and homeostasis of histone H3 acetylation during CBP/p300 inhibition.

Elife 2021 Mar 11;10. Epub 2021 Mar 11.

Molecular Biology Institute, UCLA, Los Angeles, United States.

Regulation of RNA polymerase II (Pol2) elongation in the promoter-proximal region is an important and ubiquitous control point for gene expression in metazoans. We report that transcription of the adenovirus 5 E4 region is regulated during the release of paused Pol2 into productive elongation by recruitment of the super-elongation complex, dependent on promoter H3K18/27 acetylation by CBP/p300. We also establish that this is a general transcriptional regulatory mechanism that applies to ~7% of expressed protein-coding genes in primary human airway epithelial cells. Read More

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The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold.

Mol Plant 2021 Mar 6. Epub 2021 Mar 6.

Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB/FHUC, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No 168 km. 0, Paraje El Pozo, Santa Fe 3000, Argentina. Electronic address:

Plant long noncoding RNAs (lncRNAs) have emerged as important regulators of chromatin dynamics, impacting on transcriptional programs leading to different developmental outputs. The lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO) directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation, leading to transcriptional shifts. Here, we show that APOLO recognizes the locus encoding the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and controls RHD6 transcriptional activity, leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4. Read More

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ELOVL6 promoter binding sites directly targeted by sterol regulatory element binding protein 1 in fatty acid synthesis of goat mammary epithelial cells.

J Dairy Sci 2021 May 6;104(5):6253-6266. Epub 2021 Mar 6.

Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.

The elongation of long-chain fatty acid family member 6 (ELOVL6) gene plays an important role in the synthesis of long-chain saturated and monounsaturated fatty acids. Although some studies have revealed that ELOVL6 is the target of sterol regulatory element binding protein 1 (SREBP1; gene name SREBF1) in rodents, the mechanism underlying ELOVL6 regulation during lactation in dairy goats remains unknown. The present study aimed to investigate the transcriptional regulation mechanism of ELOVL6 in goat mammary epithelial cells (GMEC). Read More

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Interaction of replication factor Sld3 and histone acetyl transferase Esa1 alleviates gene silencing and promotes the activation of late and dormant replication origins.

Authors:
Seiji Tanaka

Genetics 2021 Mar;217(1):1-11

School of Environmental Science and Engineering, Kochi University of Technology, 185 Miyanokuchi, Tosayamada, Kami, Kochi 782-8502, Japan.

DNA replication in eukaryotes is a multi-step process that consists of three main reactions: helicase loading (licensing), helicase activation (firing), and nascent DNA synthesis (elongation). Although the contributions of some chromatin regulatory factors in the licensing and elongation reaction have been determined, their functions in the firing reaction remain elusive. In the budding yeast Saccharomyces cerevisiae, Sld3, Sld7, and Cdc45 (3-7-45) are rate-limiting in the firing reaction and simultaneous overexpression of 3-7-45 causes untimely activation of late and dormant replication origins. Read More

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Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development.

Authors:
Matthew E Pipkin

Immunol Rev 2021 Mar 7;300(1):100-124. Epub 2021 Mar 7.

Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA.

Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. Read More

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Simplicity is the Ultimate Sophistication-Crosstalk of Post-translational Modifications on the RNA Polymerase II.

J Mol Biol 2021 Mar 5:166912. Epub 2021 Mar 5.

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States; The Institute for Cellular and Molecular Biology. University of Texas at Austin, Austin, TX 78712, United States. Electronic address:

The highly conserved C-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises a consensus heptad (YSPTSPS) repeated multiple times. Despite the simplicity of its sequence, the essential CTD domain orchestrates eukaryotic transcription and co-transcriptional processes, including transcription initiation, elongation, and termination, and mRNA processing. These distinct facets of the transcription cycle rely on specific post-translational modifications (PTM) of the CTD, in which five out of the seven residues in the heptad repeat are subject to phosphorylation. Read More

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Npac Is a Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells.

Genomics Proteomics Bioinformatics 2021 Mar 3. Epub 2021 Mar 3.

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China. Electronic address:

Chromatin modification contributes to pluripotency maintenance in embryonic stem cells (ESCs). However, the related mechanisms remain obscure. Here, we show that Npac, a "reader" of histone H3 lysine 36 trimethylation (H3K36me3), is required to maintain mouse ESC (mESC) pluripotency since knockdown of Npac causes mESC differentiation. Read More

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