An optimized ChIP-Seq framework for profiling of histone modifications in Chromochloris zofingiensis

The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin Immunoprecipitation followed by deep sequencing (ChIP-Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome-wide histone modification patterns and transcription factor-binding sites alike. Here, we established a ChIP-Seq framework for Chr. zofingiensis yielding over 20 million high quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA-protein crosslinking. We used this ChIP-Seq framework to generate a genome-wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA-Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP-Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis.

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Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer’s disease

Acta Neuropathologica Communications ◽

10.1186/s40478-021-01199-2 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Joseph S. Reddy ◽

Mariet Allen ◽

Charlotte C. G. Ho ◽

Stephanie R. Oatman ◽

Özkan İş ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Genome Wide Association Study ◽

Transcriptome Profiling ◽

Brain Regions ◽

Common Finding ◽

Amyloid Angiopathy ◽

Genome Wide ◽

A Genome ◽

Male Sex

AbstractCerebral amyloid angiopathy (CAA) contributes to accelerated cognitive decline in Alzheimer’s disease (AD) dementia and is a common finding at autopsy. The APOEε4 allele and male sex have previously been reported to associate with increased CAA in AD. To inform biomarker and therapeutic target discovery, we aimed to identify additional genetic risk factors and biological pathways involved in this vascular component of AD etiology. We present a genome-wide association study of CAA pathology in AD cases and report sex- and APOE-stratified assessment of this phenotype. Genome-wide genotypes were collected from 853 neuropathology-confirmed AD cases scored for CAA across five brain regions, and imputed to the Haplotype Reference Consortium panel. Key variables and genome-wide genotypes were tested for association with CAA in all individuals and in sex and APOEε4 stratified subsets. Pathway enrichment was run for each of the genetic analyses. Implicated loci were further investigated for functional consequences using brain transcriptome data from 1,186 samples representing seven brain regions profiled as part of the AMP-AD consortium. We confirmed association of male sex, AD neuropathology and APOEε4 with increased CAA, and identified a novel locus, LINC-PINT, associated with lower CAA amongst APOEε4-negative individuals (rs10234094-C, beta = −3.70 [95% CI −0.49—−0.24]; p = 1.63E-08). Transcriptome profiling revealed higher LINC-PINT expression levels in AD cases, and association of rs10234094-C with altered LINC-PINT splicing. Pathway analysis indicates variation in genes involved in neuronal health and function are linked to CAA in AD patients. Further studies in additional and diverse cohorts are needed to assess broader translation of our findings.

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Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

10.1101/2021.05.12.443750 ◽

2021 ◽

Author(s):

Tanzeem Fatima ◽

Rangachari Krishnan ◽

Ashutosh Srivastava ◽

Vageeshbabu S. Hanur ◽

M. Srinivasa Rao

Keyword(s):

