bims-crepig 2023-12-03 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023‒12‒03
twenty papers selected by
Connor Rogerson, University of Cambridge

Epigenetic pioneering by SWI/SNF family remodelers.
Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation.
SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors.
Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens.
Chromosome-specific maturation of the epigenome in the Drosophila male germline.
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer.
HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis.
Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells.
MSL2 ensures biallelic gene expression in mammals.
Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.
FOXP3 recognizes microsatellites and bridges DNA through multimerization.
A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription.
MAE-seq refines regulatory elements across the genome.
Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation.
MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks.
MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm.
Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer.
A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription.
Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans.
Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors.

Mol Cell. 2023 Nov 16. pii: S1097-2765(23)00916-4. [Epub ahead of print]

Epigenetic pioneering by SWI/SNF family remodelers.

Kami Ahmad, Sandipan Brahma, Steven Henikoff.

  In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.

Keywords:  ATP-dependent remodeling; cancer; chromatin; development; gene regulation; histone; nucleosome; transcription factor

DOI:  https://doi.org/10.1016/j.molcel.2023.10.045
Genome Biol. 2023 Nov 27. 24(1): 269

Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation.

Jun Wang, Xuesen Cheng, Qingnan Liang, Leah A Owen, Jiaxiong Lu, Yiqiao Zheng, Meng Wang, Shiming Chen, Margaret M DeAngelis, Yumei Li, Rui Chen.

  BACKGROUND: Systematic characterization of how genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits. To address this question, we profile gene expression and chromatin accessibility in cells from healthy retinae of 20 human donors through single-cell multiomics and genomic sequencing.RESULTS: We map eQTL, caQTL, allelic-specific expression, and allelic-specific chromatin accessibility in major retinal cell types. By integrating these results, we identify and characterize regulatory elements and genetic variants effective on gene regulation in individual cell types. The majority of identified sc-eQTLs and sc-caQTLs display cell type-specific effects, while the cis-elements containing genetic variants with cell type-specific effects are often accessible in multiple cell types. Furthermore, the transcription factors whose binding sites are perturbed by genetic variants tend to have higher expression levels in the cell types where the variants exert their effects, compared to the cell types where the variants have no impact. We further validate our findings with high-throughput reporter assays. Lastly, we identify the enriched cell types, candidate causal variants and genes, and cell type-specific regulatory mechanism underlying GWAS loci.
CONCLUSIONS: Overall, genetic effects on gene regulation are highly context dependent. Our results suggest that cell type-dependent genetic effect is driven by precise modulation of both trans-factor expression and chromatin accessibility of cis-elements. Our findings indicate hierarchical collaboration among transcription factors plays a crucial role in mediating cell type-specific effects of genetic variants on gene regulation.

Keywords:  ASCA; ASE; Cell type-specific effect; Gene regulation; Genetic variants; Single-cell multiomics; The human retina; Transcription factor collaboration; caQTL; eQTL

DOI:  https://doi.org/10.1186/s13059-023-03111-8
Nat Commun. 2023 Dec 01. 14(1): 7762

SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors.

Ning Qing Liu, Irene Paassen, Lars Custers, Peter Zeller, Hans Teunissen, Dilara Ayyildiz, Jiayou He, Juliane Laura Buhl, Eelco Wieger Hoving, Alexander van Oudenaarden, Elzo de Wit, Jarno Drost.

Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.

DOI: https://doi.org/10.1038/s41467-023-43498-3
Nat Commun. 2023 Nov 28. 14(1): 7464

Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens.

Shaela Wright, Xujie Zhao, Wojciech Rosikiewicz, Shelby Mryncza, Judith Hyle, Wenjie Qi, Zhenling Liu, Siqi Yi, Yong Cheng, Beisi Xu, Chunliang Li.

