DEVELOPMENTAL AND EVOLUTIONARY COMPARATIVE ANALYSIS OF A HOXD REGULATORY LANDSCAPE IN MAMMALS AND BIRDS

Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk rely more on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CRE sequences, an observation supported by a genome-wide comparative approach.

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Chromatin interaction analysis with updated ChIA-PET Tool (V3)

10.1101/627257 ◽

2019 ◽

Author(s):

Guoliang Li ◽

Tongkai Sun ◽

Huidan Chang ◽

Liuyang Cai ◽

Ping Hong ◽

...

Keyword(s):

Data Analysis ◽

Target Genes ◽

Sequence Data ◽

Interaction Analysis ◽

Regulatory Elements ◽

Chromatin Interaction ◽

Data Set ◽

Chromatin Interactions ◽

A Genome ◽

Public Data

AbstractUnderstanding chromatin interactions is important since they create chromosome conformation and link the cis- and trans-regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. Previously we developed ChIA-PET Tool in 2010 for ChIA-PET data analysis. Here we present the updated version of ChIA-PET Tool (V3), is a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes the short-read data and long-read ChIA-PET data with multithreading and generates the statistics of results in a HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze a specific ChIA-PET data set with it. At present, other ChIA-PET data analysis tools have developed including ChiaSig, MICC, Mango and ChIA-PET2 and so on. We compared our tool with other tools using the same public data set in the same machine. Most of peaks detected by ChIA-PET Tool V3 overlap with those from other tools. There is higher enrichment for significant chromatin interactions of ChIA-PET Tool V3 in APA plot. ChIA-PET Tool V3 is open source and is available at GitHub (https://github.com/GuoliangLi-HZAU/ChIA-PET_Tool_V3/).

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Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant

Genes ◽

10.3390/genes13010024 ◽

2021 ◽

Vol 13 (1) ◽

pp. 24

Author(s):

Jianfei Wu ◽

Fan Gao ◽

Tongtong Li ◽

Haixia Guo ◽

Li Zhang ◽

...

Keyword(s):

Target Genes ◽

Regulatory Element ◽

Regulatory Elements ◽

Auxin Response ◽

Higher Plant ◽

Response Factors ◽

Auxin Response Factors ◽

Genome Wide ◽

A Genome ◽

Almost All

Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.

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Integrative analysis of epigenetics data identifies gene-specific regulatory elements

10.1101/585125 ◽

2019 ◽

Cited By ~ 2

Author(s):

Florian Schmidt ◽

Alexander Marx ◽

Marie Hebel ◽

Martin Wegner ◽

Nina Baumgarten ◽

...

Keyword(s):

Transcriptional Regulation ◽

Cell Types ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Genome Wide ◽

A Genome ◽

Gene Level ◽

Regulatory Landscape ◽

Regulatory Sites ◽

Validation Experiments

AbstractUnderstanding the complexity of transcriptional regulation is a major goal of computational biology. Because experimental linkage of regulatory sites to genes is challenging, computational methods considering epigenomics data have been proposed to create tissue-specific regulatory maps. However, we showed that these approaches are not well suited to account for the variations of the regulatory landscape between cell-types. To overcome these drawbacks, we developed a new method called STITCHIT, that identifies and links putative regulatory sites to genes. Within STITCHIT, we consider the chromatin accessibility signal of all samples jointly to identify regions exhibiting a signal variation related to the expression of a distinct gene. STITCHIToutperforms previous approaches in various validation experiments and was used with a genome-wide CRISPR-Cas9 screen to prioritize novel doxorubicin-resistance genes and their associated non-coding regulatory regions. We believe that our work paves the way for a more refined understanding of transcriptional regulation at the gene-level.

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The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development

Blood ◽

10.1182/blood-2009-01-200048 ◽

2009 ◽

Vol 113 (22) ◽

pp. 5456-5465 ◽

Cited By ~ 81

Author(s):

Nicola K. Wilson ◽

Diego Miranda-Saavedra ◽

Sarah Kinston ◽

Nicolas Bonadies ◽

Samuel D. Foster ◽

...

