U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

PubAg

Main content area

You searched for: Subject "chromatin" Remove constraint Subject: "chromatin"
Start Over

Search

10,100  Search Results

« Previous | 1 - 20 of 10,100 |
Number of results to display per page

Search Results

1. Improved sperm DNA integrity and altered fat metabolism and intestinal morphology in Nile tilapia (Oreochromis niloticus) males fed rations with purified nucleotide

Author:
Robie Allan Bombardelli; Juliano Kelvin dos Santos Henriques; Marta Margarete Cestari; Antônio Ernesto Meister Luz Marques; Taís Voelkl Chagas; Fabio Meurer
Source:
Aquaculture 2023 v.562 pp. 738682
ISSN:
0044-8486
Subject:
chromatin,   etc   ; DNA; Oreochromis niloticus; aquaculture; blood glucose; diet; digestible energy; digestible protein; enterocytes; fish; gonadosomatic index; hepatosomatic index; high density lipoprotein; lipid content; lipid metabolism; liver; morphometry; muscles; nucleotides; testes; triacylglycerols; visceral fat; viscosity;     Show all 23 Subjects
Abstract:
... In this study, we assessed the health, growth, sperm characteristics, and intestinal, liver, and testicular morphology of Nile tilapia (Oreochromis niloticus) males fed rations containing purified nucleotides (NT). A total of 420 females (286 ± 7.15 g) and 140 males (536 ± 13.4 g) were used. Fish were fed on extruded ration (280 g digestible protein kg⁻¹; 11.72 M joule (MJ) of digestible energy kg ...
DOI:
10.1016/j.aquaculture.2022.738682

2. “Stripe” transcription factors provide accessibility to co-binding partners in mammalian genomes

Author:
Yongbing Zhao; Supriya V. Vartak; Andrea Conte; Xiang Wang; David A. Garcia; Evan Stevens; Seol Kyoung Jung; Kyong-Rim Kieffer-Kwon; Laura Vian; Timothy Stodola; Francisco Moris; Laura Chopp; Silvia Preite; Pamela L. Schwartzberg; Joseph M. Kulinski; Ana Olivera; Christelle Harly; Avinash Bhandoola; Elisabeth F. Heuston; David M. Bodine; Raul Urrutia; Arpita Upadhyaya; Matthew T. Weirauch; Gordon Hager; Rafael Casellas
Source:
Molecular cell 2022 v.82 no.18 pp. 3398-3411.e11
ISSN:
1097-2765
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; DNA; genome; humans; mice; transcriptome;     Show all 7 Subjects
Abstract:
... Regulatory elements activate promoters by recruiting transcription factors (TFs) to specific motifs. Notably, TF-DNA interactions often depend on cooperativity with colocalized partners, suggesting an underlying cis-regulatory syntax. To explore TF cooperativity in mammals, we analyze ∼500 mouse and human primary cells by combining an atlas of TF motifs, footprints, ChIP-seq, transcriptomes, and a ...
DOI:
10.1016/j.molcel.2022.06.029

3. Polymerase η Recruits DHX9 Helicase to Promote Replication across Guanine Quadruplex Structures

Author:
Feng Tang; Yinan Wang; Zi Gao; Shiyuan Guo; Yinsheng Wang
Source:
Journal of the American Chemical Society 2022 v.144 no.31 pp. 14016-14020
ISSN:
1520-5126
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; DNA; DNA-directed DNA polymerase; guanine;     Show all 5 Subjects
Abstract:
... DNA polymerase η (Pol η) catalyzes accurate bypass of ultraviolet light-induced cyclobutane pyrimidine dimers, and it also functions in several other related processes, including bypassing DNA with unusual structures. Here, we performed unbiased proteome-wide profiling of Pol η-interacting proteins by using two independent approaches, i.e., proximity labeling and affinity pull-down followed by LC- ...
DOI:
10.1021/jacs.2c05312

4. Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome

Author:
Mehran Karimzadeh; Michael M. Hoffman
Source:
Genome biology 2022 v.23 no.1 pp. 126
ISSN:
1474-760X
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; gene expression; genome; genomics; prediction; transcription factors; transcriptome;     Show all 8 Subjects
Abstract:
... Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble known TF sequence motifs, and many TFs are not sequence-specific. We developed Virtual ChIP-seq, which predicts binding of individual TFs in new cell types, integrating learned association ...
DOI:
10.1186/s13059-022-02690-2

5. Releasing the trap: How the segregase p97 extracts PARP1 from chromatin

Author:
Maximilian J. Götz; Julian Stingele
Source:
Molecular cell 2022 v.82 no.5 pp. 889-890
ISSN:
1097-2765
Subject:
chromatin,   etc   ; adenosinetriphosphatase; cytotoxicity;     Show all 3 Subjects
Abstract:
... Krastev et al. (2022) identify a cellular mechanism that counteracts cytotoxic trapping of PARP1 induced by clinical PARP inhibitors. SUMO-targeted ubiquitylation of trapped PARP1 is shown to trigger the enzymes’ extraction from chromatin by the p97 ATPase. ...
DOI:
10.1016/j.molcel.2022.02.012

6. Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells

Author:
Geng G. Tian; Xinyan Zhao; Changliang Hou; Wenhai Xie; Xiaoyong Li; Yinjuan Wang; Lijuan Wang; Hua Li; Xiaodong Zhao; Jing Li; Ji Wu
Source:
Cellular and molecular life sciences 2022 v.79 no.1 pp. 22
ISSN:
1420-682X
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; RNA; adults; females; gene expression; germ cells; mice; sequence analysis;     Show all 9 Subjects
Abstract:
... The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female ...
DOI:
10.1007/s00018-021-04107-y

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

Author:
Sue Yu; Jia Li; Guanxu Ji; Zhen Long Ng; Jiamin Siew; Wan Ning Lo; Ying Ye; Yuan Yuan Chew; Yun Chau Long; Wensheng Zhang; Ernesto Guccione; Yuin Han Loh; Zhi-Hong Jiang; Henry Yang; Qiang Wu
Source:
Genomics, proteomics & bioinformatics 2022 v.20 no.1 pp. 110-128
ISSN:
1672-0229
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; RNA; bioinformatics; fibroblasts; genes; genomics; histones; lysine; mice; proteomics; transcription (genetics);     Show all 12 Subjects
Abstract:
... 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. Depletion of Npac in mouse embryonic fibroblasts (MEFs) inhibit ...
DOI:
10.1016/j.gpb.2020.08.004

8. Chromatin Unlimited: An Evolutionary View of Chromatin

Author:
Yasushi Hiraoka
Source:
Epigenomes 2022 v.6 no.1 pp. -
ISSN:
2075-4655
Subject:
chromatin,   etc   ; epigenetics; eukaryotic cells;     Show all 3 Subjects
Abstract:
... Chromatin is a fundamental and highly conserved structure that carries genetic and epigenetic information in eukaryotic cells [...] ...
DOI:
10.3390/epigenomes6010002

9. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression

Author:
Ioannis Sanidas; Hanjun Lee; Purva H. Rumde; Gaylor Boulay; Robert Morris; Gabriel Golczer; Marcelo Stanzione; Soroush Hajizadeh; Jun Zhong; Meagan B. Ryan; Ryan B. Corcoran; Benjamin J. Drapkin; Miguel N. Rivera; Nicholas J. Dyson; Michael S. Lawrence
Source:
Molecular cell 2022 v.82 no.18 pp. 3333-3349.e9
ISSN:
1097-2765
Subject:
chromatin,   etc   ; cell cycle; phosphorylation;     Show all 3 Subjects
Abstract:
... The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, ...
DOI:
10.1016/j.molcel.2022.07.014

10. Pro-apoptotic and anti-apoptotic regulation mediated by deubiquitinating enzymes

Author:
Hae-Seul Choi; Kwang-Hyun Baek
Source:
Cellular and molecular life sciences 2022 v.79 no.2 pp. 117
ISSN:
1420-682X
Subject:
chromatin,   etc   ; apoptosis; cancer therapy;     Show all 3 Subjects
Abstract:
... Although damaged cells can be repaired, cells that are considered unlikely to be repaired are eliminated through apoptosis, a type of predicted cell death found in multicellular organisms. Apoptosis is a structured cell death involving alterations to the cell morphology and internal biochemical changes. This process involves the expansion and cracking of cells, changes in cell membranes, nuclear f ...
DOI:
10.1007/s00018-022-04132-5

