HOX13-dependent chromatin accessibility modulates the target repertoires of the HOX factors

ABSTRACTHox genes encode essential transcription factors that control patterning during embryonic development. Distinct combinations of nested Hox expression domains establish cell and tissue identities1–3. Consequently, spatial or temporal de-regulation of Hox genes can cause severe alterations of the body plan3. While HOX factors have very similar DNA binding motifs, their binding specificity is, in part, mediated by co-factors4–6. Yet, the interplay between HOX binding specificities and the cellular context remains largely elusive. To gain insight into this question, we took advantage of developing limbs for which the differential expression of Hox genes is well-characterized7. We show that the transcription factors HOXA13 and HOXD13 (hereafter referred as HOX13) allow another HOX factor, HOXA11, to bind loci initially assumed to be HOX13-specific. Importantly, HOXA11 is unable to bind these loci in distal limbs lacking HOX13 function indicating that HOX13 modulates HOXA11 target repertoire. In addition, we find that the HOX13 factors implement the distal limb developmental program by triggering chromatin opening, a defining property of pioneer factors8,9. Finally, single cell analysis of chromatin accessibility reveals that HOX13 factors pioneer chromatin opening in a lineage specific manner. Together, our data uncover a new mechanism underlying HOX binding specificity, whereby tissue-specific variations in the target repertoire of HOX factors rely, at least in part, on HOX13-dependent chromatin accessibility.

Download Full-text

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Nucleic Acids Research ◽

10.1093/nar/gkz627 ◽

2019 ◽

Vol 47 (17) ◽

pp. 9069-9086 ◽

Cited By ~ 10

Author(s):

Filippo M Cernilogar ◽

Stefan Hasenöder ◽

Zeyang Wang ◽

Katharina Scheibner ◽

Ingo Burtscher ◽

...

Keyword(s):

Transcription Factors ◽

Binding Sites ◽

Specific Binding ◽

Embryonic Stem ◽

Chromatin Accessibility ◽

Specific Binding Sites ◽

Nucleosomal Dna ◽

Cell Type Specific ◽

Chromatin Opening ◽

Selection Of

Abstract Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

Download Full-text

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

10.1101/607721 ◽

2019 ◽

Cited By ~ 1

Author(s):

Filippo M. Cernilogar ◽

Stefan Hasenöder ◽

Zeyang Wang ◽

Katharina Scheibner ◽

Ingo Burtscher ◽

...

Keyword(s):

Transcription Factors ◽

Binding Sites ◽

Specific Binding ◽

Embryonic Stem ◽

Chromatin Accessibility ◽

Specific Binding Sites ◽

Nucleosomal Dna ◽

Cell Type Specific ◽

Chromatin Opening ◽

Selection Of

AbstractPioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

Download Full-text

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.

Download Full-text

RNA-Seq Analysis Illuminates the Early Stages of Plasmodium Liver Infection

mBio ◽

10.1128/mbio.03234-19 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Maria Toro-Moreno ◽

Kayla Sylvester ◽

Tamanna Srivastava ◽

Dora Posfai ◽

Emily R. Derbyshire

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Redox Homeostasis ◽

Early Time ◽

Rna Seq ◽

Binding Motifs ◽

Liver Stage ◽

Content Type ◽

Dna Binding Motifs ◽

Causative Agents

ABSTRACT The apicomplexan parasites Plasmodium spp. are the causative agents of malaria, a disease that poses a significant global health burden. Plasmodium spp. initiate infection of the human host by transforming and replicating within hepatocytes. This liver stage (LS) is poorly understood compared to other Plasmodium life stages, which has hindered our ability to target these parasites for disease prevention. We conducted an extensive transcriptome sequencing (RNA-Seq) analysis throughout the Plasmodium berghei LS, covering as early as 2 h postinfection (hpi) and extending to 48 hpi. Our data revealed that hundreds of genes are differentially expressed at 2 hpi and that multiple genes shown to be important for later infection are upregulated as early as 12 hpi. Using hierarchical clustering along with coexpression analysis, we identified clusters functionally enriched for important liver-stage processes such as interactions with the host cell and redox homeostasis. Furthermore, some of these clusters were highly correlated to the expression of ApiAP2 transcription factors, while showing enrichment of mostly uncharacterized DNA binding motifs. This finding indicates potential LS targets for these transcription factors, while also hinting at alternative uncharacterized DNA binding motifs and transcription factors during this stage. Our work presents a window into the previously undescribed transcriptome of Plasmodium upon host hepatocyte infection to enable a comprehensive view of the parasite’s LS. These findings also provide a blueprint for future studies that extend hypotheses concerning LS gene function in P. berghei to human-infective Plasmodium parasites. IMPORTANCE The LS of Plasmodium infection is an asymptomatic yet necessary stage for producing blood-infective parasites, the causative agents of malaria. Blocking the liver stage of the life cycle can prevent clinical malaria, but relatively less is known about the parasite’s biology at this stage. Using the rodent model P. berghei, we investigated whole-transcriptome changes occurring as early as 2 hpi of hepatocytes. The transcriptional profiles of early time points (2, 4, 12, and 18 hpi) have not been accessible before due to the technical challenges associated with liver-stage infections. Our data now provide insights into these early parasite fluxes that may facilitate establishment of infection, transformation, and replication in the liver.

Download Full-text

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

Nucleic Acids Research ◽

10.1093/nar/gku1228 ◽

2014 ◽

Vol 42 (22) ◽

pp. 13500-13512 ◽

Cited By ~ 28

Author(s):

Mario Pujato ◽

Fabien Kieken ◽

Amanda A. Skiles ◽

Nikos Tapinos ◽

Andras Fiser

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

3D Models ◽

Binding Motifs ◽

Dna Binding Motifs

Download Full-text

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Nature Communications ◽

10.1038/s41467-020-20883-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Run Jin ◽

Samantha Klasfeld ◽

Yang Zhu ◽

Meilin Fernandez Garcia ◽

Jun Xiao ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Cell Fate ◽

Chromatin Accessibility ◽

Binding Motifs ◽

Chromatin Remodelers ◽

Pioneer Transcription Factor ◽

Chromatin Reprogramming

AbstractMaster transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY ‘unlocks’ chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.

Download Full-text

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

10.1101/2020.03.16.994418 ◽

2020 ◽

Cited By ~ 1

Author(s):

Run Jin ◽

Samantha Klasfeld ◽

Meilin Fernandez Garcia ◽

Jun Xiao ◽

Soon-Ki Han ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Cell Fate ◽

Chromatin Accessibility ◽

Binding Motifs ◽

Chromatin Remodelers ◽

Pioneer Transcription Factor ◽

Chromatin Reprogramming

ABSTRACTMaster transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet no bonafide pioneer transcription factor has - been identified in this kingdom. Here we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds in a sequence-specific manner and with high affinity to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1, where it co-occupies DNA with histones. Moreover, the LFY DNA contact helix shares defining properties with those of strong nucleosome binding pioneer factors. At the AP1 locus, LFY unlocks chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later and require activity of additional, non-pioneer transcription, factors. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between plant and animal pioneer transcription factors. Further analyses aimed at elucidating the defining characteristics of pioneer transcription factors will allow harnessing these for enhanced cell fate reprogramming.

Download Full-text

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

10.1101/2020.02.28.969261 ◽

2020 ◽

Author(s):

Christina B. Azodi ◽

John P. Lloyd ◽

Shin-Han Shiu

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Drought Stress ◽

Transcriptional Response ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Combined Stress ◽

Binding Motifs ◽

Powerful Approach ◽

The Individual

ABSTRACTPlants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic, synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility, histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.

Download Full-text