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Saeki N, Inui-Yamamoto C, Ikeda Y, Kanai R, Hata K, Itoh S, Inubushi T, Akiyama S, Ohba S, Abe M. Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice. Hum Mol Genet 2024; 33:1618-1629. [PMID: 38899779 DOI: 10.1093/hmg/ddae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.
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Affiliation(s)
- Naoya Saeki
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Chizuko Inui-Yamamoto
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Rinna Kanai
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Fixed Prosthodontics and Orofacial Function, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shousaku Itoh
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shigehisa Akiyama
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Makoto Abe
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
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Hong H, Mocci E, Kamp K, Zhu S, Cain KC, Burr RL, Perry JA, Heitkemper MM, Weaver-Toedtman KR, Dorsey SG. Genetic Variations in TrkB.T1 Isoform and Their Association With Somatic and Psychological Symptoms in Individuals With IBS. THE JOURNAL OF PAIN 2024:104634. [PMID: 39004388 DOI: 10.1016/j.jpain.2024.104634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024]
Abstract
Irritable bowel syndrome (IBS), a disorder of gut-brain interaction, is often comorbid with somatic pain and psychological disorders. Dysregulated signaling of brain-derived neurotrophic factor (BDNF) and its receptor, tropomyosin-related kinase B (TrkB), has been implicated in somatic-psychological symptoms in individuals with IBS. We investigated the association of 10 single-nucleotide polymorphisms (SNPs) in the regulatory 3' untranslated region of neurotrophic receptor tyrosine kinase-2 (NTRK2) kinase domain-deficient truncated isoform (TrkB.T1) and BDNF Val66Met SNP with somatic and psychological symptoms and quality-of-life (QoL) in a cohort from the United States (IBS, n = 464; healthy controls, n = 156). We found that the homozygous recessive genotype (G/G) of rs2013566 in individuals with IBS is associated with worsened somatic symptoms, including headache, back pain, joint pain, muscle pain, and somatization as well as diminished sleep quality, energy level, and overall QoL. Validation using United Kingdom BioBank data confirmed the association of rs2013566 with an increased likelihood of headache. Several SNPs (rs1627784, rs1624327, and rs1147198) showed significant associations with muscle pain in our U.S. cohort. These 4 SNPs are predominantly located in H3K4Me1-enriched regions, suggesting their enhancer and/or transcription regulation potential. Our findings suggest that genetic variation within the 3' untranslated region region of the TrkB.T1 isoform may contribute to comorbid conditions in individuals with IBS, resulting in a spectrum of somatic and psychological symptoms impacting their QoL. These findings advance our understanding of the genetic interaction between BDNF/TrkB pathways and somatic-psychological symptoms in IBS, highlighting the importance of further exploring this interaction for potential clinical applications. PERSPECTIVE: This study aims to understand the genetic effects on IBS-related symptoms across somatic, psychological, and quality-of-life (QoL) domains, validated by United Kingdom BioBank data. The rs2013566 homozygous recessive genotype correlates with worsened somatic symptoms and reduced QoL, emphasizing its clinical significance.
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Affiliation(s)
- Hyejeong Hong
- Department of Biobehavioral Health Sciences, University of Pennsylvania School of Nursing, Philadelphia, PA
| | - Evelina Mocci
- Department of Pain and Translational Symptom Science, University of Maryland School of Nursing, Baltimore, MD
| | - Kendra Kamp
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing, Seattle, WA
| | - Shijun Zhu
- Department of Organizational Systems and Adult Health, University of Maryland School of Nursing, Baltimore, MD
| | - Kevin C Cain
- Department of Biostatistics, University of Washington School of Nursing, Seattle, WA
| | - Robert L Burr
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing, Seattle, WA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Margaret M Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing, Seattle, WA
| | - Kristen R Weaver-Toedtman
- Department of Biobehavioral Health and Nursing Science, University of South Carolina College of Nursing, Columbia, SC
| | - Susan G Dorsey
- Department of Pain and Translational Symptom Science, University of Maryland School of Nursing, Baltimore, MD.