Transcriptome Profiling ◽

Santalum Album ◽

Rna Seq ◽

Improvement Program ◽

East Indian ◽

Kegg Pathways ◽

Oil Biosynthesis ◽

Genome Wide ◽

A Genome ◽

Santalum Album L

East Indian Sandalwood (Santalum album L.) is highly valued for its heartwood and its oil. There have been no efforts to comparative study of high and low oil yielding genetically identical sandalwood trees grown in similar climatic condition. Thus we intend to study a genome wide transcriptome analysis to identify the corresponding genes involved in high oil biosynthesis in S. album. In this study, 15 years old S. album (SaSHc and SaSLc) genotypes were targeted for analysis to understand the contribution of genetic background on high oil biosynthesis in S. album. A total of 28,959187 and 25,598869 raw PE reads were generated by the Illumina sequencing. 2.12 million and 1.811 million coding sequences were obtained in respective accessions. Based on the GO terms, functional classification of the CDS 21262, & 18113 were assigned into 26 functional groups of three GO categories; (4,168; 3,641) for biological process (5,758;4,971) cellular component and (5,108;4,441) for molecular functions. Total 41,900 and 36,571 genes were functionally annotated and KEGG pathways of the DEGs resulted 213 metabolic pathways. In this, 14 pathways were involved in secondary metabolites biosynthesis pathway in S. album. Among 237 cytochrome families, nine groups of cytochromes were participated in high oil biosynthesis. 16,665 differentially expressed genes were commonly detected in both the accessions (SaHc and SaSLc). The results showed that 784 genes were upregulated and 339 genes were downregulated in SaHc whilst 635 upregulated 299 downregulated in SaSLc S. album. RNA-Seq results were further validated by quantitative RT-PCR. Maximum Blast hits were found to be against Vitis vinifera. From this study we have identified additional number of cytochrome family in SaHc. The accessibility of a RNA-Seq for high oil yielding sandalwood accessions will have broader associations for the conservation and selection of superior elite samples/populations for further genetic improvement program.

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A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs

Genomics ◽

10.1016/j.ygeno.2012.05.013 ◽

2012 ◽

Vol 100 (2) ◽

pp. 116-124 ◽

Cited By ~ 37

Author(s):

Ke Xu ◽

Jing Liu ◽

Mingzhu Fan ◽

Wei Xin ◽

Yuxin Hu ◽

...

Keyword(s):

Transcriptome Profiling ◽

Multiple Organs ◽

Molecular Events ◽

Genome Wide ◽

A Genome ◽

Callus Initiation

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Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice

International Journal of Molecular Sciences ◽

10.3390/ijms21155492 ◽

2020 ◽

Vol 21 (15) ◽

pp. 5492 ◽

Cited By ~ 1

Author(s):

Yu Jin Jung ◽

Jong Hee Kim ◽

Hyo Ju Lee ◽

Dong Hyun Kim ◽

Jihyeon Yu ◽

...

Keyword(s):

Gene Expression Analysis ◽

Transcriptome Profiling ◽

Rna Seq ◽

Loss Of Function ◽

Amino Acid Motif ◽

Dwarf Phenotype ◽

Genome Wide ◽

A Genome ◽

Mutant Lines ◽

Genome Wide Gene Expression

The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA20OX2 (Gibberellin oxidase) and GA3OX2, were increased in the edited mutant plants, suggesting that GA20OX2 acts as a convert of GA12 signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.

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Expression of MSX1, HOXA11 and TP53I3 in the endometrium associated with the onset of pregnancy after repeated failed IVF attempts in patients with tubo-peritoneal factor infertility

GYNECOLOGY ◽

10.26442/20795696.2020.1.200028 ◽

2020 ◽

Vol 22 (1) ◽

pp. 23-28

Author(s):

Ekaterina A. Knyazeva ◽

Maria V. Kuznetsova ◽

Olga V. Burmenskaya ◽

Andrey E. Donnikov ◽

Elena A. Kalinina

Keyword(s):

