Organizational properties of a functional mammalian cis-regulome

Mapping Intimacies ◽

10.1101/550897 ◽

2019 ◽

Author(s):

Virendra K. Chaudhri ◽

Krista Dienger-Stambaugh ◽

Zhiguo Wu ◽

Mahesh Shrestha ◽

Harinder Singh

Keyword(s):

Transcription Factor ◽

B Cells ◽

Dna Binding ◽

Chromatin Accessibility ◽

Motif Analysis ◽

Transcription Profiles ◽

Genomic Analyses ◽

Enhancer Function ◽

Chromatin Profiling ◽

Accessible Chromatin

AbstractMammalian genomic states are distinguished by their chromatin and transcription profiles. Most genomic analyses rely on chromatin profiling to infer cis-regulomes controlling distinctive cellular states. By coupling FAIRE-seq with STARR-seq and integrating Hi-C we assemble a functional cis-regulome for activated murine B-cells. Within 55,130 accessible chromatin regions we delineate 9,989 active enhancers communicating with 7,530 promoters. The cis-regulome is dominated by long range enhancer-promoter interactions (>100kb) and complex combinatorics, implying rapid evolvability. Genes with multiple enhancers display higher rates of transcription and multi-genic enhancers manifest graded levels of H3K4me1 and H3K27ac in poised and activated states, respectively. Motif analysis of pathway-specific enhancers reveals diverse transcription factor (TF) codes controlling discrete processes. The cis-regulome strikingly enriches for combinatorial DNA binding regions of lineage determining TFs. Their genomic binding patterns reveal that onset of chromatin accessibility is associated with binding of simpler combinations whereas enhancer function requires greater complexity.

Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data

Nucleic Acids Research ◽

10.1093/nar/gkx358 ◽

2017 ◽

Vol 45 (10) ◽

pp. 5666-5677 ◽

Cited By ~ 5

Author(s):

Mahdi Zamanighomi ◽

Zhixiang Lin ◽

Yong Wang ◽

Rui Jiang ◽

Wing Hung Wong

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Dna Binding ◽

Gene Expression Data ◽

Chromatin Accessibility ◽

Expression Data ◽

Binding Motifs ◽

Dna Binding Domains ◽

Binding Domains ◽

Transcription Factor Binding Motifs

ATAC-seq with unique molecular identifiers improves quantification and footprinting

Communications Biology ◽

10.1038/s42003-020-01403-4 ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Tao Zhu ◽

Keyan Liao ◽

Rongfang Zhou ◽

Chunjiao Xia ◽

Weibo Xie

Keyword(s):

Transcription Factor ◽

High Throughput ◽

High Throughput Sequencing ◽

Pcr Amplification ◽

Chromatin Accessibility ◽

Link Type ◽

Pcr Duplicates ◽

Identify Transcription Factor ◽

Accessible Chromatin ◽

Accurate Quantification

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq in our study. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.

Effects of aging on DNA-binding activity of the E47 transcription factor in splenic B cells

Mechanisms of Ageing and Development ◽

10.1016/j.mad.2003.11.004 ◽

2004 ◽

Vol 125 (2) ◽

pp. 111-112 ◽

Cited By ~ 6

Author(s):

Daniela Frasca ◽

Diep Nguyen ◽

Richard L. Riley ◽

Bonnie B. Blomberg

Keyword(s):

Transcription Factor ◽

B Cells ◽

Dna Binding ◽

Binding Activity ◽

Dna Binding Activity ◽

Effects Of Aging

One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

Epigenetics & Chromatin ◽

10.1186/s13072-021-00427-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Udayakumar S. Vishnu ◽

Pierre-Olivier Estève ◽

Hang Gyeong Chin ◽

Sriharsa Pradhan

Keyword(s):

Mammalian Cells ◽

Molecular Subtypes ◽

Downstream Processing ◽

Chromatin Accessibility ◽

One Pot ◽

Tn5 Transposon ◽

Chromatin Profiling ◽

Nicking Enzyme ◽

Accessible Chromatin ◽

Enzymatic Fragmentation

Abstract Background Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples. Results One-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility. Conclusion One-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn’t require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation.

Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated

10.1101/798454 ◽

2019 ◽

Cited By ~ 1

Author(s):

Markus Nevil ◽

Tyler J. Gibson ◽

Constantine Bartolutti ◽

Anusha Iyengar ◽

Melissa M Harrison

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Chromatin Accessibility ◽

Mitotic Chromosomes ◽

Developmentally Regulated ◽

Regulatory Modules ◽

Pioneer Factor ◽

Pioneer Factors ◽

Coordinate Changes ◽

Accessible Chromatin

AbstractThe dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor, Grainy head (Grh). Grh is expressed throughout Drosophila development and functions as a pioneer factor in the larvae. We demonstrated that Grh remains bound to condensed mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking either maternal or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and is likely influenced by additional factors expressed at a given developmental stage.

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

PeerJ ◽

10.7717/peerj.4040 ◽

2017 ◽

Vol 5 ◽

pp. e4040 ◽

Cited By ~ 8

Author(s):

Zeeshan Ahmed ◽

Duygu Ucar

Keyword(s):

Chromatin Accessibility ◽

Clinical Samples ◽

Open Chromatin ◽

Data Generation ◽

Desktop Application ◽

Feature Based ◽

Cross Platform ◽

Chromatin Profiling ◽

User Friendly ◽

Accessible Chromatin

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations.

TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer

Science Immunology ◽

10.1126/sciimmunol.aau7523 ◽

2019 ◽

Vol 4 (34) ◽

pp. eaau7523 ◽

Cited By ~ 13

Author(s):

Chan-Wang J. Lio ◽

Vipul Shukla ◽

Daniela Samaniego-Castruita ◽

Edahi González-Avalos ◽

Abhijit Chakraborty ◽

...