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Saito A, Tahara R, Hirose M, Kadota M, Hasegawa A, Kondo S, Kato H, Amano T, Yoshiki A, Ogura A, Kiyosawa H. Inter-subspecies mouse F1 hybrid embryonic stem cell lines newly established for studies of allelic imbalance in gene expression. Exp Anim 2024; 73:310-318. [PMID: 38447983 PMCID: PMC11254486 DOI: 10.1538/expanim.24-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Allele-specific monoallelic gene expression is a unique phenomenon and a great resource for analyzing gene regulation. To study this phenomenon, we established new embryonic stem (ES) cell lines derived from F1 hybrid blastocysts from crosses between four mouse subspecies (Mus musculus domesticus, C57BL/6; M. musculus molossinus, MSM/Ms; M. musculus musculus, PWK; M. musculus castaneus, HMI/Ms) and analyzed the expression levels of undifferentiated pluripotent stem cell markers and karyotypes of each line. To demonstrate the utility of our cell lines, we analyzed the allele-specific expression pattern of the Inpp5d gene as an example. The allelic expression depended on the parental alleles; this dependence could be a consequence of differences in compatibility between cis- and trans-elements of the Inpp5d gene from different subspecies. The use of parental mice from four subspecies greatly enhanced genetic polymorphism. The F1 hybrid ES cells retained this polymorphism not only in the Inpp5d gene, but also at a genome-wide level. As we demonstrated for the Inpp5d gene, the established cell lines can contribute to the analysis of allelic expression imbalance based on the incompatibility between cis- and trans-elements and of phenotypes related to this incompatibility.
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Affiliation(s)
- Ayaka Saito
- Laboratory for Genome Science, Department of Life Science, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Ryosuke Tahara
- Laboratory for Genome Science, Department of Life Science, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Masayo Kadota
- Experimental Animal Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shinji Kondo
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
| | - Hidemasa Kato
- Department of Developmental Biology and Functional Genomics, Graduate School of Medicine, Ehime University, 454 Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Takanori Amano
- Next Generation Human Disease Model Team, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, BioResource Research Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Hidenori Kiyosawa
- Laboratory for Genome Science, Department of Life Science, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
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Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024; 46:e2300210. [PMID: 38715516 DOI: 10.1002/bies.202300210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Understanding the influence of cis-regulatory elements on gene regulation poses numerous challenges given complexities stemming from variations in transcription factor (TF) binding, chromatin accessibility, structural constraints, and cell-type differences. This review discusses the role of gene regulatory networks in enhancing understanding of transcriptional regulation and covers construction methods ranging from expression-based approaches to supervised machine learning. Additionally, key experimental methods, including MPRAs and CRISPR-Cas9-based screening, which have significantly contributed to understanding TF binding preferences and cis-regulatory element functions, are explored. Lastly, the potential of machine learning and artificial intelligence to unravel cis-regulatory logic is analyzed. These computational advances have far-reaching implications for precision medicine, therapeutic target discovery, and the study of genetic variations in health and disease.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ioannis Mouratidis
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nikol Chantzi
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Yasin Uzun
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
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5
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Roy Chowdhury N, Gurevich V, Shamay M. KSHV genome harbors both constitutive and lytically induced enhancers. J Virol 2024; 98:e0017924. [PMID: 38695538 PMCID: PMC11237633 DOI: 10.1128/jvi.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 06/14/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis-regulatory elements, such as enhancers and silencers, can regulate gene expression in a position- and orientation-independent manner. Open chromatin is another characteristic feature of enhancers. To systematically search for enhancers, we cloned all the open chromatin regions in the KSHV genome downstream of the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency-associated nuclear antigen promoter. Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron regions, where ORF29 Intron is a tissue-specific enhancer. The following promoters: OriLyt-L, PANp, ALTp, and the terminal repeats (TRs) acted as lytically induced enhancers. The expression of the replication and transcription activator (RTA), the master regulator of the lytic cycle, was sufficient to induce the activity of lytic enhancers in uninfected cells. We propose that the TRs that span about 24 kbp region serve as a "viral super-enhancer" that integrates the repressive effect of the latency-associated nuclear antigen (LANA) with the activating effect of RTA. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The silencer and enhancers described here provide an additional layer to the complex gene regulation of herpesviruses.IMPORTANCEIn this study, we performed a systematic functional assay to identify cis-regulatory elements within the genome of the oncogenic herpesvirus, Kaposi's sarcoma-associated herpesvirus (KSHV). Similar to other herpesviruses, KSHV presents both latent and lytic phases. Therefore, our assays were performed in uninfected cells, during latent infection, and under lytic conditions. We identified two constitutive enhancers, one of which seems to be a tissue-specific enhancer. In addition, four lytically induced enhancers, which are all responsive to the replication and transcription activator (RTA), were identified. Furthermore, a silencer was identified between the major latency promoter and the lytic gene locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The terminal repeats, spanning a region of about 24 kbp, seem like a "viral super-enhancer" that integrates the repressive effect of the latency-associated nuclear antigen (LANA) with the activating effect of RTA to regulate latency to lytic transition.
