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Article ; Online: ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors.

Boyd, Joseph / Rodriguez, Princess / Schjerven, Hilde / Frietze, Seth

2021 Volume 14, Issue 1, Page(s) 366

Abstract: Objective: Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio ... ...

Abstract	Objective: Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio using fewer number of cells compared to ChIP-seq. The results from CUT&RUN and other related sequence enrichment assays requires comprehensive quality control (QC) and comparative analysis of data quality across replicates. While several computational tools currently exist for read mapping and analysis, a systematic reporting of data quality is lacking. Our aims were to (1) compare methods for using frozen versus fresh cells for CUT&RUN and (2) to develop an easy-to-use pipeline for assessing data quality. Results: We compared a workflow for CUT&RUN with fresh and frozen samples, and present an R package called ssvQC for quality control and comparison of data quality derived from CUT&RUN and other enrichment-based sequence data. Using ssvQC, we evaluate results from different CUT&RUN protocols for transcription factors and histone modifications from fresh and frozen tissue samples. Overall, this process facilitates evaluation of data quality across datasets and permits inspection of peak calling analysis, replicate analysis of different data types. The package ssvQC is readily available at https://github.com/FrietzeLabUVM/ssvQC .
MeSH term(s)	Chromatin Immunoprecipitation ; High-Throughput Nucleotide Sequencing ; Histone Code ; Quality Control ; Transcription Factors ; Workflow
Chemical Substances	Transcription Factors
Language	English
Publishing date	2021-09-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/s13104-021-05781-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Artifact Removal in Histopathology Images

Dahan, Cameron / Christodoulidis, Stergios / Vakalopoulou, Maria / Boyd, Joseph

2022

Abstract: In the clinical setting of histopathology, whole-slide image (WSI) artifacts frequently arise, distorting regions of interest, and having a pernicious impact on WSI analysis. Image-to-image translation networks such as CycleGANs are in principle capable ... ...

Abstract	In the clinical setting of histopathology, whole-slide image (WSI) artifacts frequently arise, distorting regions of interest, and having a pernicious impact on WSI analysis. Image-to-image translation networks such as CycleGANs are in principle capable of learning an artifact removal function from unpaired data. However, we identify a surjection problem with artifact removal, and propose an weakly-supervised extension to CycleGAN to address this. We assemble a pan-cancer dataset comprising artifact and clean tiles from the TCGA database. Promising results highlight the soundness of our method. Comment: Corrected typos, small modification of Figure 1 (+ reflected in Section 2.1), results unchanged
Keywords	Electrical Engineering and Systems Science - Image and Video Processing ; Computer Science - Computer Vision and Pattern Recognition
Publishing date	2022-11-29
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Thyroid hormone dependent transcriptional programming by TRβ requires SWI/SNF chromatin remodelers.

Gillis, Noelle E / Boyd, Joseph R / Tomczak, Jennifer A / Frietze, Seth / Carr, Frances E

Nucleic acids research

2022 Volume 50, Issue 3, Page(s) 1382–1395

Abstract: Transcriptional regulation in response to thyroid hormone (3,5,3'-triiodo-l-thyronine, T3) is a dynamic and cell-type specific process that maintains cellular homeostasis and identity in all tissues. However, our understanding of the mechanisms of ... ...

Abstract	Transcriptional regulation in response to thyroid hormone (3,5,3'-triiodo-l-thyronine, T3) is a dynamic and cell-type specific process that maintains cellular homeostasis and identity in all tissues. However, our understanding of the mechanisms of thyroid hormone receptor (TR) actions at the molecular level are actively being refined. We used an integrated genomics approach to profile and characterize the cistrome of TRβ, map changes in chromatin accessibility, and capture the transcriptomic changes in response to T3 in normal human thyroid cells. There are significant shifts in TRβ genomic occupancy in response to T3, which are associated with differential chromatin accessibility, and differential recruitment of SWI/SNF chromatin remodelers. We further demonstrate selective recruitment of BAF and PBAF SWI/SNF complexes to TRβ binding sites, revealing novel differential functions in regulating chromatin accessibility and gene expression. Our findings highlight three distinct modes of TRβ interaction with chromatin and coordination of coregulator activity.
MeSH term(s)	Chromatin/genetics ; Chromatin Assembly and Disassembly ; Gene Expression Regulation ; Humans ; Thyroid Hormone Receptors beta/genetics ; Thyroid Hormone Receptors beta/metabolism ; Thyroid Hormones ; Transcription Factors/metabolism
Chemical Substances	Chromatin ; Thyroid Hormone Receptors beta ; Thyroid Hormones ; Transcription Factors
Language	English
Publishing date	2022-01-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab1287
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Article ; Online: peaksat: an R package for ChIP-seq peak saturation analysis.

Boyd, Joseph R / Gao, Cong / Quinn, Kathleen / Fritz, Andrew / Stein, Janet / Stein, Gary / Glass, Karen / Frietze, Seth

BMC genomics

2023 Volume 24, Issue 1, Page(s) 43

Abstract: Background: Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental ... ...