11. Identification of the accessible chromatin regions in six tissues in the soybean

Author:
Mingkun Huang; Ling Zhang; Limeng Zhou; Wai-Shing Yung; Zhili Wang; Zhixia Xiao; Qianwen Wang; Xin Wang; Man-Wah Li; Hon-Ming Lam
Source:
Genomics 2022 v.114 no.3 pp. 110364
ISSN:
0888-7543
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; flower buds; flowers; genes; genomics; leaf buds; sequence analysis; soybeans; transcription factors;     Show all 10 Subjects
Abstract:
... Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hen ...
DOI:
10.1016/j.ygeno.2022.110364

12. BindVAE: Dirichlet variational autoencoders for de novo motif discovery from accessible chromatin

Author:
Meghana Kshirsagar; Han Yuan; Juan Lavista Ferres; Christina Leslie
Source:
Genome biology 2022 v.23 no.1 pp. 174
ISSN:
1474-760X
Subject:
chromatin,   etc   ; genome; genomics; nucleotide sequences;     Show all 4 Subjects
Abstract:
... We present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can disentangle an input DNA sequence into distinct latent factors that encode cell-type specific in vivo binding signals for individual TFs, composite patterns for TFs involved in cooperative bindi ...
DOI:
10.1186/s13059-022-02723-w

13. Oncohistones: Exposing the nuances and vulnerabilities of epigenetic regulation

Author:
Michelle M. Mitchener; Tom W. Muir
Source:
Molecular cell 2022 v.82 no.16 pp. 2925-2938
ISSN:
1097-2765
Subject:
chromatin,   etc   ; DNA; epigenetics; histones; humans;     Show all 5 Subjects
Abstract:
... Work over the last decade has uncovered a new layer of epigenetic dysregulation. It is now appreciated that somatic missense mutations in histones, the packaging agents of genomic DNA, are often associated with human pathologies, especially cancer. Although some of these “oncohistone” mutations are thought to be key drivers of cancer, the impacts of the majority of them on disease onset and progre ...
DOI:
10.1016/j.molcel.2022.07.008

14. ATACing single cells with phages

Author:
Patrick Maschmeyer; Simon Haas
Source:
Molecular cell 2022 v.82 no.2 pp. 234-236
ISSN:
1097-2765
Subject:
chromatin,   etc   ; mitochondrial DNA; protein synthesis;     Show all 3 Subjects
Abstract:
... Fiskin et al. (2021) developed a “multi-omics” approach that integrates phage-displayed single-domain antibodies (“nanobodies”) with the assay for transposase-accessible chromatin (PHAGE-ATAC) to simultaneously determine protein expression, chromatin accessibility, and mitochondrial DNA mutations (for clonal tracing) in single cells. ...
DOI:
10.1016/j.molcel.2021.12.028

15. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

Author:
Xiaolin Wei; Yu Xiang; Derek T. Peters; Choiselle Marius; Tongyu Sun; Ruocheng Shan; Jianhong Ou; Xin Lin; Feng Yue; Wei Li; Kevin W. Southerland; Yarui Diao
Source:
Molecular cell 2022 v.82 no.6 pp. 1225-1238.e6
ISSN:
1097-2765
Subject:
chromatin,   etc   ; DNA; genes; humans; muscles; transposases;     Show all 6 Subjects
Abstract:
... The long-range interactions of cis-regulatory elements (cREs) play a central role in gene regulation. cREs can be characterized as accessible chromatin sequences. However, it remains technically challenging to comprehensively identify their spatial interactions. Here, we report a new method HiCAR (Hi-C on accessible regulatory DNA), which utilizes Tn5 transposase and chromatin proximity ligation, ...
DOI:
10.1016/j.molcel.2022.01.023