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Affiliation(s)
- Nilabja Roy Chowdhury
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Vyacheslav Gurevich
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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6
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Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS. Massively parallel characterization of regulatory elements in the developing human cortex. Science 2024; 384:eadh0559. [PMID: 38781390 DOI: 10.1126/science.adh0559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
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Affiliation(s)
- Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sean Whalen
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marilyn Steyert
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94158, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Daniela A Pereira
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
- Graduate Program of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Davide Capauto
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Alex A Pollen
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94158, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
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7
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Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
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Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. Cell Rep 2024; 43:113907. [PMID: 38461417 PMCID: PMC11005513 DOI: 10.1016/j.celrep.2024.113907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/29/2023] [Accepted: 02/19/2024] [Indexed: 03/12/2024] Open
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is sexually dimorphic, with increased incidence in females. A genome-wide association study identified a female-specific AIS susceptibility locus near the PAX1 gene. Here, we use mouse enhancer assays, three mouse enhancer knockouts, and subsequent phenotypic analyses to characterize this region. Using mouse enhancer assays, we characterize a sequence, PEC7, which overlaps the AIS-associated variant, and find it to be active in the tail tip and intervertebral disc. Removal of PEC7 or Xe1, a known sclerotome enhancer nearby, or deletion of both sequences lead to a kinky tail phenotype only in the Xe1 and combined (Xe1+PEC7) knockouts, with only the latter showing a female sex dimorphic phenotype. Extensive phenotypic characterization of these mouse lines implicates several differentially expressed genes and estrogen signaling in the sex dimorphic bias. In summary, our work functionally characterizes an AIS-associated locus and dissects the mechanism for its sexual dimorphism.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rory R Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mai Nobuhara
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Murray
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Xin Ruan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan J Rios
- Center for Translational Research, Scottish Rite for Children, Dallas, TX 75390, USA; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A Wise
- Center for Translational Research, Scottish Rite for Children, Dallas, TX 75390, USA; Department of Orthopedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
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9
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Liu S, Luo H, Zhang P, Li Y, Hao D, Zhang S, Song T, Xu T, He S. Adaptive Selection of Cis-regulatory Elements in the Han Chinese. Mol Biol Evol 2024; 41:msae034. [PMID: 38377343 PMCID: PMC10917166 DOI: 10.1093/molbev/msae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024] Open
Abstract
Cis-regulatory elements have an important role in human adaptation to the living environment. However, the lag in population genomic cohort studies and epigenomic studies, hinders the research in the adaptive analysis of cis-regulatory elements in human populations. In this study, we collected 4,013 unrelated individuals and performed a comprehensive analysis of adaptive selection of genome-wide cis-regulatory elements in the Han Chinese. In total, 12.34% of genomic regions are under the influence of adaptive selection, where 1.00% of enhancers and 2.06% of promoters are under positive selection, and 0.06% of enhancers and 0.02% of promoters are under balancing selection. Gene ontology enrichment analysis of these cis-regulatory elements under adaptive selection reveals that many positive selections in the Han Chinese occur in pathways involved in cell-cell adhesion processes, and many balancing selections are related to immune processes. Two classes of adaptive cis-regulatory elements related to cell adhesion were in-depth analyzed, one is the adaptive enhancers derived from neanderthal introgression, leads to lower hyaluronidase level in skin, and brings better performance on UV-radiation resistance to the Han Chinese. Another one is the cis-regulatory elements regulating wound healing, and the results suggest the positive selection inhibits coagulation and promotes angiogenesis and wound healing in the Han Chinese. Finally, we found that many pathogenic alleles, such as risky alleles of type 2 diabetes or schizophrenia, remain in the population due to the hitchhiking effect of positive selections. Our findings will help deepen our understanding of the adaptive evolution of genome regulation in the Han Chinese.
