IU Indianapolis ScholarWorks :: Browsing by Subject "Chromatin"

Browsing by Subject "Chromatin"

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Adipocyte-Specific ATAC-Seq with Adipose Tissues Using Fluorescence-Activated Nucleus Sorting
(MyJove Corporation, 2023-03-17) Kim, Kyungchan; Taleb, Solaema; So, Jisun; Wann, Jamie; Roh, Hyun Cheol; Biochemistry and Molecular Biology, School of Medicine
Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is a robust technique that enables genome-wide chromatin accessibility profiling. This technique has been useful for understanding the regulatory mechanisms of gene expression in a range of biological processes. Although ATAC-seq has been modified for different types of samples, there have not been effective modifications of ATAC-seq methods for adipose tissues. Challenges with adipose tissues include the complex cellular heterogeneity, large lipid content, and high mitochondrial contamination. To overcome these problems, we have developed a protocol that allows adipocyte-specific ATAC-seq by employing fluorescence-activated nucleus sorting with adipose tissues from the transgenic reporter Nuclear tagging and Translating Ribosome Affinity Purification (NuTRAP) mouse. This protocol produces high-quality data with minimal wasted sequencing reads while reducing the amount of nucleus input and reagents. This paper provides detailed step-by-step instructions for the ATAC-seq method validated for the use of adipocyte nuclei isolated from mouse adipose tissues. This protocol will aid in the investigation of chromatin dynamics in adipocytes upon diverse biological stimulations, which will allow for novel biological insights.
AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency
(Oxford University Press, 2022) Jafari, Elham; Johnson, Travis; Wang, Yue; Liu, Yunlong; Huang, Kun; Wang, Yijie; Biostatistics and Health Data Science, School of Medicine
Motivation: The integrative analysis of single-cell gene expression and chromatin accessibility measurements is essential for revealing gene regulation, but it is one of the key challenges in computational biology. Gene expression and chromatin accessibility are measurements from different modalities, and no common features can be directly used to guide integration. Current state-of-the-art methods lack practical solutions for finding heterogeneous clusters. However, previous methods might not generate reliable results when cluster heterogeneity exists. More importantly, current methods lack an effective way to select hyper-parameters under an unsupervised setting. Therefore, applying computational methods to integrate single-cell gene expression and chromatin accessibility measurements remains difficult. Results: We introduce AIscEA-Alignment-based Integration of single-cell gene Expression and chromatin Accessibility-a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency. AIscEA first defines a ranked similarity score to quantify the biological consistency between cell clusters across measurements. AIscEA then uses the ranked similarity score and a novel permutation test to identify cluster alignment across measurements. AIscEA further utilizes graph alignment for the aligned cell clusters to align the cells across measurements. We compared AIscEA with the competing methods on several benchmark datasets and demonstrated that AIscEA is highly robust to the choice of hyper-parameters and can better handle the cluster heterogeneity problem. Furthermore, AIscEA significantly outperforms the state-of-the-art methods when integrating real-world SNARE-seq and scMultiome-seq datasets in terms of integration accuracy. Availability and implementation: AIscEA is available at https://figshare.com/articles/software/AIscEA_zip/21291135 on FigShare as well as {https://github.com/elhaam/AIscEA} onGitHub.
