NAR Genom Bioinform. 2021 Jun 17;3(2):lqab052. doi: 10.1093/nargab/lqab052. eCollection 2021 Jun.

ABSTRACT

cis-regulatory modules(CRMs) formed by clusters of transcription factor (TF) binding sites (TFBSs) are as important as coding sequences in specifying phenotypes of humans. It is essential to categorize all CRMs and constituent TFBSs in the genome. In contrast to most existing methods that predict CRMs in specific cell types using epigenetic marks, we predict a largely cell type agonistic but more comprehensive map of CRMs and constituent TFBSs in the gnome by integrating all available TF ChIP-seq datasets. Our method is able to partition 77.47% of genome regions covered by available 6092 datasets into a CRM candidate (CRMC) set (56.84%) and a non-CRMC set (43.16%). Intriguingly, the predicted CRMCs are under strong evolutionary constraints, while the non-CRMCs are largely selectively neutral, strongly suggesting that the CRMCs are likely cis-regulatory, while the non-CRMCs are not. Our predicted CRMs are under stronger evolutionary constraints than three state-of-the-art predictions (GeneHancer, EnhancerAtlas and ENCODE phase 3) and substantially outperform them for recalling VISTA enhancers and non-coding ClinVar variants. We estimated that the human genome might encode about 1.47M CRMs and 68M TFBSs, comprising about 55% and 22% of the genome, respectively; for both of which, we predicted 80%. Therefore, the cis-regulatory genome appears to be more prevalent than originally thought.

PMID:34159315 | PMC:PMC8210889 | DOI:10.1093/nargab/lqab052

J Biol Chem. 2021 Jun 19:100901. doi: 10.1016/j.jbc.2021.100901. Online ahead of print.

ABSTRACT

Alx1, a homeodomain (HD)-containing transcription factor, is a highly conserved regulator of skeletogenesis in echinoderms. In sea urchins, Alx1 plays a central role in the differentiation of embryonic primary mesenchyme cells (PMCs) and positively regulates the transcription of most biomineralization genes expressed by these cells. The alx1 gene arose via duplication and acquired a skeletogenic function distinct from its paralog (alx4) through the exonization of a 41-amino acid motif (the D2 domain). Alx1 and Alx4 contain glutamine-50 paired-type HDs, which interact preferentially with palindromic binding sites in vitro. ChIP-seq studies have shown, however, that Alx1 binds both to palindromic and half-sites in vivo. To address this apparent discrepancy and to explore the function of the D2 domain, we used an endogenous cis-regulatory module (CRM) associated with Sp-mtmmpb, a gene that encodes a PMC-specific metalloprotease, to analyze the DNA binding properties of Alx1. We find that Alx1 forms dimeric complexes on TAAT-containing half-sites by a mechanism distinct from the well-known mechanism of dimerization on palindromic sites. We used transgenic reporter assays to analyze the functional roles of half-sites in vivo and demonstrate that two sites with partially redundant functions are essential for the PMC-specific activity of the Sp-mtmmpb CRM. Lastly, we show that the D2 domain influences the DNA binding properties of Alx1 in vitro, suggesting that the exonization of this motif may have facilitated the acquisition of new transcriptional targets and consequently a novel developmental function.

PMID:34157281 | DOI:10.1016/j.jbc.2021.100901

Development. 2020 Jan 1:dev.187922. doi: 10.1242/dev.187922. Online ahead of print.

ABSTRACT

Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, Orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells utilize a cohort of TFs with different expression patterns, and multiple CRMs with different chromatin configurations, to precisely regulate the expression of Otx2.

PMID:34004867 | DOI:10.1242/dev.187922

Development. 2020 Jan 1:dev.185009. doi: 10.1242/dev.185009. Online ahead of print.

ABSTRACT

The 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). Prior work established that Grh is expressed throughout Drosophila development and is a pioneer factor in the larva. We demonstrated that Grh remains bound to mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking maternal and/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 likely influenced by additional factors expressed at a given developmental stage.

