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Article ; Online: Perfect and imperfect views of ultraconserved sequences.

Snetkova, Valentina / Pennacchio, Len A / Visel, Axel / Dickel, Diane E

2021 Volume 23, Issue 3, Page(s) 182–194

Abstract: Across the human genome, there are nearly 500 'ultraconserved' elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes. Remarkably, the majority of these sequences are non-coding, and many ... ...

Abstract	Across the human genome, there are nearly 500 'ultraconserved' elements: regions of at least 200 contiguous nucleotides that are perfectly conserved in both the mouse and rat genomes. Remarkably, the majority of these sequences are non-coding, and many can function as enhancers that activate tissue-specific gene expression during embryonic development. From their first description more than 15 years ago, their extreme conservation has both fascinated and perplexed researchers in genomics and evolutionary biology. The intrigue around ultraconserved elements only grew with the observation that they are dispensable for viability. Here, we review recent progress towards understanding the general importance and the specific functions of ultraconserved sequences in mammalian development and human disease and discuss possible explanations for their extreme conservation.
MeSH term(s)	Animals ; Conserved Sequence/physiology ; Embryonic Development/genetics ; Enhancer Elements, Genetic ; Female ; Genome/genetics ; Genomics/methods ; Genomics/trends ; History, 21st Century ; Humans ; Mammals/genetics ; Mice ; Pregnancy ; Rats
Language	English
Publishing date	2021-11-11
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2035157-4
ISSN	1471-0064 ; 1471-0056
ISSN (online)	1471-0064
ISSN	1471-0056
DOI	10.1038/s41576-021-00424-x
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Article ; Online: Single cell evaluation of endocardial Hand2 gene regulatory networks reveals HAND2-dependent pathways that impact cardiac morphogenesis.

George, Rajani M / Firulli, Beth A / Podicheti, Ram / Rusch, Douglas B / Mannion, Brandon J / Pennacchio, Len A / Osterwalder, Marco / Firulli, Anthony B

Development (Cambridge, England)

2023 Volume 150, Issue 3

Abstract: The transcription factor HAND2 plays essential roles during cardiogenesis. Hand2 endocardial deletion (H2CKO) results in tricuspid atresia or double inlet left ventricle with accompanying intraventricular septum defects, hypo-trabeculated ventricles and ... ...

Abstract	The transcription factor HAND2 plays essential roles during cardiogenesis. Hand2 endocardial deletion (H2CKO) results in tricuspid atresia or double inlet left ventricle with accompanying intraventricular septum defects, hypo-trabeculated ventricles and an increased density of coronary lumens. To understand the regulatory mechanisms of these phenotypes, single cell transcriptome analysis of mouse E11.5 H2CKO hearts was performed revealing a number of disrupted endocardial regulatory pathways. Using HAND2 DNA occupancy data, we identify several HAND2-dependent enhancers, including two endothelial enhancers for the shear-stress master regulator KLF2. A 1.8 kb enhancer located 50 kb upstream of the Klf2 TSS imparts specific endothelial/endocardial expression within the vasculature and endocardium. This enhancer is HAND2-dependent for ventricular endocardium expression but HAND2-independent for Klf2 vascular and valve expression. Deletion of this Klf2 enhancer results in reduced Klf2 expression within ventricular endocardium. These data reveal that HAND2 functions within endocardial gene regulatory networks including shear-stress response.
MeSH term(s)	Animals ; Mice ; Endocardium/metabolism ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Morphogenesis/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; Hand2 protein, mouse
Language	English
Publishing date	2023-02-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.201341
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Article ; Online: Increased enhancer-promoter interactions during developmental enhancer activation in mammals.

Chen, Zhuoxin / Snetkova, Valentina / Bower, Grace / Jacinto, Sandra / Clock, Benjamin / Dizehchi, Atrin / Barozzi, Iros / Mannion, Brandon J / Alcaina-Caro, Ana / Lopez-Rios, Javier / Dickel, Diane E / Visel, Axel / Pennacchio, Len A / Kvon, Evgeny Z

Nature genetics

2024 Volume 56, Issue 4, Page(s) 675–685

Abstract: Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during ... ...

Abstract	Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
MeSH term(s)	Animals ; Mice ; Enhancer Elements, Genetic/genetics ; Promoter Regions, Genetic/genetics ; Transcriptional Activation/genetics ; Mammals/genetics ; Chromatin/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2024-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-024-01681-2
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Article: Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity.

Kosicki, Michael / Cintrón, Dianne Laboy / Page, Nicholas F / Georgakopoulos-Soares, Ilias / Akiyama, Jennifer A / Plajzer-Frick, Ingrid / Novak, Catherine S / Kato, Momoe / Hunter, Riana D / von Maydell, Kianna / Barton, Sarah / Godfrey, Patrick / Beckman, Erik / Sanders, Stephan J / Pennacchio, Len A / Ahituv, Nadav

bioRxiv : the preprint server for biology

2024

Abstract: Genetic studies find hundreds of thousands of noncoding variants associated with psychiatric disorders. Massively parallel reporter assays (MPRAs) ... ...