Accumulating evidence indicates that HOXA9 dysregulation is necessary and sufficient for leukemic transformation and maintenance. However, it remains largely unknown how HOXA9, as a homeobox transcriptional factor, binds to noncoding regulatory sequences and controls the downstream genes. Here, we conduct dropout CRISPR screens against 229 HOXA9-bound peaks identified by ChIP-seq. Integrative data analysis identifies reproducible noncoding hits, including those located in the distal enhancer of FLT3 and intron of CDK6. The Cas9-editing and dCas9-KRAB silencing of the HOXA9-bound sites significantly reduce corresponding gene transcription and impair cell proliferation in vitro, and in vivo by transplantation into NSG female mice. In addition, RNA-seq, Q-PCR analysis, chromatin accessibility change, and chromatin conformation evaluation uncover the noncoding regulation mechanism of HOXA9 and its functional downstream genes. In summary, our work improves our understanding of how HOXA9-associated transcription programs reconstruct the regulatory network specifying MLL-r dependency.

DOI: https://doi.org/10.1038/s41467-023-43264-5
Elife. 2023 Nov 30. pii: RP89373. [Epub ahead of print]12

Chromosome-specific maturation of the epigenome in the Drosophila male germline.

James T Anderson, Steven Henikoff, Kami Ahmad.

  Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.

Keywords:  D. melanogaster; chromatin; chromosomes; gene expression; gene regulation; genetics; genomics; germline development

DOI:  https://doi.org/10.7554/eLife.89373
Nucleic Acids Res. 2023 Nov 28. pii: gkad1126. [Epub ahead of print]

Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer.

Laura Helminen, Jasmin Huttunen, Melina Tulonen, Niina Aaltonen, Einari A Niskanen, Jorma J Palvimo, Ville Paakinaho.

Treatment of prostate cancer relies predominantly on the inhibition of androgen receptor (AR) signaling. Despite the initial effectiveness of the antiandrogen therapies, the cancer often develops resistance to the AR blockade. One mechanism of the resistance is glucocorticoid receptor (GR)-mediated replacement of AR function. Nevertheless, the mechanistic ways and means how the GR-mediated antiandrogen resistance occurs have remained elusive. Here, we have discovered several crucial features of GR action in prostate cancer cells through genome-wide techniques. We detected that the replacement of AR by GR in enzalutamide-exposed prostate cancer cells occurs almost exclusively at pre-accessible chromatin sites displaying FOXA1 occupancy. Counterintuitively to the classical pioneer factor model, silencing of FOXA1 potentiated the chromatin binding and transcriptional activity of GR. This was attributed to FOXA1-mediated repression of the NR3C1 (gene encoding GR) expression via the corepressor TLE3. Moreover, the small-molecule inhibition of coactivator p300's enzymatic activity efficiently restricted GR-mediated gene regulation and cell proliferation. Overall, we identified chromatin pre-accessibility and FOXA1-mediated repression as important regulators of GR action in prostate cancer, pointing out new avenues to oppose steroid receptor-mediated antiandrogen resistance.

DOI: https://doi.org/10.1093/nar/gkad1126
Nat Commun. 2023 Nov 29. 14(1): 7759

HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis.

Michael F Emmons, Richard L Bennett, Alberto Riva, Kanchan Gupta, Larissa Anastasio Da Costa Carvalho, Chao Zhang, Robert Macaulay, Daphne Dupéré-Richér, Bin Fang, Edward Seto, John M Koomen, Jiannong Li, Y Ann Chen, Peter A Forsyth, Jonathan D Licht, Keiran S M Smalley.

Melanomas can adopt multiple transcriptional states. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity. Here, we identify stress-induced HDAC8 activity as driving melanoma brain metastasis development. Exposure of melanocytes and melanoma cells to multiple stresses increases HDAC8 activation leading to a neural crest-stem cell transcriptional state and an amoeboid, invasive phenotype that increases seeding to the brain. Using ATAC-Seq and ChIP-Seq we show that increased HDAC8 activity alters chromatin structure by increasing H3K27ac and enhancing accessibility at c-Jun binding sites. Functionally, HDAC8 deacetylates the histone acetyltransferase EP300, causing its enzymatic inactivation. This, in turn, increases binding of EP300 to Jun-transcriptional sites and decreases binding to MITF-transcriptional sites. Inhibition of EP300 increases melanoma cell invasion, resistance to stress and increases melanoma brain metastasis development. HDAC8 is identified as a mediator of transcriptional co-factor inactivation and chromatin accessibility that drives brain metastasis.