Keyword(s):

Transcription Factor ◽

B Cells ◽

Cell Activation ◽

Chromatin Accessibility ◽

Dna Demethylation ◽

Bzip Transcription Factor ◽

Epigenetic Mark ◽

Enhancer Activity ◽

Activation Induced Deaminase ◽

Tet Enzymes

TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). Here, we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, which encodes the activation-induced cytidine deaminase (AID) enzyme essential for CSR. TET enzymes deposit 5hmC, facilitate DNA demethylation, and maintain chromatin accessibility at two TET-responsive enhancer elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Our data identify the bZIP transcription factor, ATF-like (BATF) as a key transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF facilitates TET recruitment to this Aicda enhancer. Our study emphasizes the importance of TET enzymes for bolstering AID expression and highlights 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.

Conserved epigenetic programming and enhanced heme metabolism drive memory B cell reactivation

10.1101/2021.01.20.427446 ◽

2021 ◽

Author(s):

Madeline J. Price ◽

Christopher D. Scharer ◽

Anna K. Kania ◽

Troy D. Randall ◽

Jeremy M. Boss

Keyword(s):

B Cells ◽

Plasma Cells ◽

Ex Vivo ◽

Chromatin Accessibility ◽

Memory B Cells ◽

List Type ◽

Differentiation Potential ◽

Altered Expression ◽

Genes Encoding ◽

Accessible Chromatin

ABSTRACTMemory B cells (MBCs) have enhanced capabilities to differentiate to plasma cells and generate a rapid burst of antibodies upon secondary stimulation. To determine if MBCs harbor an epigenetic landscape that contributes to increased differentiation potential, we derived the chromatin accessibility and transcriptomes of influenza-specific IgM and IgG MBCs compared to naïve cells. MBCs possessed an accessible chromatin architecture surrounding plasma cell specific genes, as well as altered expression of transcription factors and genes encoding cell cycle, chemotaxis, and signal transduction processes. Intriguingly, this MBC signature was conserved between humans and mice. MBCs of both species possessed a heightened heme signature compared to naïve cells. Differentiation in the presence of hemin enhanced oxidative phosphorylation metabolism and MBC differentiation into antibody secreting plasma cells. Thus, these data define conserved MBC transcriptional and epigenetic signatures that include a central role for heme and multiple other pathways in augmenting MBC reactivation potential.Key PointsInfluenza-specific memory B cells have accessible chromatin structure.Human and mouse memory B cells upregulate heme metabolic pathways.Heme enhances PC differentiation and augments mitochondrial metabolism in ex vivo.

Assessing chromatin accessibility in maize using ATAC-seq

10.1101/526079 ◽

2019 ◽

Author(s):

Yi-Jing Lee ◽

Pearl Chang ◽

Jui-Hsien Lu ◽

Pao-Yang Chen ◽

Chung-Ju Rachel Wang

Keyword(s):

Cell Sorting ◽

High Throughput Sequencing ◽

Crop Improvement ◽

Practical Method ◽

Chromatin Accessibility ◽

Crop Species ◽

Chromatin Profiling ◽

Key Steps ◽

Accessible Chromatin ◽

Complex Genome

Background: Maize is an important crop that has a complex genome. A better understanding of maize chromatin architecture provides great opportunities for crop improvement, because chromatin accessibility influences gene expression, thereby affecting agricultural traits. The newly developed method for chromatin profiling, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), has been developed to investigate chromatin accessibility. Result: We adapt this method by testing parameters of several key steps and generate the first ATAC-seq protocol for maize. We demonstrate that purification of maize nuclei to eliminate organelles can be achieved without the need for cell sorting, and that only a standard bench-top centrifuge is required for sample preparation. Finally, our sequence analyses confirm that our protocol of ATAC-seq can be successfully used to assess the chromatin landscape in maize. Conclusion: The ATAC-seq provides a useful technique to study the chromatin accessibility. Given the parameters tested in our study, it can be a simple and practical method for maize and may be a foundation for similar studies in other crop species.

ATAC-seq with unique molecular identifiers improves quantification and footprinting

10.1101/2020.10.22.351478 ◽

2020 ◽

Author(s):

Tao Zhu ◽

Keyan Liao ◽

Rongfang Zhou ◽

Chunjiao Xia ◽

Weibo Xie

Keyword(s):

Transcription Factor ◽

High Throughput ◽

High Throughput Sequencing ◽

Pcr Amplification ◽

Chromatin Accessibility ◽

Link Type ◽

Pcr Duplicates ◽

Identify Transcription Factor ◽

Accessible Chromatin ◽

Accurate Quantification

AbstractATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) provides an efficient way to analyze nucleosome-free regions and has been applied widely to identify transcription factor footprints. Both applications rely on the accurate quantification of insertion events of the hyperactive transposase Tn5. However, due to the presence of the PCR amplification, it is impossible to accurately distinguish independently generated identical Tn5 insertion events from PCR duplicates using the standard ATAC-seq technique. Removing PCR duplicates based on mapping coordinates introduces an increasing bias towards highly accessible chromatin regions. To overcome this limitation, we establish a UMI-ATAC-seq technique by incorporating unique molecular identifiers (UMIs) into standard ATAC-seq procedures. In our study, UMI-ATAC-seq can rescue about 20% of reads that are mistaken as PCR duplicates in standard ATAC-seq, which helps identify an additional 50% or more of footprints. We demonstrate that UMI-ATAC-seq could more accurately quantify chromatin accessibility and significantly improve the sensitivity of identifying transcription factor footprints. An analytic pipeline is developed to facilitate the application of UMI-ATAC-seq, and it is available at https://github.com/tzhu-bio/UMI-ATAC-seq.