Abstract	Genetic studies find hundreds of thousands of noncoding variants associated with psychiatric disorders. Massively parallel reporter assays (MPRAs) and
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.22.590634
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Article: Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation

Li, Shan / Kvon, Evgeny Z / Visel, Axel / Pennacchio, Len A / Ovcharenko, Ivan

Genome biology. 2019 Dec., v. 20, no. 1

2019

Abstract: BACKGROUND: Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations ( ... ...

Abstract	BACKGROUND: Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations (deMs) in enhancer sequences. Here, we focus on elucidating the mechanism underlying the different densities of deMs in human enhancers. RESULTS: We identify two classes of enhancers based on the density of nucleotides prone to deMs. Firstly, fragile enhancers with abundant deM nucleotides are associated with the immune system and regular cellular maintenance. Secondly, stable enhancers with only a few deM nucleotides are associated with the development and regulation of TFs and are evolutionarily conserved. These two classes of enhancers feature different regulatory programs: the binding sites of pioneer TFs of FOX family are specifically enriched in stable enhancers, while tissue-specific TFs are enriched in fragile enhancers. Moreover, stable enhancers are more tolerant of deMs due to their dominant employment of homotypic TF binding site (TFBS) clusters, as opposed to the larger-extent usage of heterotypic TFBS clusters in fragile enhancers. Notably, the sequence environment and chromatin context of the cognate motif, other than the motif itself, contribute more to the susceptibility to deMs of TF binding. CONCLUSIONS: This dichotomy of enhancer activity is conserved across different tissues, has a specific footprint in epigenetic profiles, and argues for a bimodal evolution of gene regulatory programs in vertebrates. Specifically encoded stable enhancers are evolutionarily conserved and associated with development, while differently encoded fragile enhancers are associated with the adaptation of species.
Keywords	binding sites ; chromatin ; enhancer elements ; epigenetics ; evolutionary adaptation ; genes ; humans ; immune system ; mutation ; nucleotides ; tissues ; transcription factors
Language	English
Dates of publication	2019-12
Size	p. 140.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-019-1750-z
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Article ; Online: HAND transcription factors cooperatively specify the aorta and pulmonary trunk.

Vincentz, Joshua W / Firulli, Beth A / Toolan, Kevin P / Osterwalder, Marco / Pennacchio, Len A / Firulli, Anthony B

Developmental biology

2021 Volume 476, Page(s) 1–10

Abstract: Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart ...

Abstract	Congenital heart defects (CHDs) affecting the cardiac outflow tract (OFT) constitute a significant cause of morbidity and mortality. The OFT develops from migratory cell populations which include the cardiac neural crest cells (cNCCs) and secondary heart field (SHF) derived myocardium and endocardium. The related transcription factors HAND1 and HAND2 have been implicated in human CHDs involving the OFT. Although Hand1 is expressed within the OFT, Hand1 NCC-specific conditional knockout mice (H1CKOs) are viable. Here we show that these H1CKOs present a low penetrance of OFT phenotypes, whereas SHF-specific Hand1 ablation does not reveal any cardiac phenotypes. Further, HAND1 and HAND2 appear functionally redundant within the cNCCs, as a reduction/ablation of Hand2 on an NCC-specific H1CKO background causes pronounced OFT defects. Double conditional Hand1 and Hand2 NCC knockouts exhibit persistent truncus arteriosus (PTA) with 100% penetrance. NCC lineage-tracing and Sema3c in situ mRNA expression reveal that Sema3c-expressing cells are mis-localized, resulting in a malformed septal bridge within the OFTs of H1CKO;H2CKO embryos. Interestingly, Hand1 and Hand2 also genetically interact within the SHF, as SHF H1CKOs on a heterozygous Hand2 background exhibit Ventricular Septal Defects (VSDs) with incomplete penetrance. Previously, we identified a BMP, HAND2, and GATA-dependent Hand1 OFT enhancer sufficient to drive reporter gene expression within the nascent OFT and aorta. Using these transcription inputs as a probe, we identify a novel Hand2 OFT enhancer, suggesting that a conserved BMP-GATA dependent mechanism transcriptionally regulates both HAND factors. These findings support the hypothesis that HAND factors interpret BMP signaling within the cNCCs to cooperatively coordinate OFT morphogenesis.
MeSH term(s)	Animals ; Aorta/embryology ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Cardiac Output/physiology ; Cell Movement/genetics ; Gene Expression Regulation, Developmental/genetics ; Heart/embryology ; Heart Defects, Congenital/genetics ; Heart Defects, Congenital/metabolism ; Homeodomain Proteins/metabolism ; Mice ; Mice, Knockout ; Myocardium/metabolism ; Myocytes, Cardiac/metabolism ; Neural Crest/metabolism ; Phenotype ; Signal Transduction/genetics ; Transcription Factors/genetics
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Hand1 protein, mouse ; Hand2 protein, mouse ; Homeodomain Proteins ; Transcription Factors ; helix-loop-helix protein, eHAND
Language	English
Publishing date	2021-03-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2021.03.011
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Article ; Online: Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.

