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4. Prediction of histone post-translational modification patterns based on nascent transcription data.

Author

Wang, Zhong, Chivu, Alexandra G, Choate, Lauren A, Rice, Edward J, Miller, Donald C, Chu, Tinyi, Chou, Shao-Pei, Kingsley, Nicole B, Petersen, Jessica L, Finno, Carrie J, Bellone, Rebecca R, Antczak, Douglas F, Lis, John T, and Danko, Charles G

Subjects
Chromatin, Nucleosomes, Histones, Protein Processing, Post-Translational, Histone Code, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The role of histone modifications in transcription remains incompletely understood. Here, we examine the relationship between histone modifications and transcription using experimental perturbations combined with sensitive machine-learning tools. Transcription predicted the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. Blocking transcription rapidly removed two punctate marks, H3K4me3 and H3K27ac, from chromatin indicating that transcription is required for active histone modifications. Transcription was also required for maintenance of H3K27me3, consistent with a role for RNA in recruiting PRC2. A subset of DNase-I-hypersensitive sites were refractory to prediction, precluding models where transcription initiates pervasively at any open chromatin. Our results, in combination with past literature, support a model in which active histone modifications serve a supportive, rather than an essential regulatory, role in transcription.

Published
2022

12. Supplementary Figure from SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis

Author

Leung, Wilfred, primary, Teater, Matt, primary, Durmaz, Ceyda, primary, Meydan, Cem, primary, Chivu, Alexandra G., primary, Chadburn, Amy, primary, Rice, Edward J., primary, Muley, Ashlesha, primary, Camarillo, Jeannie M., primary, Arivalagan, Jaison, primary, Li, Ziyi, primary, Flowers, Christopher R., primary, Kelleher, Neil L., primary, Danko, Charles G., primary, Imielinski, Marcin, primary, Dave, Sandeep S., primary, Armstrong, Scott A., primary, Mason, Christopher E., primary, and Melnick, Ari M., primary

Published
2023
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13. Data from SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis

Author

Leung, Wilfred, primary, Teater, Matt, primary, Durmaz, Ceyda, primary, Meydan, Cem, primary, Chivu, Alexandra G., primary, Chadburn, Amy, primary, Rice, Edward J., primary, Muley, Ashlesha, primary, Camarillo, Jeannie M., primary, Arivalagan, Jaison, primary, Li, Ziyi, primary, Flowers, Christopher R., primary, Kelleher, Neil L., primary, Danko, Charles G., primary, Imielinski, Marcin, primary, Dave, Sandeep S., primary, Armstrong, Scott A., primary, Mason, Christopher E., primary, and Melnick, Ari M., primary

Published
2023
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14. Evolution of promoter-proximal pausing enabled a new layer of transcription control

Author

Chivu, Alexandra G., primary, Abuhashem, Abderhman, additional, Barshad, Gilad, additional, Rice, Edward J., additional, Leger, Michelle M., additional, Vill, Albert C., additional, Wong, Wilfred, additional, Brady, Rebecca, additional, Smith, Jeramiah J., additional, Wikramanayake, Athula H., additional, Arenas-Mena, César, additional, Brito, Ilana L., additional, Ruiz-Trillo, Iñaki, additional, Hadjantonakis, Anna-Katerina, additional, Lis, John T., additional, Lewis, James J., additional, and Danko, Charles G., additional

Published
2023
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15. Additional file 2 of GDNF-RET signaling and EGR1 form a positive feedback loop that promotes tamoxifen resistance via cyclin D1

Author

Marks, Brooke A., Pipia, Ilissa M., Mukai, Chinatsu, Horibata, Sachi, Rice, Edward J., Danko, Charles G., and Coonrod, Scott A.

Abstract

Additional file 2: Figure S1. Cell viability of TamSEGR1-OE and TamSVc cells in the presence of 1uM TAM. Data are represented as mean ± SEM. Figure S2. Western blot from Fig. 4 showing edges of membrane. Figure S3. Cell viability assay in TamS cells showing the four treatment controls corresponding to Fig. 7 (vehicle, rGDNF, TAM, and Palbociclib treatment).

