scholarly journals Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms

2019 ◽  
Author(s):  
Laura E McKnight ◽  
Johnathan G Crandall ◽  
Thomas B Bailey ◽  
Orion GB Banks ◽  
Kona N Orlandi ◽  
...  
Keyword(s):  
Leukemia Cell ◽  
Leukemia Cell Line ◽  
Model Organisms ◽  
Dna Fragments ◽  
Chemical Waste ◽  
Genome Wide ◽  
Solid Agar ◽  
Eukaryotic Dna ◽  
Nucleosome Mapping ◽  
The Relationship

AbstractEukaryotic DNA is packaged into nucleosomes, the smallest repeating unit of chromatin. The positions of nucleosomes determine the relative accessibility of genomic DNA. Several protocols exist for mapping nucleosome positions in eukaryotic genomes in order to study the relationship between chromatin structure and DNA-dependent processes. These nucleosome mapping protocols can be laborious and, at minimum, require two to three days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for mapping nucleosomes from S. cerevisiae liquid culture or from patches on solid agar. This method isolates nucleosome-sized footprints in three hours using 1.5 ml tubes with minimal chemical waste. We validate that these footprints match those produced by previously published methods and we demonstrate that our protocol works for N. crassa and S. pombe. A slightly modified protocol can be used for isolation of nucleosome-protected DNA fragments from a variety of wild fungal specimens thereby providing a simple, easily multiplexed and unified strategy to map nucleosome positions in model and non-model fungi. Finally, we demonstrate recovery of nucleosome footprints from the diploid myeloid leukemia cell line PLB-985 in less than three hours using an abbreviated version of the same protocol. With reduced volume and incubation times and a streamlined workflow, the described method should be compatible with high-throughput, automated creation of MNase-seq libraries. We believe this simple validated method for rapidly producing sequencing-ready nucleosome footprints from a variety of organisms will make nucleosome mapping studies widely accessible to researchers globally.

scholarly journals HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

2020 ◽  
Author(s):  
Jonathan D. Rosen ◽  
Yuchen Yang ◽  
Armen Abnousi ◽  
Jiawen Chen ◽  
Michael Song ◽  
...  
Keyword(s):  
Cell Line ◽  
Leukemia Cell ◽  
Embryonic Stem ◽  
Cell Types ◽  
Brain Cell ◽  
Leukemia Cell Line ◽  
Human Lymphoblastoid Cell ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Cost Efficient

AbstractHiChIP and PLAC-seq are emerging technologies for studying genome-wide long-range chromatin interactions mediated by protein of interest, enabling more sensitive and cost-efficient interrogation of protein-centric chromatin conformation. However, due to the unbalanced read distribution introduced by protein immunoprecipitation, existing reproducibility measures developed for Hi-C data are not appropriate for the analysis of HiChIP and PLAC-seq data.Here, we present HPRep, a stratified and weighted correlation metric derived from normalized contact counts, to quantify reproducibility in HiChIP and PLAC-seq data. We applied HPRep to multiple real datasets and demonstrate that HPRep outperforms existing reproducibility measures developed for Hi-C data. Specifically, we applied HPRep to H3K4me3 PLAC-seq data from mouse embryonic stem cells and mouse brain tissues, as well as H3K27ac HiChIP data from human lymphoblastoid cell line GM12878 and leukemia cell line K562, showing that HPRep can more clearly separate among pseudo-replicates, real replicates, and non-replicates. Furthermore, in an H3K4me3 PLAC-seq dataset consisting of 11 samples from four human brain cell types, HPRep demonstrates expected clustering of data which could not be achieved by existing methods developed for Hi-C data, highlighting the need of a reproducibility metric tailored to HiChIP and PLAC-seq data.

scholarly journals Naphthylchalcones induce apoptosis and caspase activation in a leukemia cell line: The relationship between mitochondrial damage, oxidative stress, and cell death

2010 ◽  
Vol 18 (22) ◽  
pp. 8026-8034 ◽  
Author(s):  
Evelyn Winter ◽  
Louise Domeneghini Chiaradia ◽  
Clarissa A.S. de Cordova ◽  
Ricardo José Nunes ◽  
Rosendo Augusto Yunes ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Cell Death ◽  
Cell Line ◽  
Leukemia Cell ◽  
Mitochondrial Damage ◽  
Leukemia Cell Line ◽  
Caspase Activation ◽  
The Relationship

scholarly journals Dysregulated bcl-2 expression inhibits apoptosis but not differentiation of retinoic acid-induced HL-60 granulocytes

Blood ◽  
1994 ◽  
Vol 84 (2) ◽  
pp. 440-445 ◽  
Author(s):  
JR Park ◽  
K Robertson ◽  
DD Hickstein ◽  
S Tsai ◽  
DM Hockenbery ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Life Span ◽  
Myeloid Leukemia ◽  
Leukemia Cell ◽  
Leukemia Cell Line ◽  
Over Expression ◽  
Limited Life ◽  
Regulatory Controls ◽  
The Relationship ◽  
Myeloid Leukemia Cell