DOI: https://doi.org/10.1038/s41467-023-43519-1
Cell Genom. 2023 Nov 08. 3(11): 100424

Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells.

Michael J G Milevskiy, Hannah D Coughlan, Serena R Kane, Timothy M Johanson, Somayeh Kordafshari, Wing Fuk Chan, Minhsuang Tsai, Elliot Surgenor, Stephen Wilcox, Rhys S Allan, Yunshun Chen, Geoffrey J Lindeman, Gordon K Smyth, Jane E Visvader.

  Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.

Keywords:  chromatin looping; enhancer; epigenetics; mammary gland; polycomb; stem cells; transcription factors

DOI:  https://doi.org/10.1016/j.xgen.2023.100424
Nature. 2023 Nov 29.

MSL2 ensures biallelic gene expression in mammals.

Yidan Sun, Meike Wiese, Raed Hmadi, Remzi Karayol, Janine Seyfferth, Juan Alfonso Martinez Greene, Niyazi Umut Erdogdu, Ward Deboutte, Laura Arrigoni, Herbert Holz, Gina Renschler, Naama Hirsch, Arion Foertsch, Maria Felicia Basilicata, Thomas Stehle, Maria Shvedunova, Chiara Bella, Cecilia Pessoa Rodrigues, Bjoern Schwalb, Patrick Cramer, Thomas Manke, Asifa Akhtar.

In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.

DOI: https://doi.org/10.1038/s41586-023-06781-3
Nucleic Acids Res. 2023 Nov 28. pii: gkad1121. [Epub ahead of print]

Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.

Zilong Li, Tamar Schlick.

The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.

DOI: https://doi.org/10.1093/nar/gkad1121
Nature. 2023 Nov 29.

FOXP3 recognizes microsatellites and bridges DNA through multimerization.

Wenxiang Zhang, Fangwei Leng, Xi Wang, Ricardo N Ramirez, Jinseok Park, Christophe Benoist, Sun Hur.

FOXP3 is a transcription factor that is essential for the development of regulatory T cells, a branch of T cells that suppress excessive inflammation and autoimmunity1-5. However, the molecular mechanisms of FOXP3 remain unclear. Here we here show that FOXP3 uses the forkhead domain-a DNA-binding domain that is commonly thought to function as a monomer or dimer-to form a higher-order multimer after binding to TnG repeat microsatellites. The cryo-electron microscopy structure of FOXP3 in a complex with T3G repeats reveals a ladder-like architecture, whereby two double-stranded DNA molecules form the two 'side rails' bridged by five pairs of FOXP3 molecules, with each pair forming a 'rung'. Each FOXP3 subunit occupies TGTTTGT within the repeats in a manner that is indistinguishable from that of FOXP3 bound to the forkhead consensus motif (TGTTTAC). Mutations in the intra-rung interface impair TnG repeat recognition, DNA bridging and the cellular functions of FOXP3, all without affecting binding to the forkhead consensus motif. FOXP3 can tolerate variable inter-rung spacings, explaining its broad specificity for TnG-repeat-like sequences in vivo and in vitro. Both FOXP3 orthologues and paralogues show similar TnG repeat recognition and DNA bridging. These findings therefore reveal a mode of DNA recognition that involves transcription factor homomultimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.

DOI: https://doi.org/10.1038/s41586-023-06793-z
Nat Genet. 2023 Nov 30.

A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription.

Vladimir Seplyarskiy, Evan M Koch, Daniel J Lee, Joshua S Lichtman, Harding H Luan, Shamil R Sunyaev.