16. The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist

Author:
Jack A. Collora; Ya-Chi Ho
Source:
Cell 2022 v.185 no.2 pp. 227-229
ISSN:
0092-8674
Subject:
chromatin,   etc   ; HIV infections; proviruses; transcription (genetics);     Show all 4 Subjects
Abstract:
... The shock-and-kill strategy reactivates HIV-1 latent reservoir for immune clearance. Einkauf et al. found that some HIV-1-infected cells that persist and proliferate have transcriptionally active HIV-1 in permissive chromatin. Silent proviruses in repressive chromatin resist reactivation. Understanding HIV-1-chromatin interactions and how transcriptionally active HIV-1-infected cells survive is a ...
DOI:
10.1016/j.cell.2021.12.038

17. CCCTC-binding factor is an upstream regulator of the pluripotency factor Oct4 and functions in active transcription of linc1253 and linc1356 genes in pluripotent cells

Author:
Feng Wang; Baiquan Ci; Yangzi Wang
Source:
Gene expression patterns 2022 v.43 pp. 119230
ISSN:
1567-133X
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; data collection; gene expression; genomics; mice; models; quantitative polymerase chain reaction; transcription (genetics); transcription factors;     Show all 10 Subjects
Abstract:
... The embryonic stem cell- (ESC) specific transcription factor Oct4 is a well-known master regulator of pluripotency. The aim of this study was to identify upstream regulators of Oct4 and explore their functional link in regulating lincRNA expression in ESCs. By quantitative real-time PCR (RT-qPCR) analysis upon CCCTC-binding factor (CTCF) or Oct4 knockdown, here, we found that the chromatin insulat ...
DOI:
10.1016/j.gep.2021.119230

18. Mapping histone modification-dependent protein interactions with chemical proteomics

Author:
Yanmei Chen; Yi Wang
Source:
Trends in biochemical sciences 2022 v.47 no.3 pp. 189-193
ISSN:
0968-0004
Subject:
chromatin,   etc   ; epigenetics; histones; proteomics; transcription (genetics);     Show all 5 Subjects
Abstract:
... Post-translational modifications (PTMs) of histones play essential roles in chromatin function and epigenetic regulation. Determining the interaction partners of these modifications is crucial to understanding transcriptional processes related to diverse developmental and pathological cues. We discuss how chemical proteomics can be applied to the simultaneous and global exploration of these intera ...
DOI:
10.1016/j.tibs.2021.11.002

19. Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants

Author:
Fernando Baile; Ángeles Gómez-Zambrano; Myriam Calonje
Source:
Plant communications 2022 v.3 no.1 pp. 100267
ISSN:
2590-3462
Subject:
chromatin,   etc   ; eukaryotic cells; gene expression; histones;     Show all 4 Subjects
Abstract:
... The evolutionary conserved Polycomb Group (PcG) repressive system comprises two central protein complexes, PcG repressive complex 1 (PRC1) and PRC2. These complexes, through the incorporation of histone modifications on chromatin, have an essential role in the normal development of eukaryotes. In recent years, a significant effort has been made to characterize these complexes in the different king ...
DOI:
10.1016/j.xplc.2021.100267

20. Genome-wide identification of functional enhancers and their potential roles in pig breeding

Author:
Yinqiao Wu; Yuedong Zhang; Hang Liu; Yun Gao; Yuyan Liu; Ling Chen; Lu Liu; David M. Irwin; Chunhui Hou; Zhongyin Zhou; Yaping Zhang
Source:
Journal of animal science and biotechnology 2022 v.13 no.1 pp. 75
ISSN:
2049-1891
Subject:
chromatin; chromatin immunoprecipitation,   etc   ; alkaline phosphatase; animal models; biomedical research; biotechnology; epithelium; evolution; genes; histone code; histones; kidneys; muscles; swine; testes;     Show all 15 Subjects
Abstract:
... BACKGROUND: The pig is an economically important livestock species and is a widely applied large animal model in medical research. Enhancers are critical regulatory elements that have fundamental functions in evolution, development and disease. Genome-wide quantification of functional enhancers in the pig is needed. RESULTS: We performed self-transcribing active regulatory region sequencing (STARR ...
DOI:
10.1186/s40104-022-00726-y