Gene Expression ◽

Transcriptome Profiling ◽

Endometrial Receptivity ◽

In Vitro Fertilisation ◽

Ivf Outcome ◽

Program Outcomes ◽

Implantation Window ◽

Genome Wide ◽

A Genome

Relevance. The success of the in vitro fertilisation (IVF) program, among other factors, depends on the readiness of the endometrium to accept the embryo. It is believed that this is possible during the so-called implantation window, the timing of which can be shifted under the influence of various factors. Evaluation of endometrial receptivity and the implantation window based on analysis of endometrial gene expression before embryo transfer is a promising approach for predicting the likelihood of pregnancy in IVF programs. Aim. To construct a classifier based on the expression of endometrial genes for predicting the outcome of an IVF program in patients with tubal-peritoneal infertility factor and repeated failed IVF attempts in history. Materials and methods. Before the IVF program, a genome-wide transcriptome profiling of endometrial samples of 15 women with tubal-perioneal infertility factor and repeated unsuccessful IVF attempts in history was carried out using Affymetrix arrays. Potential genes capable of classifying IVF program outcomes were selected, after which the expression of these genes was analyzed by qPCR-RT in the endometrium of 47 women to construct IVF outcome classifiers based on the expression of pairs or triples of genes. Results. A classifier based on the expression of the triple of genes MSX1 (HOX7), HOXA11, and TP53I3 made it possible to determine the onset of pregnancy in an IVF program with a sensitivity of 73% and a specificity of 71% with an area under the ROC-curve (AUC) of 0.738 (95% confidence interval 0.5770.898). Earlier, a relationship was found between the expression of these genes and receptivity of the endometrium, which suggests that these genes play a role in the onset of the implantation window. Conclusions. The use of a classifier based on the genes MSX1 (HOX7), HOXA11, and TP53I3 can determine the readiness of the endometrium to accept an embryo and create an individual prognosis of the outcome of an IVF program in women with tubal-peritoneal infertility factor and repeated failed IVF attempts in history.

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Identification and characterization of Hoxa9 binding sites in hematopoietic cells

Blood ◽

10.1182/blood-2011-03-341081 ◽

2012 ◽

Vol 119 (2) ◽

pp. 388-398 ◽

Cited By ~ 119

Author(s):

Yongsheng Huang ◽

Kajal Sitwala ◽

Joel Bronstein ◽

Daniel Sanders ◽

Monisha Dandekar ◽

...

Keyword(s):

Transcriptional Activation ◽

Binding Sites ◽

Enhancer Activity ◽

Transcription Start Sites ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

P300 Binding ◽

Histone H3k4

The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified the binding sites for Hoxa9 and the Hox cofactor Meis1 on a genome-wide level and profiled their associated epigenetic modifications and transcriptional targets. Hoxa9 and the Hox cofactor Meis1 cobind at hundreds of highly evolutionarily conserved sites, most of which are distant from transcription start sites. These sites show high levels of histone H3K4 monomethylation and CBP/P300 binding characteristic of enhancers. Furthermore, a subset of these sites shows enhancer activity in transient transfection assays. Many Hoxa9 and Meis1 binding sites are also bound by PU.1 and other lineage-restricted transcription factors previously implicated in establishment of myeloid enhancers. Conditional Hoxa9 activation is associated with CBP/P300 recruitment, histone acetylation, and transcriptional activation of a network of proto-oncogenes, including Erg, Flt3, Lmo2, Myb, and Sox4. Collectively, this work suggests that Hoxa9 regulates transcription by interacting with enhancers of genes important for hematopoiesis and leukemia.

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Nuclease deficiencies alter plasma cell-free DNA methylation profiles

Genome Research ◽

10.1101/gr.275426.121 ◽

2021 ◽

pp. gr.275426.121

Author(s):

Diana Siao Cheng Han ◽

Meng Ni ◽

Rebecca Wing Yan Chan ◽

Danny Ka Lok Wong ◽

Linda T Hiraki ◽

...

Keyword(s):

Fragment Size ◽

Cpg Islands ◽

Periodic Pattern ◽

Open Chromatin ◽

Cell Free Dna ◽

Free Dna ◽

Genome Wide ◽

A Genome ◽

Wide Scale ◽

Deficient Mice

The effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation was explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild-type cfDNA, cfDNA in Dnase1l3-deficient mice was significantly hypomethylated, while cfDNA in Dnase1-deficient mice was hypermethylated. The cfDNA hypomethylation in Dnase1l3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in Dnase1-deficient mice, demonstrating the preference of DNASE1 to cleave in hypomethylated OCRs and CGIs. We also observed a substantial decrease of fragment ends and coverage at methylated CpGs in the absence of DNASE1L3, thereby demonstrating that DNASE1L3 prefers to cleave at methylated CpGs. Furthermore, we found that methylation levels of cfDNA varied by fragment size in a periodic pattern, with cfDNA of specific sizes being more hypomethylated and enriched for OCRs and CGIs. These findings were confirmed in DNASE1L3-deficient human cfDNA. Thus, we have found that nuclease-mediated cfDNA fragmentation markedly affected cfDNA methylation level on a genome-wide scale. This work provides a foundational understanding of the relationship between methylation, nuclease biology and cfDNA fragmentation.