De novo mutations occur at substantially different rates depending on genomic location, sequence context and DNA strand. The success of methods to estimate selection intensity, infer demographic history and map rare disease genes, depends strongly on assumptions about the local mutation rate. Here we present Roulette, a genome-wide mutation rate model at basepair resolution that incorporates known determinants of local mutation rate. Roulette is shown to be more accurate than existing models. We use Roulette to refine the estimates of population growth within Europe by incorporating the full range of human mutation rates. The analysis of significant deviations from the model predictions revealed a tenfold increase in mutation rate in nearly all genes transcribed by polymerase III (Pol III), suggesting a new mutagenic mechanism. We also detected an elevated mutation rate within transcription factor binding sites restricted to sites actively used in testis and residing in promoters.

DOI: https://doi.org/10.1038/s41588-023-01562-0
Nucleic Acids Res. 2023 Dec 01. pii: gkad1129. [Epub ahead of print]

MAE-seq refines regulatory elements across the genome.

Xiusheng Zhu, Qitong Huang, Lei Huang, Jing Luo, Qing Li, Dashuai Kong, Biao Deng, Yi Gu, Xueyan Wang, Chenying Li, Siyuan Kong, Yubo Zhang.

Proper cell fate determination relies on precise spatial and temporal genome-wide cooperation between regulatory elements (REs) and their targeted genes. However, the lengths of REs defined using different methods vary, which indicates that there is sequence redundancy and that the context of the genome may be unintelligible. We developed a method called MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, MAE-seq was used to identify 626879, 541617 and 554826 25-bp enhancers in mouse embryonic stem cells (mESCs), C2C12 and HEK 293T, respectively. Using ∼1.6 trillion 25 bp DNA fragments and screening 12 billion cells, we identified 626879 as active enhancers in mESCs as an example. Comparative analysis revealed that most of the histone modification datasets were annotated by MAE-Seq loci. Furthermore, 33.85% (212195) of the identified enhancers were identified as de novo ones with no epigenetic modification. Intriguingly, distinct chromatin states dictate the requirement for dissimilar cofactors in governing novel and known enhancers. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements, Enhanced resolution facilitated the identification of numerous cell-specific enhancers and their accurate annotation as super enhancers. Moreover, we characterized novel elements capable of augmenting gene activity. By integrating with high-resolution Hi-C data, over 55.64% of novel elements may have a distal association with different targeted genes. For example, we found that the Cdh1 gene interacts with one novel and two known REs in mESCs. The biological effects of these interactions were investigated using CRISPR-Cas9, revealing their role in coordinating Cdh1 gene expression and mESC proliferation. Our study presents an experimental approach to refine the REs at 25-bp resolution, advancing the precision of genome annotation and unveiling the underlying genome context. This novel approach not only advances our understanding of gene regulation but also opens avenues for comprehensive exploration of the genomic landscape.

DOI: https://doi.org/10.1093/nar/gkad1129
Genome Biol. 2023 Nov 28. 24(1): 264

Methylation-directed regulatory networks determine enhancing and silencing of mutation disease driver genes and explain inter-patient expression variation.

Yifat Edrei, Revital Levy, Daniel Kaye, Anat Marom, Bernhard Radlwimmer, Asaf Hellman.

  BACKGROUND: Common diseases manifest differentially between patients, but the genetic origin of this variation remains unclear. To explore possible involvement of gene transcriptional-variation, we produce a DNA methylation-oriented, driver-gene-wide dataset of regulatory elements in human glioblastomas and study their effect on inter-patient gene expression variation.RESULTS: In 175 of 177 analyzed gene regulatory domains, transcriptional enhancers and silencers are intermixed. Under experimental conditions, DNA methylation induces enhancers to alter their enhancing effects or convert into silencers, while silencers are affected inversely. High-resolution mapping of the association between DNA methylation and gene expression in intact genomes reveals methylation-related regulatory units (average size = 915.1 base-pairs). Upon increased methylation of these units, their target-genes either increased or decreased in expression. Gene-enhancing and silencing units constitute cis-regulatory networks of genes. Mathematical modeling of the networks highlights indicative methylation sites, which signified the effect of key regulatory units, and add up to make the overall transcriptional effect of the network. Methylation variation in these sites effectively describe inter-patient expression variation and, compared with DNA sequence-alterations, appears as a major contributor of gene-expression variation among glioblastoma patients.
CONCLUSIONS: We describe complex cis-regulatory networks, which determine gene expression by summing the effects of positive and negative transcriptional inputs. In these networks, DNA methylation induces both enhancing and silencing effects, depending on the context. The revealed mechanism sheds light on the regulatory role of DNA methylation, explains inter-individual gene-expression variation, and opens the way for monitoring the driving forces behind deferential courses of cancer and other diseases.