Published
2023
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17. RNA polymerase II and PARP1 shape enhancer-promoter contacts

Author

Barshad, Gilad, primary, Lewis, James J., additional, Chivu, Alexandra G., additional, Abuhashem, Abderhman, additional, Krietenstein, Nils, additional, Rice, Edward J., additional, Rando, Oliver J., additional, Hadjantonakis, Anna-Katerina, additional, and Danko, Charles G., additional

Published
2022
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24. SETD2 Haploinsufficiency Enhances Germinal Center–Associated AICDA Somatic Hypermutation to Drive B-cell Lymphomagenesis

Author

Leung, Wilfred, primary, Teater, Matt, additional, Durmaz, Ceyda, additional, Meydan, Cem, additional, Chivu, Alexandra G., additional, Chadburn, Amy, additional, Rice, Edward J., additional, Muley, Ashlesha, additional, Camarillo, Jeannie M., additional, Arivalagan, Jaison, additional, Li, Ziyi, additional, Flowers, Christopher R., additional, Kelleher, Neil L., additional, Danko, Charles G., additional, Imielinski, Marcin, additional, Dave, Sandeep S., additional, Armstrong, Scott A., additional, Mason, Christopher E., additional, and Melnick, Ari M., additional

Published
2022
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25. E-Protein Inhibition in ILC2 Development Shapes the Function of Mature ILC2s during Allergic Airway Inflammation

Author

Barshad, Gilad, primary, Webb, Lauren M., additional, Ting, Hung-An, additional, Oyesola, Oyebola O., additional, Onyekwere, Oluomachi G., additional, Lewis, James J., additional, Rice, Edward J., additional, Matheson, Macy K., additional, Sun, Xiao-Hong, additional, von Moltke, Jakob, additional, Danko, Charles G., additional, and Tait Wojno, Elia D., additional

Published
2022
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27. Additional file 2 of Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Author

Blumberg, Amit, Yixin Zhao, Huang, Yi-Fei, Dukler, Noah, Rice, Edward J., Chivu, Alexandra G., Krumholz, Katie, Danko, Charles G., and Siepel, Adam

Subjects
genetic processes, natural sciences
Abstract

Additional file 2: Figure S1. Correlation of PRO-seq and RNA-seq replicates in K562 cells. Figure S2. Correlation of exonic reads from RNA-seq with either PRO-seq or intronic reads. Figures S3-S4. Scatter plots of PRO-seq vs. RNA-seq for intron-containing (Figure S3) or intron-less (Figure S4) transcription units in K562 cells. Figure S5. Scatter plots of PRO-seq vs. RNA-seq for lincRNAs and protein-coding mRNAs in K562 cells after matching by PRO-seq signal. Figures S6-S7. Scatter plots of PRO-seq vs. RNA-seq for transcription units in K562 cells (Figure S6) or HeLa cells (Figure S7). Figure S8. Scatter plots of PRO-seq vs. RNA-seq for mRNAs and lincRNAs in K562 cells before and after correcting for elongation rate. Figure S9. Intronic half-life vs. TimeLapse-seq half-life. Figure S10. Empirical cumulative distribution functions (eCDFs) for estimated half-lives of predicted targets of miR-125-5p and miR-19-3p vs. non-targets. Figure S11. Correlation of estimated RNA half-lives under various methods. Figure S12. Correlation of PRO-seq-based half-lives (T1/2PR, x-axis) vs. estimates from TimeLapse-seq (T1/2TLS, y-axis) after correcting for elongation rate. Figures S13-S14. SEM results for features of intron-containing (Figure S13) or intron-less (Figure S14) transcription units in K562. Figure S15. Estimated half-lives for intron-containing and intron-less transcription units. Figure S16. SEM results for features of intron-containing transcripts in K562 cells, with and without a correction for elongation rate. Figure S17. Multiple linear regression (MLR) for features of transcription units versus RNA stability in K562 cells. Figures S18-S19. DNA word enrichments in stable transcripts for protein-coding mRNAs (Figure S18) or lincRNAs (Figure S19). Figure S20. G+C content in intervals downstream of the TSS for various classes of transcription units. Figure S21. DNA word enrichments in stable transcripts for eRNAs. Figure S22. DNA methylation in lincRNAs of various stability levels. Figure S23. Sequence Stability Index of intron-containing versus intron-less genes. Figures S24-S25. Sequence Stability Index (SSI) for mRNAs (Figure S24) or lincRNAs (Figure S25) of various stability classes. Figures S26-S27. Histone modification signals for protein-coding mRNAs of various stability classes. Half-live estimations are based on published data (Figure S26) or newly collected data for this study (Figure S27). Figures S28-S29. Estimated SEM coefficients for transcription (λn; top) and half-life (μn; bottom) for 11 histone modifications. It’s assayed by ChIP-seq in the 500 bases (Figure S28) or 1000-1500 bases (Figure S29) downstream of the TSS. Figures S30-S31. Estimated SEM coefficients for transcription (λn; top) and half-life (μn; bottom) for 11 histone modifications. It’s based either on published data (Figure S30) or on the newly collected PRO-seq and RNA-seq data (Figure S31).

Published
2021
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29. Additional file 6 of Identification and prediction of developmental enhancers in sea urchin embryos

Author

Arenas-Mena, César, Miljovska, Sofija, Rice, Edward J., Gurges, Justin, Shashikant, Tanvi, Wang, Zihe, Ercan, Sevinç, and Danko, Charles G.