Keyword(s):

Stem Cell ◽

Regulatory Networks ◽

Transcriptional Control ◽

Target Genes ◽

Fetal Liver ◽

Bioinformatic Analysis ◽

Regulatory Elements ◽

Hematopoietic Stem ◽

A Genome

The basic helix-loop-helix transcription factor Scl/Tal1 controls the development and subsequent differentiation of hematopoietic stem cells (HSCs). However, because few Scl target genes have been validated to date, the underlying mechanisms have remained largely unknown. In this study, we have used ChIP-Seq technology (coupling chromatin immunoprecipitation with deep sequencing) to generate a genome-wide catalog of Scl-binding events in a stem/progenitor cell line, followed by validation using primary fetal liver cells and comprehensive transgenic mouse assays. Transgenic analysis provided in vivo validation of multiple new direct Scl target genes and allowed us to reconstruct an in vivo validated network consisting of 17 factors and their respective regulatory elements. By coupling ChIP-Seq in model cell lines with in vivo transgenic validation and sophisticated bioinformatic analysis, we have identified a widely applicable strategy for the reconstruction of stem cell regulatory networks in which biologic material is otherwise limiting. Moreover, in addition to revealing multiple previously unrecognized links to known HSC regulators, as well as novel links to genes not previously implicated in HSC function, comprehensive transgenic analysis of regulatory elements provided substantial new insights into the transcriptional control of several important hematopoietic regulators, including Cbfa2t3h/Eto2, Cebpe, Nfe2, Zfpm1/Fog1, Erg, Mafk, Gfi1b, and Myb.

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Organization and Regulation of the Human Genome

Blood ◽

10.1182/blood.v128.22.sci-16.sci-16 ◽

2016 ◽

Vol 128 (22) ◽

pp. SCI-16-SCI-16

Author(s):

Bing Ren

Keyword(s):

Gene Regulation ◽

Long Range ◽

Genome Organization ◽

Mammalian Cells ◽

Target Genes ◽

Critical Role ◽

Cell Types ◽

Regulatory Elements ◽

Chromatin Organization ◽

Specific Gene

Abstract The 3-dimensional (3D) chromatin organization plays a critical role in gene regulation. Great strides have been made recently to characterize and identify cis regulatory elements from epigenome profiles in different cell types and tissues, but efforts have just begun to functionally characterize these long-range control elements. Mapping interactions between enhancers and promoters, and understanding how the 3D landscape of the genome constrains such interactions is fundamental to our understanding of genome function. I will present recent findings related to 3D genome organization in mammalian cells, with a particular focus on how chromatin organization contributes to transcriptional regulation. I will describe higher-order organizational features that are observed at the level of both the whole chromosome and individual loci. I will highlight changes in genome organization that occur during the course of differentiation, and discuss the functional relationship between chromatin architecture and gene regulation. Taken together, mounting evidence now shows that the genome organization plays an essential role in orchestrating the lineage-specific gene expression programs through modulating long- range interactions between enhancers and target genes. Disclosures Ren: Arima Genomics, Inc.: Equity Ownership, Patents & Royalties; Eli Lilly: Employment.

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The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila

10.1101/373308 ◽

2018 ◽

Author(s):

Arya Zandvakili ◽

Juli Uhl ◽

Ian Campbell ◽

Yuntao Charlie Song ◽

Brian Gebelein

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Dna Sequences ◽

Binding Sites ◽

Target Genes ◽

Hox Genes ◽

Regulatory Elements ◽

Protease Gene ◽

Precise Integration

AbstractHox genes encode a family of transcription factors that, despite having similar in vitro DNA binding preferences, regulate distinct genetic programs along the metazoan anterior-posterior axis. To better define mechanisms of Hox specificity, we compared and contrasted the ability of abdominal Hox factors to regulate two cis-regulatory elements within the Drosophila embryo. Both the Ultrabithorax (Ubx) and Abdominal-A (Abd-A) Hox factors form cooperative complexes with the Extradenticle (Exd) and Homothorax (Hth) transcription factors to repress the distal-less leg selector gene via the DCRE, whereas only Abd-A interacts with Exd and Hth on the RhoA element to activate a rhomboid serine protease gene that stimulates Epidermal Growth Factor secretion. By swapping binding sites between these elements, we found that the RhoA Exd/Hth/Hox site configuration that mediates Abd-A specific activation can also convey transcriptional repression by both Ubx and Abd-A when placed into the DCRE, but only in one orientation. We further show that the orientation and spacing of Hox sites relative to additional transcription factor binding sites within the RhoA and DCRE elements is critical to mediate appropriate cell- and segment-specific output. These results indicate that the interaction between Hox, Exd, and Hth neither determines activation vs repression specificity nor defines Ubx vs Abd-A specificity. Instead the precise integration of Hox sites with additional TF inputs is required for accurate transcriptional output. Taken together, these studies provide new insight into the mechanisms of Hox target and regulatory specificity as well as the constraints placed on regulatory elements to convey appropriate outputs.Author SummaryThe Hox genes encode a family of transcription factors that give cells within each region along the developing body plan a unique identity in animals from worms to mammals. Surprisingly, however, most of the Hox factors bind the same or highly similar DNA sequences. These findings raise a paradox: How can proteins that have highly similar DNA binding properties perform different functions in the animal by regulating different sets of target genes? In this study, we address this question by studying how two Hox factors regulate the expression of target genes that specify leg development and the making of liver-like cells in the developing fly. By comparing and contrasting how Hox target genes are activated and/or repressed, we found that the same Hox binding sites can mediate either activation or repression in a manner that depends upon context. In addition, we found that a Hox binding site that is normally regulated by only one Hox factor, can also be used by more than one Hox factor swapped into another target gene. These findings indicate that the specificity of a Hox factor to regulate target genes does not rely solely upon DNA binding specificity but also requires regulatory specificity.