Keywords:  Cancer driver genes; Cis-regulatory elements; DNA methylations; Enhancers; Expression variation; Gene regulation; Gene regulatory-domains; Glioblastoma; Silencers

DOI:  https://doi.org/10.1186/s13059-023-03094-6
PLoS One. 2023 ;18(11): e0294724

MORA and EnsembleTFpredictor: An ensemble approach to reveal functional transcription factor regulatory networks.

Kevin Boyer, Louis Li, Tiandao Li, Bo Zhang, Guoyan Zhao.

MOTIVATION: Our study aimed to identify biologically relevant transcription factors (TFs) that control the expression of a set of co-expressed or co-regulated genes.RESULTS: We developed a fully automated pipeline, Motif Over Representation Analysis (MORA), to detect enrichment of known TF binding motifs in any query sequences. MORA performed better than or comparable to five other TF-prediction tools as evaluated using hundreds of differentially expressed gene sets and ChIP-seq datasets derived from known TFs. Additionally, we developed EnsembleTFpredictor to harness the power of multiple TF-prediction tools to provide a list of functional TFs ranked by prediction confidence. When applied to the test datasets, EnsembleTFpredictor not only identified the target TF but also revealed many TFs known to cooperate with the target TF in the corresponding biological systems. MORA and EnsembleTFpredictor have been used in two publications, demonstrating their power in guiding experimental design and in revealing novel biological insights.

DOI: https://doi.org/10.1371/journal.pone.0294724
Comput Biol Med. 2023 Nov 25. pii: S0010-4825(23)01218-0. [Epub ahead of print]168 107753

MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm.

Zhe Liu, Hiu-Man Wong, Xingjian Chen, Jiecong Lin, Shixiong Zhang, Shankai Yan, Fuzhou Wang, Xiangtao Li, Ka-Chun Wong.

  BACKGROUND: Trans-acting factors are of special importance in transcription regulation, which is a group of proteins that can directly or indirectly recognize or bind to the 8-12 bp core sequence of cis-acting elements and regulate the transcription efficiency of target genes. The progressive development in high-throughput chromatin capture technology (e.g., Hi-C) enables the identification of chromatin-interacting sequence groups where trans-acting DNA motif groups can be discovered. The problem difficulty lies in the combinatorial nature of DNA sequence pattern matching and its underlying sequence pattern search space.METHOD: Here, we propose to develop MotifHub for trans-acting DNA motif group discovery on grouped sequences. Specifically, the main approach is to develop probabilistic modeling for accommodating the stochastic nature of DNA motif patterns.
RESULTS: Based on the modeling, we develop global sampling techniques based on EM and Gibbs sampling to address the global optimization challenge for model fitting with latent variables. The results reflect that our proposed approaches demonstrate promising performance with linear time complexities.
CONCLUSION: MotifHub is a novel algorithm considering the identification of both DNA co-binding motif groups and trans-acting TFs. Our study paves the way for identifying hub TFs of stem cell development (OCT4 and SOX2) and determining potential therapeutic targets of prostate cancer (FOXA1 and MYC). To ensure scientific reproducibility and long-term impact, its matrix-algebra-optimized source code is released at http://bioinfo.cs.cityu.edu.hk/MotifHub.

Keywords:  Cancer; Hi-C; Probabilistic modeling algorithm; Stem cell development; Trans-acting DNA motif group

DOI:  https://doi.org/10.1016/j.compbiomed.2023.107753
Genome Biol. 2023 Nov 27. 24(1): 268

Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer.