Subjects
animal structures, fungi, embryonic structures
Abstract

Additional file 6: Fig. S4. Evaluation of models for CRMs overlapping and not overlapping promoters. A, 12 h embryo and, B, 20 h embryo models trained and tested with CRMs not overlapping promoters. C, 12 h embryo and, D, 20 h embryo models trained and tested with CRMs overlapping promoters.

Published
2021
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32. Additional file 7 of Identification and prediction of developmental enhancers in sea urchin embryos

Author

Arenas-Mena, César, Miljovska, Sofija, Rice, Edward J., Gurges, Justin, Shashikant, Tanvi, Wang, Zihe, Ercan, Sevinç, and Danko, Charles G.

Abstract

Additional file 7: Fig. S5. Quantitative prediction of enhancer activity from ATAC and PRO-seq data. Plot of the hold-out predicted and actual reporter expression of linear regression models using ATAC and PRO-seq signal in 12 h and 20 h stages. Violin/Box-plots of R2 values, with the average indicated underneath.

Published
2021
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33. Additional file 8 of Identification and prediction of developmental enhancers in sea urchin embryos

Author

Arenas-Mena, César, Miljovska, Sofija, Rice, Edward J., Gurges, Justin, Shashikant, Tanvi, Wang, Zihe, Ercan, Sevinç, and Danko, Charles G.

Subjects
sense organs, skin and connective tissue diseases
Abstract

Additional file 8: Fig. S6. Summary 12 to 20 h mRNA expression changes of regulatory genes. The fold change in the mRNA expression levels quantified at high resolution for 31 of the 37 genes used in this study [33].

Published
2021
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35. Additional file 4 of Identification and prediction of developmental enhancers in sea urchin embryos

Author

Arenas-Mena, César, Miljovska, Sofija, Rice, Edward J., Gurges, Justin, Shashikant, Tanvi, Wang, Zihe, Ercan, Sevinç, and Danko, Charles G.

Abstract

Additional file 4: Fig. S2. PRO-, Pol II ChIP- and ATAC-seq at onecut, gcm, gatae and delta. A, onecut, the entire region was scanned for enhancer activity by overlapping reporter constructs averaging 2.23 Kb [40]. Similar snapshots are taken for other regulatory genes whose regulatory elements were primarily selected based on evolutionary sequence conservation rather than an unbiased tiling scan.

Published
2021
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36. Additional file 5 of Identification and prediction of developmental enhancers in sea urchin embryos

Author

Arenas-Mena, César, Miljovska, Sofija, Rice, Edward J., Gurges, Justin, Shashikant, Tanvi, Wang, Zihe, Ercan, Sevinç, and Danko, Charles G.

Subjects
fungi, embryonic structures
Abstract

Additional file 5: Fig. S3. The enhancer activity of promoter-overlapping CRMs is independent of their orientation. A, the concurrent orientation of the promoter in the GFP reporter construct and the promoter of promoter-overlapping CRMs could in principle result in transcripts reaching to the coding region of the reporter that could confound CRM driven transcription (red dashed line) with enhancer activity (black dotted line). In both cases the reporter enhancer activity of CRMs containing endogenous promoters should be diminished due to enhancer sharing between both promoters. Correlation of Pol II accumulation at endogenous promoters (purple ovals) and reporter expression is expected for CRMs that contain necessary enhancers and endogenous promoters. B, the difference of expression between CRMs in concurrent and divergent reporter construct orientation is not significant (ns) in 12 and 24 h embryos, Wilcox test p-values of 0.67 and 0.14, respectively.

Published
2021
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40. Accurate imputation of histone modifications using transcription

Author

Wang, Zhong, Chivu, Alexandra G., Choate, Lauren A., Rice, Edward J., Miller, Donald C., Chu, Tinyi, Chou, Shao-Pei, Kingsley, Nicole B., Petersen, Jessica L., Finno, Carrie J., Bellone, Rebecca R., Antczak, Douglas F., and Danko, Charles G.

Abstract

We trained a sensitive machine learning tool to infer the distribution of histone marks using maps of nascent transcription. Transcription captured the variation in active histone marks and complex chromatin states, like bivalent promoters, down to single-nucleosome resolution and at an accuracy that rivaled the correspondence between independent ChIP-seq experiments. The relationship between active histone marks and transcription was conserved in all cell types examined, allowing individual labs to annotate active functional elements in mammals with similar richness as major consortia. Using imputation as an interpretative tool uncovered cell-type specific differences in how the PRC2-dependent repressive mark, H3K27me3, corresponds to transcription, and revealed that transcription initiation requires both chromatin accessibility and an active chromatin environment demonstrating that initiation is less promiscuous than previously thought.