PMID:34004769 | DOI:10.1242/dev.185009

Nat Commun. 2021 May 7;12(1):2557. doi: 10.1038/s41467-021-22821-w.

ABSTRACT

The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.

PMID:33963188 | DOI:10.1038/s41467-021-22821-w

Development. 2021 May 1;148(9):dev198549. doi: 10.1242/dev.198549. Epub 2021 Apr 30.

ABSTRACT

The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC RPC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.

PMID:33929509 | DOI:10.1242/dev.198549

Commun Biol. 2021 Apr 6;4(1):442. doi: 10.1038/s42003-021-01970-0.

ABSTRACT

Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC .

PMID:33824393 | DOI:10.1038/s42003-021-01970-0

Nat Genet. 2021 Apr 1. doi: 10.1038/s41588-021-00816-z. Online ahead of print.

ABSTRACT

Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM-promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM-promoter interactions in defining transcriptional states, as well as distinct cell types.

PMID:33795867 | DOI:10.1038/s41588-021-00816-z

Hum Gene Ther. 2021 Mar 26. doi: 10.1089/hum.2020.325. Online ahead of print.

ABSTRACT

Duchenne muscular dystrophy (DMD) is an X-linked recessive disease that affects 1:5000 live male births and is characterised by muscle wasting. By the age of 13 years, affected individuals are often wheelchair bound and suffer from respiratory and cardiac failure which results in premature death. Although the administration of corticosteroids and ventilation can relieve the symptoms and extend the patients' lifespan, currently no cure exists for DMD. Among the different approaches under pre-clinical and clinical testing, gene therapy using Adeno-Associated Viral (AAV) vectors is one of the most promising. In this study, we delivered intravenously AAV9 vectors expressing the microdystrophin MD1 (ΔR4-R23/ΔCT) under control of the synthetic muscle specific promoter Spc5-12 and assessed the effect of adding a cardiac-specific cis-regulatory module (designated as CS-CRM4) on its expression profile in skeletal and cardiac muscles. Results show that Spc5-12 promoter, in combination with an AAV serotype that has high tropism for the heart, drives high MD1 expression levels in cardiac muscle in mdx mice. The additional regulatory element CS-CRM4 can further improve MD1 expression in cardiac muscles but its effect is dose-dependent and enhancement becomes evident only at lower vector doses.

PMID:33765840 | DOI:10.1089/hum.2020.325

Expression pattern determines regulatory logic.

PLoS One. 2021;16(1):e0244864

Authors: Mora-Martinez C

Abstract
Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.

PMID: 33395445 [PubMed - as supplied by publisher]

Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers.

Dev Dyn. 2020 Dec 30;:

Authors: Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA

Abstract
BACKGROUND: The zinc finger-containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogeneic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue-specific enhancers for Gli family including Gli2 through direct tetrapod-teleost comparisons.
RESULTS: Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved non-coding elements in human GLI2 containing locus. Zebrafish-based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins.
CONCLUSION: Taken together with our previous findings, this study suggests that Hh-signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis-regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. This article is protected by copyright. All rights reserved.

PMID: 33381902 [PubMed - as supplied by publisher]

Inhibition of LncRNA MAAT Controls Multiple Types of Muscle Atrophy by Cis and Trans-regulatory Actions.

Mol Ther. 2020 Dec 03;:

Authors: Li J, Yang T, Tang H, Sha Z, Chen R, Chen L, Yu Y, Rowe GC, Das S, Xiao J

Abstract
Muscle atrophy is associated with worse outcomes in a variety of diseases. Identification of a common therapeutic target would address a significant unmet clinical need. Here we identify a lncRNA (muscle atrophy associated transcript, lncMAAT) as a common regulator of skeletal muscle atrophy. LncMAAT is down-regulated in multiple types of muscle atrophy models both in vivo (denervation, AngII, fasting, immobilization, and aging induced muscle atrophy) and in vitro (AngII, H2O2 and TNFα induced muscle atrophy). Gain and loss of function analysis both in vitro and in vivo reveals that down-regulation of lncMAAT is sufficient to induce muscle atrophy, while overexpression of lncMAAT can ameliorate multiple types of muscle atrophy. Mechanistically, lncMAAT negatively regulates the transcription of miR-29b through SOX6 by a trans-regulatory module, and increases the expression of the neighboring gene Mbnl1 by a cis-regulatory module. Therefore, overexpression of lncMAAT may represent a promising therapy for muscle atrophy induced by different stimuli.