Analysis of differentiation capacity of Cfp1 null embyronic stem cells
(2014) Bowen, Tamara R.; Skalnik, David Gordon; Marrs, James; Chang, Hua-Chen
Epigenetics is defined as “the study of stable, often heritable, changes that influence gene expression that are not mediated by DNA sequence” (Fingerman et al., 2013). Epigenetic marks such as covalent histone modifications and DNA methylation are important for maintaining chromatin structure and epigenetic inheritance. Several proteins have been found to bind and/ or regulate epigenetic marks. One such protein, CXXC finger protein 1 (Cfp1) is an important chromatin regulator that binds to unmethylated CpG islands. It has been found to be essential for mammalian development. Mice lacking Cfp1 exhibit an embryonic- lethal phenotype. However, the function of Cfp1 can be studied using Cfp1 Null mouse ES cells, which are viable. Thus far, Cfp1 has been shown to be important for cell growth, cytosine methylation, histone modifications, subnuclear localization of Set1A histone H3K4 methyltransferase, and cellular differentiation. When Cfp1 Null ES cells are induced to differentiate by removal of Leukemia Inhibitory Factor (LIF), the cells are not able to turn off pluripotency markers such as Oct4 and alkaline phosphatase and fail to express differentiation markers such as Gata4 and Brachyury. In this study, we used established protocols to further examine the differentiation capacity of Cfp1 Null cells. Specifically, we tested the ability of Cfp1 Null ES cells to retain stem cell properties in the absence of LIF, differentiate into cardiomyocytes in the presence of TGF-β2 and differentiate into neuron precursors in the presence of retinoic acid (RA). While the differentiation effects of RA were inconclusive, Null cells were able to start differentiating in the absence of LIF, either as individual cells or EBs, and the presence of TGF-β2 when seeded on gelatin coated tissue culture dishes. However, no difference was seen between cells treated without LIF and those treated with TGF-β2. In both conditions, only a small portion of cells were able to differentiate, while the majority of the cell population retained stem cell characteristics. Cell growth and the differentiation capacity of Cfp1 Null cells were also compromised in comparison to WT cells. Thus, further supporting the need for the correct epigenetic patterns maintained by Cfp1 during cellular differentiation.
BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms
(Elsevier, 2020-12-03) Barish, Scott; Barakat, Tahsin Stefan; Michel, Brittany C.; Mashtalir, Nazar; Phillips, Jennifer B.; Valencia, Alfredo M.; Ugur, Berrak; Wegner, Jeremy; Scott, Tiana M.; Bostwick, Brett; Murdock, David R.; Dai, Hongzheng; Perenthaler, Elena; Nikoncuk, Anita; van Slegtenhorst, Marjon; Brooks, Alice S.; Keren, Boris; Nava, Caroline; Mignot, Cyril; Douglas, Jessica; Rodan, Lance; Nowak, Catherine; Ellard, Sian; Stals, Karen; Lynch, Sally Ann; Faoucher, Marie; Lesca, Gaetan; Edery, Patrick; Engleman, Kendra L.; Zhou, Dihong; Thiffault, Isabelle; Herriges, John; Gass, Jennifer; Louie, Raymond J.; Stolerman, Elliot; Washington, Camerun; Vetrini, Francesco; Otsubo, Aiko; Pratt, Victoria M.; Conboy, Erin; Treat, Kayla; Shannon, Nora; Camacho, Jose; Wakeling, Emma; Yuan, Bo; Chen, Chun-An; Rosenfeld, Jill A.; Westerfield, Monte; Wangler, Michael; Yamamoto, Shinya; Kadoch, Cigall; Scott, Daryl A.; Bellen, Hugo J.; Medical and Molecular Genetics, School of Medicine
SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.
Canonical histone H2Ba and H2A.X dimerize in an opposite genomic localization to H2A.Z/H2B.Z dimers in Toxoplasma gondii
(Elsevier, 2014-10) Bogado, Silvina S.; Dalmasso, Carolina; Ganuza, Agustina; Kim, Kami; Sullivan, William J., Jr.; Angel, Sergio O.; Vanagas, Laura; Department of Pharmacology and Toxicology, IU School of Medicine
Histone H2Ba of Toxoplasma gondii was expressed as recombinant protein (rH2Ba) and used to generate antibody in mouse that is highly specific. Antibody recognizing rH2Ba detects a single band in tachyzoite lysate of the expected molecular weight (12kDa). By indirect immunofluorescence (IFA) in in vitro grown tachyzoites and bradyzoites, the signal was detected only in the parasite nucleus. The nucleosome composition of H2Ba was determined through co-immunoprecipitation assays. H2Ba was detected in the same immunocomplex as H2A.X, but not with H2A.Z. Through chromatin immunoprecipitation (ChIP) assays and qPCR, it was observed that H2Ba is preferentially located at promoters of inactive genes and silent regions, accompanying H2A.X and opposed to H2A.Z/H2B.Z dimers.
