scholarly journals HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

2021 ◽  
Vol 4 (3) ◽  
pp. 49
Author(s):  
Tomas Zelenka ◽  
Charalampos Spilianakis
Keyword(s):  
T Cells ◽  
Long Range ◽  
Three Dimensional ◽  
Cell Types ◽  
Range Interaction ◽  
Chromatin Interactions ◽  
Optimized Protocol ◽  
Long Range Interaction ◽  
Chromatin Compactness ◽  
Detailed Protocol

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

scholarly journals Human PRE-PIK3C2B exhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marks

2020 ◽  
Author(s):  
Jayant Maini ◽  
Ankit Kumar Pathak ◽  
Kausik Bhattacharyya ◽  
Narendra Kumar ◽  
Ankita Narang ◽  
...  
Keyword(s):  
Long Range ◽  
Meta Analysis ◽  
Range Interaction ◽  
Dual Nature ◽  
Polycomb Response Element ◽  
Chromatin Interactions ◽  
Long Range Interaction ◽  
Intergenic Regions ◽  
Genomic Regions ◽  
Transcriptional Start Sites

AbstractHuman PRE-PIK3C2B is a dual nature polycomb response element that interacts with both polycomb as well as trithorax members. In the current study, using 4C-Seq (Capturing Circular Chromosomal Conformation-Sequencing), we identified long-range chromatin interactions associated with PRE-PIK3C2B and validated them with 3C-PCR. We identified both intra-as well as inter-chromosomal interactions, a large proportion of which were found to be closely distributed around transcriptional start sites (TSS). A significant number of interactions were also found to be associated with heterochromatic regions. Meta-analysis of ENCODE ChIP-Seq data identified an overall enrichment of YY1, CTCF as well as histone modification such as H3K4me3 and H3K27me marks in different cell lines. Almost 90% interactions were derived from either intronic or intergenic regions. among which large proportions of intronic interactors were either unique sequences or LINE/SINE derived. In case of intergenic interactions, majority of the interaction were associated with LINE/SINE repeats. We further found that genes proximal to the interactor sequences were co-expressed, they showed reduced expression. To the best of our knowledge this is one of the early demonstrations of long-range interaction of PRE sequences in human genome.

scholarly journals Improving chromatin-interaction prediction using single-cell open-chromatin profile and making insight about the cis-regulatory landscape of the human brain

2020 ◽  
Author(s):  
Neetesh Pandey ◽  
Omkar Chandra ◽  
Shreya Mishra ◽  
Vibhor Kumar
Keyword(s):  
Human Brain ◽  
Single Cell ◽  
Long Range ◽  
Target Genes ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Open Chromatin ◽  
Range Interaction ◽  
Chromatin Interactions ◽  
A Cell

AbstractSingle-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell-type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local chromatin-interactions despite the fact that long-range interaction among genomic sites plays a significant role in gene regulation. Here, we propose a method that predicts both local and long-range interactions among genomic sites using single-cell open chromatin profiles. Using our method’s better sensitivity, we could predict almost 0.7 million interactions among genomic sites across 7 cell-types in the human brain. The chromatin-interactions estimated in the human brain revealed surprising but useful insight about target genes of human-accelerated-elements and disease-associated mutations.

Phase transformation and Raman spectra in BaTiO3 nanocrystals

2002 ◽  
Vol 718 ◽  
Author(s):  
Jian Yu ◽  
X. J. Meng ◽  
J.L. Sun ◽  
G.S. Wang ◽  
J.H. Chu
Keyword(s):  
Particle Size ◽  
Phase Transformation ◽  
Low Temperature ◽  
Long Range ◽  
Lattice Expansion ◽  
Inversion Symmetry ◽  
Range Interaction ◽  
Cooperative Phenomena ◽  
Long Range Interaction ◽  
Hydrothermal Methods

AbstractIn this paper, size-induced ferroelectricit yweakening, phase transformation, and anomalous lattice expansion are observed in nanocrystalline BaTiO3 (nc-BaTiO3) deriv ed b y low temperature hydrothermal methods, and they are w ellunderstood using the terms of the long-range interaction and its cooperative phenomena altered by particle size in covalen t ionic nanocrystals. In cubic nc-BaTiO3, five modes centerd at 186, 254, 308, 512 and 716 cm-1 are observed Raman active in cubic nanophase, and they are attributed to local rhombohedral distortion breaking inversion-symmetry in cubic nanophase. The254 and 308 cm-1 modes are significantly affected not only by the concentration of hydroxyl defects, but also their particular configuration. And the 806 cm-1 modes found to be closely associated with OH - absorbed on grain boundaries.

scholarly journals Inverse Problem for Ising Connection Matrix with Long-Range Interaction

Mathematics ◽  
2021 ◽  
Vol 9 (14) ◽  
pp. 1624
Author(s):  
Leonid Litinskii ◽  
Boris Kryzhanovsky
Keyword(s):  
Inverse Problem ◽  
Long Range ◽  
Random Number ◽  
Connection Matrix ◽  
Range Interaction ◽  
Connection Matrices ◽  
Ising Systems ◽  
Long Range Interaction ◽  
Matrix Spectrum ◽  
Analytical Expressions

In the present paper, we examine Ising systems on d-dimensional hypercube lattices and solve an inverse problem where we have to determine interaction constants of an Ising connection matrix when we know a spectrum of its eigenvalues. In addition, we define restrictions allowing a random number sequence to be a connection matrix spectrum. We use the previously obtained analytical expressions for the eigenvalues of Ising connection matrices accounting for an arbitrary long-range interaction and supposing periodic boundary conditions.

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