Li, Shan / Kvon, Evgeny Z / Visel, Axel / Pennacchio, Len A / Ovcharenko, Ivan

Genome biology

2019 Volume 20, Issue 1, Page(s) 140

Abstract: Background: Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations ( ... ...

Abstract	Background: Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF binding deactivating mutations (deMs) in enhancer sequences. Here, we focus on elucidating the mechanism underlying the different densities of deMs in human enhancers. Results: We identify two classes of enhancers based on the density of nucleotides prone to deMs. Firstly, fragile enhancers with abundant deM nucleotides are associated with the immune system and regular cellular maintenance. Secondly, stable enhancers with only a few deM nucleotides are associated with the development and regulation of TFs and are evolutionarily conserved. These two classes of enhancers feature different regulatory programs: the binding sites of pioneer TFs of FOX family are specifically enriched in stable enhancers, while tissue-specific TFs are enriched in fragile enhancers. Moreover, stable enhancers are more tolerant of deMs due to their dominant employment of homotypic TF binding site (TFBS) clusters, as opposed to the larger-extent usage of heterotypic TFBS clusters in fragile enhancers. Notably, the sequence environment and chromatin context of the cognate motif, other than the motif itself, contribute more to the susceptibility to deMs of TF binding. Conclusions: This dichotomy of enhancer activity is conserved across different tissues, has a specific footprint in epigenetic profiles, and argues for a bimodal evolution of gene regulatory programs in vertebrates. Specifically encoded stable enhancers are evolutionarily conserved and associated with development, while differently encoded fragile enhancers are associated with the adaptation of species.
MeSH term(s)	Adaptation, Biological ; Animals ; Enhancer Elements, Genetic ; Evolution, Molecular ; Genes, Reporter ; Hep G2 Cells ; Humans ; Mice, Transgenic ; Mutation
Language	English
Publishing date	2019-07-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-019-1750-z
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Article: Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis.

Catta-Preta, Rinaldo / Lindtner, Susan / Ypsilanti, Athena / Price, James / Abnousi, Armen / Su-Feher, Linda / Wang, Yurong / Juric, Ivan / Jones, Ian R / Akiyama, Jennifer A / Hu, Ming / Shen, Yin / Visel, Axel / Pennacchio, Len A / Dickel, Diane / Rubenstein, John L R / Nord, Alex S

bioRxiv : the preprint server for biology

2023

Abstract: Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, ... ...

Abstract	Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.
Language	English
Publishing date	2023-06-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.28.546894
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Article ; Online: Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range.

Edwards, Joseph A / Saran, Usha Bishnoi / Bonnette, Jason / MacQueen, Alice / Yin, Jun / Nguyen, Tu Uyen / Schmutz, Jeremy / Grimwood, Jane / Pennacchio, Len A / Daum, Chris / Glavina Del Rio, Tijana / Fritschi, Felix B / Lowry, David B / Juenger, Thomas E

Current biology : CB

2023 Volume 33, Issue 10, Page(s) 1926–1938.e6

Abstract: A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the ...

Abstract	A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
MeSH term(s)	Panicum/genetics ; Genome-Wide Association Study ; Microbiota ; Bacteria/genetics ; Genotype
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2023.03.078
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Article: Rare variation in noncoding regions with evolutionary signatures contributes to autism spectrum disorder risk.

Shin, Taehwan / Song, Janet H T / Kosicki, Michael / Kenny, Connor / Beck, Samantha G / Kelley, Lily / Qian, Xuyu / Bonacina, Julieta / Papandile, Frances / Antony, Irene / Gonzalez, Dilenny / Scotellaro, Julia / Bushinsky, Evan M / Andersen, Rebecca E / Maury, Eduardo / Pennacchio, Len A / Doan, Ryan N / Walsh, Christopher A

medRxiv : the preprint server for health sciences

2023

Abstract: Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally ...

Abstract	Little is known about the role of noncoding regions in the etiology of autism spectrum disorder (ASD). We examined three classes of noncoding regions: Human Accelerated Regions (HARs), which show signatures of positive selection in humans; experimentally validated neural Vista Enhancers (VEs); and conserved regions predicted to act as neural enhancers (CNEs). Targeted and whole genome analysis of >16,600 samples and >4900 ASD probands revealed that likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents share ancestry, which enriches for recessive contributions, but modestly, if at all, in simplex family structures. We identified multiple patient variants in HARs near
Language	English
Publishing date	2023-09-22
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.19.23295780
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