Characterization of protein arginine methyltransferase of TgPRMT5 in Toxoplasma gondii
(Springer Nature, 2019-05-08) Liu, Min; Li, Fen-Xiang; Li, Chun-Yuan; Li, Xiao-Cong; Chen, Long-Fei; Wu, Kun; Yang, Pei-Liang; Lai, Zhi-Fa; Liu, Ting-kai; Sullivan, William J., Jr.; Cui, Liwang; Chen, Xiao-Guang; Pharmacology and Toxicology, School of Medicine
BACKGROUND: Protein arginine methylation is a prevalent post-translational modification. The protein arginine methyltransferase family (PRMT) is involved in many cellular processes in eukaryotes, including transcriptional regulation, epigenetic regulation, RNA metabolism, and DNA damage repair. Toxoplasma gondii, an opportunistic protozoan parasite, encodes five conserved PRMTs. PRMT5 is thought to be responsible for substantial PRMT activity in T. gondii; however, it has not yet been characterized. METHODS: We tagged the 3' end of the endogenous TgPRMT5 genomic locus with sequence encoding a 3X hemagglutinin (HA) epitope. IFA and WB were performed to check the expression and subcellular localization of TgPRMT5 in tachyzoites and bradyzoites. In vitro methylation assays were performed to determine whether endogenous TgPRMT5 has arginine methyltransferase activity. RESULTS: IFA and WB results showed that T. gondii PRMT5 (TgPRMT5) was localized in the cytoplasm in the tachyzoite stage; however, it shifts largely to the nuclear compartment in the bradyzoite stage. The in vitro methylation showed that TgPRMT5 has authentic type II PRMT activity and forms monomethylarginines and symmetric dimethylarginines. CONCLUSIONS: We determined the expression and cellular localization of TgPRMT5 in tachyzoites and bradyzoites and confirmed its type II PRMT activity. We demonstrated the major changes in expression and cellular localization of TgPRMT5 during the tachyzoite and bradyzoite stages in T. gondii. Our findings suggest that TgPRMT5 protein may be involved in tachyzoite-bradyzoite transformation.
Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1
(Impact Journals, 2018-07-27) Hankey, William; Chen, Zhong; Bergman, Maxwell J.; Fernandez, Max O.; Hancioglu, Baris; Lan, Xun; Jegga, Anil G.; Zhang, Jie; Jin, Victor X.; Aronow, Bruce J.; Wang, Qianben; Groden, Joanna; Medical and Molecular Genetics, School of Medicine
Mutation of the APC gene occurs in a high percentage of colorectal tumors and is a central event driving tumor initiation in the large intestine. The APC protein performs multiple tumor suppressor functions including negative regulation of the canonical WNT signaling pathway by both cytoplasmic and nuclear mechanisms. Published reports that APC interacts with β-catenin in the chromatin fraction to repress WNT-activated targets have raised the possibility that chromatin-associated APC participates more broadly in mechanisms of transcriptional control. This screening study has used chromatin immunoprecipitation and next-generation sequencing to identify APC-associated genomic regions in colon cancer cell lines. Initial target selection was performed by comparison and statistical analysis of 3,985 genomic regions associated with the APC protein to whole transcriptome sequencing data from APC-deficient and APC-wild-type colon cancer cells, and two types of murine colon adenomas characterized by activated Wnt signaling. 289 transcripts altered in expression following APC loss in human cells were linked to APC-associated genomic regions. High-confidence targets additionally validated in mouse adenomas included 16 increased and 9 decreased in expression following APC loss, indicating that chromatin-associated APC may antagonize canonical WNT signaling at both WNT-activated and WNT-repressed targets. Motif analysis and comparison to ChIP-seq datasets for other transcription factors identified a prevalence of binding sites for the TCF7L2 and AP-1 transcription factors in APC-associated genomic regions. Our results indicate that canonical WNT signaling can collaborate with or antagonize the AP-1 transcription factor to fine-tune the expression of shared target genes in the colorectal epithelium. Future therapeutic strategies for APC-deficient colorectal cancers might be expanded to include agents targeting the AP-1 pathway.