Xiang Lin, Ji-Dong Chen, Chen-Yu Wang, Zhen Cai, Rui Zhan, Chen Yang, La-Ying Zhang, Lian-Yun Li, Yong Xiao, Ming-Kai Chen, Min Wu.

  BACKGROUND: Enhancer dysregulation is one of the important features for cancer cells. Enhancers enriched with H3K4me3 have been implicated to play important roles in cancer. However, their detailed features and regulatory mechanisms have not been well characterized.RESULTS: Here, we profile the landscape of H3K4me3-enriched enhancers (m3Es) in 43 pairs of colorectal cancer (CRC) samples. M3Es are widely distributed in CRC and averagely possess around 10% of total active enhancers. We identify 1322 gain variant m3Es and 367 lost variant m3Es in CRC. The target genes of the gain m3Es are enriched in immune response pathways. We experimentally prove that repression of CBX8 and RPS6KA5 m3Es inhibits target gene expression in CRC. Furthermore, we find histone methyltransferase MLL1 is responsible for depositing H3K4me3 on the identified Vm3Es. We demonstrate that the transcription factor AP1/JUN interacts with MLL1 and regulates m3E activity. Application of a small chemical inhibitor for MLL1 activity, OICR-9429, represses target gene expression of the identified Vm3Es, enhances anti-tumor immunity and inhibits CRC growth in an animal model.
CONCLUSIONS: Taken together, our study illustrates the genome-wide landscape and the regulatory mechanisms of m3Es in CRC, and reveals potential novel strategies for cancer treatment.

Keywords:  Colorectal cancer; Enhancers; H3K4me3; JUN; MLL1

DOI:  https://doi.org/10.1186/s13059-023-03108-3
Mol Cell. 2023 Nov 23. pii: S1097-2765(23)00920-6. [Epub ahead of print]

A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription.

Manuel Carminati, Juan B Rodríguez-Molina, M Cemre Manav, Dom Bellini, Lori A Passmore.

  Transcription termination by RNA polymerase II (RNA Pol II) is linked to RNA 3' end processing by the cleavage and polyadenylation factor (CPF or CPSF). CPF contains endonuclease, poly(A) polymerase, and protein phosphatase activities, which cleave and polyadenylate pre-mRNAs and dephosphorylate RNA Pol II to control transcription. Exactly how the RNA 3' end processing machinery is coupled to transcription remains unclear. Here, we combine in vitro reconstitution, structural studies, and genome-wide analyses to show that yeast CPF physically and functionally interacts with RNA Pol II. Surprisingly, CPF-mediated dephosphorylation promotes the formation of an RNA Pol II stalk-to-stalk homodimer in vitro. This dimer is compatible with transcription but not with the binding of transcription elongation factors. Disruption of the dimerization interface in cells causes transcription defects, including altered RNA Pol II abundance on protein-coding genes, tRNA genes, and intergenic regions. We hypothesize that RNA Pol II dimerization may provide a mechanistic basis for the allosteric model of transcription termination.

Keywords:  CPSF; X-ray crystallography; cryo-EM; phosphatase; poly(A) tail; polymerase; transcription

DOI:  https://doi.org/10.1016/j.molcel.2023.11.004
Elife. 2023 Dec 01. pii: RP84355. [Epub ahead of print]12

Dynamic compartmentalization of the pro-invasive transcription factor NHR-67 reveals a role for Groucho in regulating a proliferative-invasive cellular switch in C. elegans.

Taylor N Medwig-Kinney, Brian A Kinney, Michael A Q Martinez, Callista Yee, Sydney S Sirota, Angelina A Mullarkey, Neha Somineni, Justin Hippler, Wan Zhang, Kang Shen, Christopher Hammell, Ariel M Pani, David Q Matus.