Published
2020
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41. Additional file 3 of Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, Eunju Choi, Sams, Kelly L., Klampen, Elena Zu, Anguish, Lynne, Marks, Brooke A., Rice, Edward J., Wang, Zhong, Choate, Lauren A., Shao-Pei Chou, Kato, Yukinari, Miller, Andrew D., Danko, Charles G., and Coonrod, Scott A.

Abstract

Additional file 3. FS1. Trichrome staining quantification.

Published
2020
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42. Additional file 7 of Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, Eunju Choi, Sams, Kelly L., Klampen, Elena Zu, Anguish, Lynne, Marks, Brooke A., Rice, Edward J., Wang, Zhong, Choate, Lauren A., Shao-Pei Chou, Kato, Yukinari, Miller, Andrew D., Danko, Charles G., and Coonrod, Scott A.

Subjects
body regions, integumentary system, embryonic structures, cardiovascular system, eye diseases
Abstract

Additional file 7. FS5. Masson’s trichrome staining and IHC on serial sections from case B176 (HSA).

Published
2020
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43. Additional file 9 of Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, Eunju Choi, Sams, Kelly L., Klampen, Elena Zu, Anguish, Lynne, Marks, Brooke A., Rice, Edward J., Wang, Zhong, Choate, Lauren A., Shao-Pei Chou, Kato, Yukinari, Miller, Andrew D., Danko, Charles G., and Coonrod, Scott A.

Abstract

Additional file 9. FS7. Original gel images for Fig. 4b.

Published
2020
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44. Additional file 4 of Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, Eunju Choi, Sams, Kelly L., Klampen, Elena Zu, Anguish, Lynne, Marks, Brooke A., Rice, Edward J., Wang, Zhong, Choate, Lauren A., Shao-Pei Chou, Kato, Yukinari, Miller, Andrew D., Danko, Charles G., and Coonrod, Scott A.

Abstract

Additional file 4. FS2. ChRO-seq counts on PDPN and LAMA4 gene bodies.

Published
2020
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45. Additional file 1 of Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, Eunju Choi, Sams, Kelly L., Klampen, Elena Zu, Anguish, Lynne, Marks, Brooke A., Rice, Edward J., Wang, Zhong, Choate, Lauren A., Shao-Pei Chou, Kato, Yukinari, Miller, Andrew D., Danko, Charles G., and Coonrod, Scott A.

Abstract

Additional file 1. Supplemental methods and figure legends.

Published
2020
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47. A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)

Author

Judd, Julius, primary, Wojenski, Luke A., additional, Wainman, Lauren M., additional, Tippens, Nathaniel D., additional, Rice, Edward J., additional, Dziubek, Alexis, additional, Villafano, Geno J., additional, Wissink, Erin M., additional, Versluis, Philip, additional, Bagepalli, Lina, additional, Shah, Sagar R., additional, Mahat, Dig B., additional, Tome, Jacob M., additional, Danko, Charles G., additional, Lis, John T., additional, and Core, Leighton J., additional

Published
2020
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48. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Mukai, Chinatsu, primary, Choi, Eunju, additional, Sams, Kelly L., additional, Zu Klampen, Elena, additional, Anguish, Lynne, additional, Marks, Brooke A., additional, Rice, Edward J., additional, Wang, Zhong, additional, Choate, Lauren A., additional, Chou, Shao-Pei, additional, Kato, Yukinari, additional, Miller, Andrew, additional, Danko, Charles G., additional, and Coonrod, Scott A., additional

Published
2020
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49. Interdependence between histone marks and steps in Pol II transcription

Author

Wang, Zhong, primary, Chivu, Alexandra G., additional, Choate, Lauren A., additional, Rice, Edward J., additional, Miller, Donald C., additional, Chu, Tinyi, additional, Chou, Shao-Pei, additional, Kingsley, Nicole B., additional, Petersen, Jessica L., additional, Finno, Carrie J., additional, Bellone, Rebecca R., additional, Antczak, Douglas F., additional, Lis, John T., additional, and Danko, Charles G., additional

Published
2020
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50. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis

Author

Author), Chinatsu Mukai(New Corresponding, primary, Choi, Eunju, additional, Sams, Kelly L., additional, Zu Klampen, Elena, additional, Anguish, Lynne, additional, Marks, Brooke A., additional, Rice, Edward J., additional, Wang, Zhong, additional, Choate, Lauren A., additional, Chou, Shao-Pei, additional, Kato, Yukinari, additional, Miller, Andrew, additional, Danko, Charles G., additional, and Author), Scott A. Coonrod(Former Corresponding, additional

Published
2020
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