Decoding regulatory associations of G-quadruplex with epigenetic and transcriptomic functional components
(Frontiers Media, 2022-08-25) Fang, Shuyi; Liu, Sheng; Yang, Danzhou; Yang, Lei; Hu, Chang-Deng; Wan, Jun; BioHealth Informatics, School of Informatics and Computing
G-quadruplex (G4) has been previously observed to be associated with gene expression. In this study, we performed integrative analysis on G4 multi-omics data from in-silicon prediction and ChIP-seq in human genome. Potential G4 sites were classified into three distinguished groups, such as one group of high-confidence G4-forming locations (G4-II) and groups only containing either ChIP-seq detected G4s (G4-I) or predicted G4 motif candidates (G4-III). We explored the associations of different-confidence G4 groups with other epigenetic regulatory elements, including CpG islands, chromatin status, enhancers, super-enhancers, G4 locations compared to the genes, and DNA methylation. Our elastic net regression model revealed that G4 structures could correlate with gene expression in two opposite ways depending on their locations to the genes as well as G4-forming DNA strand. Some transcription factors were identified to be over-represented with G4 emergence. The motif analysis discovered distinct consensus sequences enriched in the G4 feet, the flanking regions of two groups of G4s. We found high GC content in the feet of high-confidence G4s (G4-II) when compared to high TA content in solely predicted G4 feet of G4-III. Overall, we uncovered the comprehensive associations of G4 formations or predictions with other epigenetic and transcriptional elements which potentially coordinate gene transcription.
Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity
(Elsevier, 2019-03-12) Aho, Erin R.; Wang, Jing; Gogliotti, Rocco D.; Howard, Gregory C.; Phan, Jason; Acharya, Pankaj; Macdonald, Jonathan D.; Cheng, Ken; Lorey, Shelly L.; Lu, Bin; Wenzel, Sabine; Foshage, Audra M.; Alvarado, Joseph; Wang, Feng; Shaw, J. Grace; Zhao, Bin; Weissmiller, April M.; Thomas, Lance R.; Vakoc, Christopher R.; Hall, Matthew D.; Hiebert, Scott W.; Liu, Qi; Stauffer, Shaun R.; Fesik, Stephen W.; Tansey, William P.; Biochemistry and Molecular Biology, School of Medicine
The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility. Here, by the discovery of potent WIN site inhibitors, we demonstrate that the WIN site links WDR5 to chromatin at a small cohort of loci, including a specific subset of ribosome protein genes. WIN site inhibitors rapidly displace WDR5 from chromatin and decrease the expression of associated genes, causing translational inhibition, nucleolar stress, and p53 induction. Our studies define a mode by which WDR5 engages chromatin and forecast that WIN site blockade could have utility against multiple cancer types.
Epigenetic and lncRNA regulation of cardiac pathophysiology
(Elsevier, 2016-03-09) Chang, Ching-Pin; Han, Pei; Medicine, School of Medicine
Our developmental studies provide an insight into the pathogenesis of heart failure in adults. These studies reveal a mechanistic link between fetal cardiomyocytes and pathologically stressed adult cardiomyocytes at the level of chromatin regulation. In embryos, chromatin-regulating factors within the cardiomyocytes respond to developmental signals to program cardiac gene expression to promote cell proliferation and inhibit premature cell differentiation. In the neonatal period, the activity of these developmental chromatin regulators is quickly turned off in cardiomyocytes, coinciding with the cessation of cell proliferation and advance in cell differentiation toward adult maturity. When the mature hearts are pathologically stressed, those chromatin regulators essential for cardiomyocyte development in embryos are reactivated, triggering gene reprogramming to a fetal-like state and pathological cardiac hypertrophy. Furthermore, in the study of chromatin regulation and cardiac gene expression, we identified a long noncoding RNA that interacts with chromatin remodeling factor to regulate the cardiac response to environmental changes. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

Browsing by Subject "Chromatin"

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