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Hox proteins have different affinities for a consensus DNA site that correlate with the positions of their genes on the hox cluster

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4532-4545.1994 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4532-4545

Author(s):

I Pellerin ◽

C Schnabel ◽

K M Catron ◽

C Abate

Keyword(s):

Dna Binding ◽

Target Genes ◽

Hox Genes ◽

Regulatory Elements ◽

Binding Properties ◽

Hox Proteins ◽

Hox Cluster ◽

Dna Binding Properties

The hox genes, members of a family of essential developmental regulators, have the intriguing property that their expression in the developing murine embryo is colinear with their chromosomal organization. Members of the hox gene family share a conserved DNA binding domain, termed the homeodomain, which mediates interactions of Hox proteins with DNA regulatory elements in the transcriptional control regions of target genes. In this study, we characterized the DNA binding properties of five representative members of the Hox family: HoxA5, HoxB4, HoxA7, HoxC8, and HoxB1. To facilitate a comparative analysis of their DNA binding properties, we produced the homeodomain regions of these Hox proteins in Escherichia coli and obtained highly purified polypeptides. We showed that these Hox proteins interact in vitro with a common consensus DNA site that contains the motif (C/G)TAATTG. We further showed that the Hox proteins recognize the consensus DNA site in vivo, as determined by their ability to activate transcription through this site in transient transfection assays. Although they interact optimally with the consensus DNA site, the Hox proteins exhibit subtle, but distinct, preferences for DNA sites that contain variations of the nucleotides within the consensus motif. In addition to their modest differences in DNA binding specificities, the Hox proteins also vary in their relative affinities for DNA. Intriguingly, their relative affinities correlate with the positions of their respective genes on the hox cluster. These findings suggest that subtle differences in DNA binding specificity combined with differences in DNA binding affinity constitute features of the "Hox code" that contribute to the selective functions of Hox proteins during murine embryogenesis.

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Hox proteins have different affinities for a consensus DNA site that correlate with the positions of their genes on the hox cluster.

Molecular and Cellular Biology ◽

10.1128/mcb.14.7.4532 ◽

1994 ◽

Vol 14 (7) ◽

pp. 4532-4545 ◽

Cited By ~ 39

Author(s):

I Pellerin ◽

C Schnabel ◽

K M Catron ◽

C Abate

Keyword(s):

Dna Binding ◽

Target Genes ◽

Hox Genes ◽

Regulatory Elements ◽

Binding Properties ◽

Hox Proteins ◽

Hox Cluster ◽

Dna Binding Properties

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Histone crotonylation-centric gene regulation

Epigenetics & Chromatin ◽

10.1186/s13072-021-00385-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kun Li ◽

Ziqiang Wang

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Gene Transcription ◽

Target Genes ◽

Regulatory Elements ◽

Related Gene ◽

Post Translational Modification ◽

Histone Lysine ◽

Dna Regulatory Elements

AbstractHistone crotonylation is a recently described post-translational modification that occurs at multiple identified histone lysine crotonylation sites. An increasing number of studies have demonstrated that histone crotonylation at DNA regulatory elements plays an important role in the activation of gene transcription. However, among others, we have shown that elevated cellular crotonylation levels result in the inhibition of endocytosis-related gene expression and pro-growth gene expression, implicating the complexity of histone crotonylation in gene regulation. Therefore, it is important to understand how histone crotonylation is regulated and how it, in turn, regulates the expression of its target genes. In this review, we summarize the regulatory factors that control histone crotonylation and discuss the role of different histone crotonylation sites in regulating gene expression, while providing novel insights into the central role of histone crotonylation in gene regulation.

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Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)

Genes ◽

10.3390/genes10070554 ◽

2019 ◽

Vol 10 (7) ◽

pp. 554 ◽

Cited By ~ 4

Author(s):

Li ◽

Sun ◽

Chang ◽

Cai ◽

Hong ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Target Genes ◽

Sequence Data ◽

Interaction Analysis ◽

Regulatory Elements ◽

Chromatin Interaction ◽

Data Set ◽

Chromatin Interactions ◽

A Genome ◽

Public Data

Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub.

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