keyword
MENU ▼
Read by QxMD icon Read
search

chromosome conformation capture

keyword
https://www.readbyqxmd.com/read/29915359/dynamic-kinetochore-size-regulation-promotes-microtubule-capture-and-chromosome-biorientation-in-mitosis
#1
Carlos Sacristan, Misbha Ud Din Ahmad, Jenny Keller, Job Fermie, Vincent Groenewold, Eelco Tromer, Alexander Fish, Roberto Melero, José María Carazo, Judith Klumperman, Andrea Musacchio, Anastassis Perrakis, Geert Jpl Kops
Faithful chromosome segregation depends on the ability of sister kinetochores to attach to spindle microtubules. The outer layer of kinetochores transiently expands in early mitosis to form a fibrous corona, and compacts following microtubule capture. Here we show that the dynein adaptor Spindly and the RZZ (ROD-Zwilch-ZW10) complex drive kinetochore expansion in a dynein-independent manner. C-terminal farnesylation and MPS1 kinase activity cause conformational changes of Spindly that promote oligomerization of RZZ-Spindly complexes into a filamentous meshwork in cells and in vitro...
June 18, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29900125/genome-wide-analysis-of-interchromosomal-interaction-probabilities-reveals-chained-translocations-and-overrepresentation-of-translocation-breakpoints-in-genes-in-a-cutaneous-t-cell-lymphoma-cell-line
#2
Anne Steininger, Grit Ebert, Benjamin V Becker, Chalid Assaf, Markus Möbs, Christian A Schmidt, Piotr Grabarczyk, Lars R Jensen, Grzegorz K Przybylski, Matthias Port, Andreas W Kuss, Reinhard Ullmann
In classical models of tumorigenesis, the accumulation of tumor promoting chromosomal aberrations is described as a gradual process. Next-generation sequencing-based methods have recently revealed complex patterns of chromosomal aberrations, which are beyond explanation by these classical models of karyotypic evolution of tumor genomes. Thus, the term chromothripsis has been introduced to describe a phenomenon, where temporarily and spatially confined genomic instability results in dramatic chromosomal rearrangements limited to segments of one or a few chromosomes...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29898989/disruption-of-a-35kb-enhancer-impairs-ctcf-binding-and-mlh1-expression-in-colorectal-cells
#3
Qing Liu, Julie A Thoms, Andrea C Nunez, Yizhou Huang, Kathy Knezevic, Deborah Packham, Rebecca C Poulos, Rachel Williams, Dominik Beck, Nicholas J Hawkins, Robyn L Ward, Jason W H Wong, Luke B Hesson, Mathew A Sloane, John Pimanda
PURPOSE: MLH1 is a major tumour suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified. EXPERIMENTAL DESIGN: Here we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1 expressing and non-expressing cells...
June 13, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29895565/chromatin-interaction-analysis-using-paired-end-tag-chia-pet-sequencing-in-tadpole-tissues
#4
Nicolas Buisine, Xiaoan Ruan, Yijun Ruan, Laurent M Sachs
Proper gene expression involves communication between the regulatory elements and promoters of genes. Today, chromosome conformation capture (3C)-based methods efficiently probe chromosome folding in the nucleus and thus provide a molecular description of physical proximity through DNA looping between enhancer(s) and their target promoter(s). One such method, chromatin interaction analysis using paired-end-tag (ChIA-PET) sequencing is a powerful high-throughput method for detection of genome-wide chromatin interactions...
June 12, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29895563/chromatin-immunoprecipitation-for-chromatin-interaction-analysis-using-paired-end-tag-chia-pet-sequencing-in-tadpole-tissues
#5
Nicolas Buisine, Xiaoan Ruan, Yijun Ruan, Laurent M Sachs
Proper gene expression involves communication between the regulatory elements and promoters of genes. Because regulatory elements can be located over a large range of genomic distances (from as close as a few hundred bp to as much as several Mb away), contact and communication between regulators and the core transcriptional machinery at promoters are mediated through DNA looping. Today, chromosome conformation capture (3C)-based methods efficiently probe chromosome folding in the nucleus and thus provide a molecular description of physical proximity between enhancer(s) and their target promoter(s)...
June 12, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29883495/genome-wide-analysis-reveals-no-evidence-of-trans-chromosomal-regulation-of-mammalian-immune-development
#6
Timothy M Johanson, Hannah D Coughlan, Aaron T L Lun, Naiara G Bediaga, Gaetano Naselli, Alexandra L Garnham, Leonard C Harrison, Gordon K Smyth, Rhys S Allan
It has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene expression and cell fate determination. Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome conformation capture. Although we readily identified stable interactions in cis, and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including previously described interactions...
June 8, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29848293/improved-accuracy-assessment-for-3d-genome-reconstructions
#7
Mark R Segal, Henrik L Bengtsson
BACKGROUND: Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genome conformation had been difficult to elucidate but the advent chromatin conformation capture assays, notably Hi-C, has transformed understanding of chromatin architecture and yielded numerous biological insights. Although most of these findings have flowed from analysis of proximity data produced by these assays, added value in generating 3D reconstructions has been demonstrated, deriving, in part, from superposing genomic features on the reconstruction...
May 30, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29796744/3d-genome-and-its-disorganization-in-diseases
#8
REVIEW
Ruifeng Li, Yuting Liu, Yingping Hou, Jingbo Gan, Pengze Wu, Cheng Li
The chromosomes in eukaryotic cells are highly folded and organized to form dynamic three-dimensional (3D) structures. In recent years, many technologies including chromosome conformation capture (3C) and 3C-based technologies (Hi-C, ChIA-PET) have been developed to investigate the 3D structure of chromosomes. These technologies are enabling research on how gene regulatory events are affected by the 3D genome structure, which is increasingly implicated in the regulation of gene expression and cellular functions...