Abstract	Background: Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to variable sequencing depth requirements across experimental conditions, it can be challenging to determine optimal sequencing depth, particularly for projects involving multiple targets or cell types. Results: We developed the peaksat R package to provide target read depth estimates for epigenomic experiments based on the analysis of peak saturation curves. We applied peaksat to establish the distinctive read depth requirements for ChIP-seq studies of histone modifications in different cell lines. Using peaksat, we were able to estimate the target read depth required per library to obtain high-quality peak calls for downstream analysis. In addition, peaksat was applied to other sequence-enrichment methods including CUT&RUN and ATAC-seq. Conclusion: peaksat addresses a need for researchers to make informed decisions about whether their sequencing data has been generated to an adequate depth and subsequently sufficient meaningful peaks, and failing that, how many more reads would be required per library. peaksat is applicable to other sequence-based methods that include calling peaks in their analysis.
MeSH term(s)	Chromatin Immunoprecipitation Sequencing/methods ; Sequence Analysis, DNA/methods ; Gene Library ; High-Throughput Nucleotide Sequencing
Language	English
Publishing date	2023-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09109-7
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Article ; Online: Ikaros Regulates microRNA Networks in Acute Lymphoblastic Leukemia

Kogut, Sophie / Paculova, Hana / Rodriguez, Princess / Boyd, Joseph / Richman, Alyssa / Palaria, Amrita / Schjerven, Hilde / Frietze, Seth

Epigenomes. 2022 Oct. 19, v. 6, no. 4

2022

Abstract: The hematopoietic transcription factor Ikaros (IKZF1) regulates normal B cell development and functions as a tumor suppressor in precursor B cell acute lymphoblastic leukemia (B-ALL). MicroRNAs (miRNAs) are small regulatory RNAs that through post- ... ...

Abstract	The hematopoietic transcription factor Ikaros (IKZF1) regulates normal B cell development and functions as a tumor suppressor in precursor B cell acute lymphoblastic leukemia (B-ALL). MicroRNAs (miRNAs) are small regulatory RNAs that through post-transcriptional gene regulation play critical roles in intracellular processes including cell growth in cancer. However, the role of Ikaros in the regulation of miRNA expression in developing B cells is unknown. In this study, we examined the Ikaros-regulated miRNA targets using human IKZF1-mutated Ph⁺ B-ALL cell lines. Inducible expression of wild-type Ikaros (the Ik1 isoform) caused B-ALL growth arrest and exit from the cell cycle. Global miRNA expression analysis revealed a total of 31 miRNAs regulated by IK1, and ChIP-seq analysis showed that Ikaros bound to several Ik1-responsive miRNA genes. Examination of the prognostic significance of miRNA expression in B-ALL indicate that the IK1-regulated miRNAs hsa-miR-26b, hsa-miR-130b and hsa-miR-4649 are significantly associated with outcome in B-ALL. Our findings establish a potential regulatory circuit between the tumor-suppressor Ikaros and the oncogenic miRNA networks in IKZF1-mutated B-ALL. These results indicate that Ikaros regulates the expression of a subset of miRNAs, of which several may contribute to B-ALL growth.
Keywords	B-lymphocytes ; cell cycle ; cell growth ; chromatin immunoprecipitation ; genes ; humans ; lymphocytic leukemia ; microRNA ; transcription factors
Language	English
Dates of publication	2022-1019
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ISSN	2075-4655
DOI	10.3390/epigenomes6040037
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: Structured State Space Models for Multiple Instance Learning in Digital Pathology

Fillioux, Leo / Boyd, Joseph / Vakalopoulou, Maria / Cournède, Paul-Henry / Christodoulidis, Stergios

2023

Abstract: Multiple instance learning is an ideal mode of analysis for histopathology data, where vast whole slide images are typically annotated with a single global label. In such cases, a whole slide image is modelled as a collection of tissue patches to be ... ...

Abstract	Multiple instance learning is an ideal mode of analysis for histopathology data, where vast whole slide images are typically annotated with a single global label. In such cases, a whole slide image is modelled as a collection of tissue patches to be aggregated and classified. Common models for performing this classification include recurrent neural networks and transformers. Although powerful compression algorithms, such as deep pre-trained neural networks, are used to reduce the dimensionality of each patch, the sequences arising from whole slide images remain excessively long, routinely containing tens of thousands of patches. Structured state space models are an emerging alternative for sequence modelling, specifically designed for the efficient modelling of long sequences. These models invoke an optimal projection of an input sequence into memory units that compress the entire sequence. In this paper, we propose the use of state space models as a multiple instance learner to a variety of problems in digital pathology. Across experiments in metastasis detection, cancer subtyping, mutation classification, and multitask learning, we demonstrate the competitiveness of this new class of models with existing state of the art approaches. Our code is available at https://github.com/MICS-Lab/s4_digital_pathology.
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning
Subject code	006
Publishing date	2023-06-27
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ikaros Regulates microRNA Networks in Acute Lymphoblastic Leukemia.