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A single-cell genomic strategy for alternative transcript start sites identification

10.1101/2021.12.09.472038 ◽

2021 ◽

Author(s):

Yanling Peng ◽

Qitong Huang ◽

Rui Kamada ◽

Keiko Ozato ◽

Yubo Zhang ◽

...

Keyword(s):

Single Cell ◽

Critical Role ◽

Genomic Analysis ◽

Cell Types ◽

Alternative Transcript ◽

Transcription Start Sites ◽

Genome Wide ◽

Alternative Transcription ◽

A Genome ◽

Alternative Tsss

Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. In the method, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNAs, then dual priming oligonucleotide system to specifically enrich TSSs for genomic analysis. We apply this method to a genome-wide study of alternative TSSs identification in two different IFN-β stimulated mouse embryonic fibroblasts (MEFs). We quantify the performance of our method and find it as accurate as other single cell methods for the detection of TSSs. Our data are also clearly discriminate two IFN-β stimulated MEFs. Moreover, our results indicate 82% expressed genes in these two cell types containing multiple TSSs, which is much higher than previous predictions based on CAGE (58%) or empirical determination (54%) in various cell types. This indicates that alternative TSSs are more pervasive than expected and implies our strategy could position them at an unprecedented sensitivity. It would be helpful for elucidating their biological insights in future.

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Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean

PeerJ ◽

10.7717/peerj.6354 ◽

2019 ◽

Vol 7 ◽

pp. e6354 ◽

Cited By ~ 6

Author(s):

Zhi Zou ◽

Xicai Zhang

Keyword(s):

Transcription Factor ◽

Stress Responses ◽

Castor Bean ◽

Ricinus Communis ◽

Transcriptome Profiling ◽

Evolutionary Analysis ◽

Physic Nut ◽

Transcription Factor Family ◽

Genome Wide ◽

A Genome

DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut (Jatropha curcas) and castor bean (Ricinus communis), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes. Phylogenetic analysis assigned these genes into nine groups representing four subfamilies, and 24 orthologous groups were also proposed based on comparison of physic nut, castor, Arabidopsis and rice Dofs. Conserved microsynteny was observed between physic nut and castor Dof-coding scaffolds, which allowed anchoring of 23 RcDof genes to nine physic nut chromosomes. In contrast to how no recent duplicate was present in castor, two tandem duplications and one gene loss were found in the Dof gene family of physic nut. Global transcriptome profiling revealed diverse patterns of Jc/RcDof genes over various tissues, and key Dof genes involved in flower development and stress response were also identified in physic nut. These findings provide valuable information for further studies of Dof genes in physic nut and castor.

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Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening

Scientific Reports ◽

10.1038/s41598-020-75004-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mary Miyaji ◽

Ryohei Furuta ◽

Osamu Hosoya ◽

Kuniaki Sano ◽

Norikazu Hara ◽

...

Keyword(s):

Model Building ◽

Mapping Technique ◽

Dna Duplexes ◽

Transcription Start Sites ◽

Genome Wide ◽

A Genome ◽

Topo Ii ◽

Type Ii Dna Topoisomerases ◽

Strand Passage ◽

Chromatin Opening

Abstract Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T- segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be derived from distant sites on the same chromosome. Due to lack of proper methodology, however, no direct evidence has been described so far. The beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. Here we devise a genome-wide mapping technique (eTIP-seq) for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It revealed that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that topo IIβ acts on crossovers to unknot the intertwined DSP sites, leading to chromatin decondensation.

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