Abstract The bcl-2-proto-oncogene appears to contribute to the development of certain malignancies by inhibiting programmed cell death (apoptosis). Mature granulocytes show a markedly limited life span and rapidly undergo apoptosis. To further define the relationship between apoptosis and granulocyte differentiation, we used retroviral vector-mediated gene transduction to introduce the normal bcl-2 gene into the HL-60 myeloid leukemia cell line and determined the response of these bcl-2- transduced HL-60 cells to the induction of granulocyte differentiation by retinoic acid (RA). Although the bcl-2-transduced HL-60 cells showed the same differentiative response to RA as did the parental HL-60 cells, the life span of the RA-induced, bcl-2-transduced HL-60 granulocytes was markedly prolonged compared with that of the RA- induced parental HL-60 granulocytes. DNA fragmentation studies indicate that this prolonged life span resulted from diminished apoptosis in the bcl-2-transduced cells. These studies indicate that bcl-2 is involved in regulating apoptosis in maturing granulocytes. Because bcl-2 over- expression did not interfere with RA-induced granulocyte differentiation, it appears that granulocyte differentiation and apoptosis are under distinct and separate regulatory controls.

scholarly journals Dysregulated bcl-2 expression inhibits apoptosis but not differentiation of retinoic acid-induced HL-60 granulocytes

Blood ◽  
1994 ◽  
Vol 84 (2) ◽  
pp. 440-445 ◽  
Author(s):  
JR Park ◽  
K Robertson ◽  
DD Hickstein ◽  
S Tsai ◽  
DM Hockenbery ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Life Span ◽  
Myeloid Leukemia ◽  
Leukemia Cell ◽  
Leukemia Cell Line ◽  
Over Expression ◽  
Limited Life ◽  
Regulatory Controls ◽  
The Relationship ◽  
Myeloid Leukemia Cell

The bcl-2-proto-oncogene appears to contribute to the development of certain malignancies by inhibiting programmed cell death (apoptosis). Mature granulocytes show a markedly limited life span and rapidly undergo apoptosis. To further define the relationship between apoptosis and granulocyte differentiation, we used retroviral vector-mediated gene transduction to introduce the normal bcl-2 gene into the HL-60 myeloid leukemia cell line and determined the response of these bcl-2- transduced HL-60 cells to the induction of granulocyte differentiation by retinoic acid (RA). Although the bcl-2-transduced HL-60 cells showed the same differentiative response to RA as did the parental HL-60 cells, the life span of the RA-induced, bcl-2-transduced HL-60 granulocytes was markedly prolonged compared with that of the RA- induced parental HL-60 granulocytes. DNA fragmentation studies indicate that this prolonged life span resulted from diminished apoptosis in the bcl-2-transduced cells. These studies indicate that bcl-2 is involved in regulating apoptosis in maturing granulocytes. Because bcl-2 over- expression did not interfere with RA-induced granulocyte differentiation, it appears that granulocyte differentiation and apoptosis are under distinct and separate regulatory controls.

scholarly journals HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets

2021 ◽  
Vol 43 (2) ◽  
pp. 1156-1170
Author(s):  
Jonathan D. Rosen ◽  
Yuchen Yang ◽  
Armen Abnousi ◽  
Jiawen Chen ◽  
Michael Song ◽  
...  
Keyword(s):  
Cell Line ◽  
Leukemia Cell ◽  
Embryonic Stem ◽  
Cell Types ◽  
Brain Cell ◽  
Leukemia Cell Line ◽  
Human Lymphoblastoid Cell ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Cost Efficient

HiChIP and PLAC-Seq are emerging technologies for studying genome-wide long-range chromatin interactions mediated by the protein of interest, enabling more sensitive and cost-efficient interrogation of protein-centric chromatin conformation. However, due to the unbalanced read distribution introduced by protein immunoprecipitation, existing reproducibility measures developed for Hi-C data are not appropriate for the analysis of HiChIP and PLAC-Seq data. Here, we present HPRep, a stratified and weighted correlation metric derived from normalized contact counts, to quantify reproducibility in HiChIP and PLAC-Seq data. We applied HPRep to multiple real datasets and demonstrate that HPRep outperforms existing reproducibility measures developed for Hi-C data. Specifically, we applied HPRep to H3K4me3 PLAC-Seq data from mouse embryonic stem cells and mouse brain tissues as well as H3K27ac HiChIP data from human lymphoblastoid cell line GM12878 and leukemia cell line K562, showing that HPRep can more clearly separate among pseudo-replicates, real replicates, and non-replicates. Furthermore, in an H3K4me3 PLAC-Seq dataset consisting of 11 samples from four human brain cell types, HPRep demonstrated the expected clustering of data that could not be achieved by existing methods developed for Hi-C data, highlighting the need for a reproducibility metric tailored to HiChIP and PLAC-Seq data.

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