Kogut, Sophie / Paculova, Hana / Rodriguez, Princess / Boyd, Joseph / Richman, Alyssa / Palaria, Amrita / Schjerven, Hilde / Frietze, Seth

Epigenomes

2022 Volume 6, Issue 4

Abstract: The hematopoietic transcription factor Ikaros ( ...

Abstract	The hematopoietic transcription factor Ikaros (
Language	English
Publishing date	2022-10-19
Publishing country	Switzerland
Document type	Journal Article
ISSN	2075-4655
ISSN (online)	2075-4655
DOI	10.3390/epigenomes6040037
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Article: Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes.

Boyd, Joseph / Nadeau, Emily A W / Kogut, Sophie / Rodriguez, Princess / Munteneau, Daniel / O'Leary, Thomas / Filler, Sara / Lockwood, Brent / Cahan, Sara Helms / Frietze, Seth

Research square

2023

Abstract: Background: RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. ... ...

Abstract	Background: RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms. Results: In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in Conclusions: Our study introduces a versatile transcriptomic analysis pipeline, TAP, designed to uniformly process RNA-seq data from any organism with a reference genome. It also highlights the significance of selecting an appropriate RNA-seq library protocol tailored to the specific research context. Background: Advances in next generation sequencing (NGS) technologies enable the comprehensive analysis of genetic sequences of organisms in a relatively cost-effective manner [1, 2]. Among these technologies, RNA-sequencing (RNA-seq) has emerged as a preeminent method to study fundamental biological mechanisms at the level of cells, tissues, and whole organisms. RNA-seq enables the detection and quantification of various RNA populations, including messenger RNA (mRNA) and various species of non-coding RNA, such as long non-coding RNA (lncRNA), as well as an assessment of features including splice junctions in RNA.
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3390128/v1
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Article: Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle.

Fritz, Andrew J / Ghule, Prachi N / Toor, Rabail / Dillac, Louis / Perelman, Jonah / Boyd, Joseph / Lian, Jane B / Gordon, Johnathan A R / Frietze, Seth / Van Wijnen, Andre / Stein, Janet L / Stein, Gary S

Critical reviews in eukaryotic gene expression

2023 Volume 33, Issue 3, Page(s) 85–97

Abstract: Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, ... ...

Abstract	Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
MeSH term(s)	Histones/metabolism ; Chromatin ; Cyclin E/genetics ; Cyclin E/metabolism ; Nuclear Proteins/genetics ; Cell Cycle Proteins/genetics ; Cell Cycle/genetics ; Epigenesis, Genetic
Chemical Substances	Histones ; Chromatin ; Cyclin E ; Nuclear Proteins ; Cell Cycle Proteins
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1071345-1
ISSN	1045-4403
ISSN	1045-4403
DOI	10.1615/CritRevEukaryotGeneExpr.2022046190
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Article: Bromodomain Proteins Epigenetically Regulate the Mitotically Associated lncRNA MANCR in Triple Negative Breast Cancer Cells.

Tracy, Kirsten M / Prior, Shannon / Trowbridge, Willem T / Boyd, Joseph R / Ghule, Prachi N / Frietze, Seth / Stein, Janet L / Stein, Gary S / Lian, Jane B

Critical reviews in eukaryotic gene expression

2023 Volume 34, Issue 2, Page(s) 61–71

Abstract: Long non-coding RNA (lncRNA)-mediated control of gene expression contributes to regulation of biological processes that include proliferation and phenotype, as well as compromised expression of genes that are functionally linked to cancer initiation and ... ...

Abstract	Long non-coding RNA (lncRNA)-mediated control of gene expression contributes to regulation of biological processes that include proliferation and phenotype, as well as compromised expression of genes that are functionally linked to cancer initiation and tumor progression. lncRNAs have emerged as novel targets and biomarkers in breast cancer. We have shown that mitotically associated lncRNA MANCR is expressed in triple-negative breast cancer (TNBC) cells and that it serves a critical role in promoting genome stability and survival in aggressive breast cancer cells. Using an siRNA strategy, we selectively depleted BRD2, BRD3, and BRD4, singly and in combination, to establish which bromodomain proteins regulate MANCR expression in TNBC cells. Our findings were confirmed by using in situ hybridization combined with immunofluorescence analysis that revealed BRD4, either alone or with BRD2 and BRD3, can support MANCR regulation of TNBC cells. Here we provide evidence for MANCR-responsive epigenetic control of super enhancers by histone modifications that are required for gene transcription to support cell survival and expression of the epithelial tumor phenotype in triple negative breast cancer cells.
MeSH term(s)	Humans ; Triple Negative Breast Neoplasms/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Cell Survival ; Gene Expression Regulation, Neoplastic ; Cell Line, Tumor ; Cell Proliferation/genetics ; Bromodomain Containing Proteins ; Cell Cycle Proteins/genetics
Chemical Substances	RNA, Long Noncoding ; Nuclear Proteins ; Transcription Factors ; BRD4 protein, human ; Bromodomain Containing Proteins ; Cell Cycle Proteins
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1071345-1
ISSN	1045-4403
ISSN	1045-4403
DOI	10.1615/CritRevEukaryotGeneExpr.2023050109
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