  A growing body of evidence suggests that cell division and basement membrane invasion are mutually exclusive cellular behaviors. How cells switch between proliferative and invasive states is not well understood. Here, we investigated this dichotomy in vivo by examining two cell types in the developing Caenorhabditis elegans somatic gonad that derive from equipotent progenitors, but exhibit distinct cell behaviors: the post-mitotic, invasive anchor cell and the neighboring proliferative, non-invasive ventral uterine (VU) cells. We show that the fates of these cells post-specification are more plastic than previously appreciated and that levels of NHR-67 are important for discriminating between invasive and proliferative behavior. Transcription of NHR-67 is downregulated following post-translational degradation of its direct upstream regulator, HLH-2 (E/Daughterless) in VU cells. In the nuclei of VU cells, residual NHR-67 protein is compartmentalized into discrete punctae that are dynamic over the cell cycle and exhibit liquid-like properties. By screening for proteins that colocalize with NHR-67 punctae, we identified new regulators of uterine cell fate maintenance: homologs of the transcriptional co-repressor Groucho (UNC-37 and LSY-22), as well as the TCF/LEF homolog POP-1. We propose a model in which the association of NHR-67 with the Groucho/TCF complex suppresses the default invasive state in non-invasive cells, which complements transcriptional regulation to add robustness to the proliferative-invasive cellular switch in vivo.

Keywords:  C. elegans; cell fate; cell invasion; developmental biology; transcription factors; transdifferentiation

DOI:  https://doi.org/10.7554/eLife.84355
Mol Cancer. 2023 Nov 28. 22(1): 190

Chromatin insulation orchestrates matrix metalloproteinase gene cluster expression reprogramming in aggressive breast cancer tumors.

Pere Llinàs-Arias, Miquel Ensenyat-Mendez, Sandra Íñiguez-Muñoz, Javier I J Orozco, Betsy Valdez, Matthew P Salomon, Chikako Matsuba, Maria Solivellas-Pieras, Andrés F Bedoya-López, Borja Sesé, Anja Mezger, Mattias Ormestad, Fernando Unzueta, Siri H Strand, Alexander D Boiko, E Shelley Hwang, Javier Cortés, Maggie L DiNome, Manel Esteller, Mathieu Lupien, Diego M Marzese.

  BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive subtype that exhibits a high incidence of distant metastases and lacks targeted therapeutic options. Here we explored how the epigenome contributes to matrix metalloprotease (MMP) dysregulation impacting tumor invasion, which is the first step of the metastatic process.METHODS: We combined RNA expression and chromatin interaction data to identify insulator elements potentially associated with MMP gene expression and invasion. We employed CRISPR/Cas9 to disrupt the CCCTC-Binding Factor (CTCF) binding site on an insulator element downstream of the MMP8 gene (IE8) in two TNBC cellular models. We characterized these models by combining Hi-C, ATAC-seq, and RNA-seq with functional experiments to determine invasive ability. The potential of our findings to predict the progression of ductal carcinoma in situ (DCIS), was tested in data from clinical specimens.
RESULTS: We explored the clinical relevance of an insulator element located within the Chr11q22.2 locus, downstream of the MMP8 gene (IE8). This regulatory element resulted in a topologically associating domain (TAD) boundary that isolated nine MMP genes into two anti-correlated expression clusters. This expression pattern was associated with worse relapse-free (HR = 1.57 [1.06 - 2.33]; p = 0.023) and overall (HR = 2.65 [1.31 - 5.37], p = 0.005) survival of TNBC patients. After CRISPR/Cas9-mediated disruption of IE8, cancer cells showed a switch in the MMP expression signature, specifically downregulating the pro-invasive MMP1 gene and upregulating the antitumorigenic MMP8 gene, resulting in reduced invasive ability and collagen degradation. We observed that the MMP expression pattern predicts DCIS that eventually progresses into invasive ductal carcinomas (AUC = 0.77, p < 0.01).
CONCLUSION: Our study demonstrates how the activation of an IE near the MMP8 gene determines the regional transcriptional regulation of MMP genes with opposing functional activity, ultimately influencing the invasive properties of aggressive forms of breast cancer.

Keywords:  ATAC-seq; Breast cancer; CTCF; Chromatin; Gene regulatory element; Hi-C; Insulator; Invasion; MMP1; MMP8; RNA-seq; cis-regulatory element

DOI:  https://doi.org/10.1186/s12943-023-01906-8