PMID: 33279721 [PubMed - as supplied by publisher]

Author Correction: BICORN: An R package for integrative inference of de novo cis-regulatory modules.

Sci Rep. 2020 Oct 07;10(1):16962

Authors: Chen X, Gu J, Neuwald AF, Hilakivi-Clarke L, Clarke R, Xuan J

Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.

PMID: 33028952 [PubMed]

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.

Cancers (Basel). 2020 Sep 30;12(10):

Authors: Overton IM, Sims AH, Owen JA, Heale BSE, Ford MJ, Lubbock ALR, Pairo-Castineira E, Essafi A

Abstract
Cell identity is governed by gene expression, regulated by transcription factor (TF) binding at cis-regulatory modules. Decoding the relationship between TF binding patterns and gene regulation is nontrivial, remaining a fundamental limitation in understanding cell decision-making. We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions. Snail and Twist are canonical drivers of epithelial to mesenchymal transition (EMT), a cell programme important in development, tumour progression and fibrosis. Predicted "neutral" (non-functional) TF binding always accounted for the majority (50% to 95%) of candidate target genes from statistically significant peaks and HOT regions had higher functional binding than most of the Snail and Twist datasets examined. Our results illuminated conserved gene networks that control epithelial plasticity in development and disease. We identified new gene functions and network modules including crosstalk with notch signalling and regulation of chromatin organisation, evidencing networks that reshape Waddington's epigenetic landscape during epithelial remodelling. Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine. Predicted invasion roles were validated using a tractable cell model, supporting our approach.

PMID: 33007944 [PubMed - as supplied by publisher]

Unusual DNA-binding properties of the Arabidopsis thaliana WRKY50 transcription factor at target gene promoters.

Plant Cell Rep. 2020 Oct 02;:

Authors: Kanofsky K, Rusche J, Eilert L, Machens F, Hehl R

Abstract
KEY MESSAGE: WRKY50 from A. thaliana requires WT-boxes at target gene promoters for activation and binding. Based on the genome-wide prediction of WRKY50 target genes and the similarity of a WRKY50 binding site to WT-boxes in microbe-associated molecular pattern (MAMP)-responsive cis-regulatory modules (CRM), four WT-box containing CRMs from the promoter region of three WRKY50 target genes were investigated for their interaction with WRKY50. These target genes are DJ1E, WRKY30 and ATBBE4. Two of the four CRMs, one from DJ1E and one from WRKY30, were able to activate reporter gene expression in the presence of WRKY50. Activation requires the WT-boxes GGACTTTT, GGACTTTG from DJ1E and GGACTTTC from WRKY30. WRKY50 does not activate a second CRM from WRKY30 and the CRM from ATBBE4, both containing the WT-box TGACTTTT. In vitro gel-shift assays demonstrate WT-box-specific binding of the WRKY50 DNA-binding domain to all four CRMs. This work shows a high flexibility of WRKY50 binding site recognition beyond the classic W-box TTGACC/T.

PMID: 33006643 [PubMed - as supplied by publisher]

Elife. 2020 Oct 2;9:e56450. doi: 10.7554/eLife.56450.

ABSTRACT

Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.

PMID:33006313 | PMC:PMC7556880 | DOI:10.7554/eLife.56450

Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis.