May 23, 2018: Cell Biology and Toxicology
https://www.readbyqxmd.com/read/29787433/investigation-of-spatial-organization-of-chromosome-territories-in-chromosome-exchange-aberrations-after-ionizing-radiation-exposure
#9
Adayabalam S Balajee, Jacob T Sanders, Rosela Golloshi, Igor Shuryak, Rachel Patton McCord, Nicholas Dainiak
Higher-order organization of the human genome is well established with chromosomes occupying distinct domains or territories in the interphase nucleus. Spatial organization of chromosome territories in the interphase nucleus occurs in a cell-type-specific manner. Since both stable and unstable aberrations induced by ionizing radiation involve the exchange of material between two or more chromosomes, this study investigated the role of spatial organization of chromosome domains in ionizing-radiation-induced chromosome translocation events...
July 2018: Health Physics
https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#10
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#11
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29767704/gene-regulation-in-the-3d-genome
#12
Yun Li, Ming Hu, Yin Shen
The spatial organization of the genome is essential for the precise control of gene expression. Recent advances in sequencing and imaging technologies allow us to explore the 3D genome and its relationship to gene regulation at an unprecedented scale. In this review, we provide an overview of lessons learned from studying the chromatin structure and their implications in communications between gene promoters and distal cis-regulatory elements, such as enhancers. We first review the current knowledge of general genome organization, followed by the importance of chromatin folding in gene regulation...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29763375/chromosomal-architecture-and-placental-expression-of-the-human-growth-hormone-gene-family-are-targeted-by-pre-pregnancy-maternal-obesity
#13
Yan Jin, Hana Vakili, SongYan Liu, Savas Menticoglou, Margaret E Bock, Peter A Cattini
The human (h) placental lactogenic hormone chorionic somatomammotropin (CS) is highly produced during pregnancy and acts as a metabolic adaptor in response to maternal insulin resistance. Maternal obesity can exacerbate this "resistance" and a >75% decrease in CS RNA levels was observed in term placentas from obese versus lean women. The genes coding for hCS (hCS-A and hCS-B) and placental growth hormone (hGH-V) as well as the hCS-L pseudogene and pituitary growth hormone (GH) gene (hGH-N) are located at a single locus on chromosome 17...
May 15, 2018: American Journal of Physiology. Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29733521/hmga2-promotes-glioma-invasion-and-poor-prognosis-via-a-long-range-chromatin-interaction
#14
Shanshan Zhang, Huibian Zhang, Lin Yu
To identify the function and underlying mechanisms of HMGA2 on the prognosis and invasion of gliomas, HMGA2 was detected by immunohistochemistry. The Kaplan-Meier and Cox's regression analysis results showed that higher HMGA2 level predicted the poorer outcomes of glioma patients. ChIP-qPCR, DNA electrophoretic mobility shift assay, chromosome conformation capture, and co-immunoprecipitation were applied to identify HMGA2-activated target sites, which were further verified by mRNA and protein expression detection...
May 7, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29723572/iteratively-improving-hi-c-experiments-one-step-at-a-time
#15
Rosela Golloshi, Jacob Sanders, Rachel Patton McCord
The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to study diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases...
April 30, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29712868/-insulin-promoter-in-human-pancreatic-%C3%AE-cells-contacts-diabetes-susceptibility-loci-and-regulates-genes-affecting-insulin-metabolism
#16
Xing Jian, Gary Felsenfeld
Both type 1 and type 2 diabetes involve a complex interplay between genetic, epigenetic, and environmental factors. Our laboratory has been interested in the physical interactions, in nuclei of human pancreatic β cells, between the insulin ( INS) gene and other genes that are involved in insulin metabolism. We have identified, using Circularized Chromosome Conformation Capture (4C), many physical contacts in a human pancreatic β cell line between the INS promoter on chromosome 11 and sites on most other chromosomes...
May 15, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29703667/entering-the-next-dimension-plant-genomes-in-3d
#17
REVIEW
Mariana Sotelo-Silveira, Ricardo A Chávez Montes, Jose R Sotelo-Silveira, Nayelli Marsch-Martínez, Stefan de Folter
After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but also differences, among them and with animals. The smallest structures, found in high-resolution maps of the Arabidopsis genome, are single genes...
April 24, 2018: Trends in Plant Science
https://www.readbyqxmd.com/read/29700467/digestion-ligation-only-hi-c-is-an-efficient-and-cost-effective-method-for-chromosome-conformation-capture
#18
Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal, Keji Yan, Yingying Lei, Liang Li, Yijun Ruan, Zhen F Fu, Guoliang Li, Gang Cao
Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments...
May 2018: Nature Genetics
https://www.readbyqxmd.com/read/29685368/principles-of-chromosome-architecture-revealed-by-hi-c
#19
REVIEW
Kyle P Eagen
Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops...
June 2018: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29674753/combining-fluorescence-imaging-with-hi-c-to-study-3d-genome-architecture-of-the-same-single-cell
#20
David Lando, Srinjan Basu, Tim J Stevens, Andy Riddell, Kai J Wohlfahrt, Yang Cao, Wayne Boucher, Martin Leeb, Liam P Atkinson, Steven F Lee, Brian Hendrich, Dave Klenerman, Ernest D Laue
Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000-100,000 chromosome contacts per single haploid genome in parallel with fluorescence images...
May 2018: Nature Protocols
keyword
keyword
82925
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"