Curr Opin Insect Sci. 2020 Sep 23;:

Authors: Niederhuber MJ, McKay DJ

Abstract
Cis-regulatory modules of metazoan genomes determine the when and where of gene expression during development. Here we discuss insights into the genetic and molecular mechanisms behind cis-regulatory module usage that have come from recent application of genomics assays to insect metamorphosis. Assays including FAIRE-seq, ATAC-seq, and CUT&RUN indicate that sequential changes in chromatin accessibility play a key role in mediating stage-specific cis-regulatory module activity and gene expression. We review the current understanding of what controls precisely coordinated changes in chromatin accessibility during metamorphosis and describe evidence that points to systemic hormone signaling as a primary signal to trigger genome-wide shifts in accessibility patterns and cis-regulatory module usage.

PMID: 32979530 [PubMed - as supplied by publisher]

The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells.

Sci Immunol. 2020 Sep 04;5(51):

Authors: Miyazaki K, Watanabe H, Yoshikawa G, Chen K, Hidaka R, Aitani Y, Osawa K, Takeda R, Ochi Y, Tani-Ichi S, Uehata T, Takeuchi O, Ikuta K, Ogawa S, Kondoh G, Lin YC, Ogata H, Miyazaki M

Abstract
Cell type-specific gene expression is driven by the interplay between lineage-specific transcription factors and cis-regulatory elements to which they bind. Adaptive immunity relies on RAG-mediated assembly of T cell receptor (TCR) and immunoglobulin (Ig) genes. Although Rag1 and Rag2 expression is largely restricted to adaptive lymphoid lineage cells, it remains unclear how Rag gene expression is regulated in a cell lineage-specific manner. Here, we identified three distinct cis-regulatory elements, a T cell lineage-specific enhancer (R-TEn) and the two B cell-specific elements, R1B and R2B By generating mice lacking either R-TEn or R1B and R2B, we demonstrate that these distinct sets of regulatory elements drive the expression of Rag genes in developing T and B cells. What these elements have in common is their ability to bind the transcription factor E2A. By generating a mouse strain that carries a mutation within the E2A binding site of R-TEn, we demonstrate that recruitment of E2A to this site is essential for orchestrating changes in chromatin conformation that drive expression of Rag genes in T cells. By mapping cis-regulatory elements and generating multiple mouse strains lacking distinct enhancer elements, we demonstrate expression of Rag genes in developing T and B cells to be driven by distinct sets of E2A-dependent cis-regulatory modules.

PMID: 32887843 [PubMed - as supplied by publisher]

Intrinsic control of muscle attachment sites matching.

Elife. 2020 Jul 24;9:

Authors: Carayon A, Bataillé L, Lebreton G, Dubois L, Pelletier A, Carrier Y, Wystrach A, Vincent A, Frendo JL

Abstract
Myogenesis is an evolutionarily conserved process. Little known, however, is how the morphology of each muscle is determined, such that movements relying upon contraction of many muscles are both precise and coordinated. Each Drosophila larval muscle is a single multinucleated fiber whose morphology reflects expression of distinctive identity Transcription Factors (iTFs). By deleting transcription cis-regulatory modules of one iTF, Collier, we generated viable muscle identity mutants, allowing live imaging and locomotion assays. We show that both selection of muscle attachment sites and muscle/muscle matching is intrinsic to muscle identity and requires transcriptional reprogramming of syncytial nuclei. Live-imaging shows that the staggered muscle pattern involves attraction to tendon cells and heterotypic muscle-muscle adhesion. Unbalance leads to formation of branched muscles, and this correlates with locomotor behavior deficit. Thus, engineering Drosophila muscle identity mutants allows to investigate, in vivo, physiological and mechanical properties of abnormal muscles.

PMID: 32706334 [PubMed - as supplied by publisher]

Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina.

Development. 2020 Jul 06;:

Authors: Chan CSK, Lonfat N, Zhao R, Davis AE, Li L, Wu MR, Lin CH, Ji Z, Cepko CL, Wang S

Abstract
Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, Orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells utilize a cohort of TFs with different expression patterns, and multiple CRMs with different chromatin configurations, to precisely regulate the expression of Otx2.

PMID: 32631829 [PubMed - as supplied by publisher]