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Affiliation(s)
- Shuai Liu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaxia Luo
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Di Hao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sijia Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingrui Song
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Shunmin He
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Federman N, Gordon EM, Chawla SP, Hall FL. Editorial: Celebrating the 200th mendel's anniversary: gene-targeted diagnostics and therapies for cancer. FRONTIERS IN MOLECULAR MEDICINE 2024; 4:1366963. [PMID: 39086436 PMCID: PMC11285536 DOI: 10.3389/fmmed.2024.1366963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 08/02/2024]
Affiliation(s)
- Noah Federman
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Erlinda M. Gordon
- Cancer Center of Southern California, Santa Monica, CA, United States
- Aveni Foundation, Santa Monica, CA, United States
| | - Sant P. Chawla
- Cancer Center of Southern California, Santa Monica, CA, United States
- Counterpoint Biomedica LLC, Santa Monica, CA, United States
| | - Frederick L. Hall
- Counterpoint Biomedica LLC, Santa Monica, CA, United States
- Delta Next-Gene, LLC, Santa Monica, CA, United States
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11
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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12
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Aparicio JG, Hopp H, Harutyunyan N, Stewart C, Cobrinik D, Borchert M. Aberrant gene expression yet undiminished retinal ganglion cell genesis in iPSC-derived models of optic nerve hypoplasia. Ophthalmic Genet 2024; 45:1-15. [PMID: 37807874 PMCID: PMC10841193 DOI: 10.1080/13816810.2023.2253902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/26/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Optic nerve hypoplasia (ONH), the leading congenital cause of permanent blindness, is characterized by a retinal ganglion cell (RGC) deficit at birth. Multifactorial developmental events are hypothesized to underlie ONH and its frequently associated neurologic and endocrine abnormalities; however, environmental influences are unclear and genetic underpinnings are unexplored. This work investigates the genetic contribution to ONH RGC production and gene expression using patient induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs). MATERIALS AND METHODS iPSCs produced from ONH patients and controls were differentiated to ROs. RGC genesis was assessed using immunofluorescence and flow cytometry. Flow-sorted BRN3+ cells were collected for RNA extraction for RNA-Sequencing. Differential gene expression was assessed using DESeq2 and edgeR. PANTHER was employed to identify statistically over-represented ontologies among the differentially expressed genes (DEGs). DEGs of high interest to ONH were distinguished by assessing function, mutational constraint, and prior identification in ONH, autism and neurodevelopmental disorder (NDD) studies. RESULTS RGC genesis and survival were similar in ONH and control ROs. Differential expression of 70 genes was identified in both DESeq2 and edgeR analyses, representing a ~ 4-fold higher percentage of DEGs than in randomized study participants. DEGs showed trends towards over-representation of validated NDD genes and ONH exome variant genes. Among the DEGs, RAPGEF4 and DMD had the greatest number of disease-relevant features. CONCLUSIONS ONH genetic background was not associated with impaired RGC genesis but was associated with DEGs exhibiting disease contribution potential. This constitutes some of the first evidence of a genetic contribution to ONH.
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Affiliation(s)
- Jennifer G. Aparicio
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Hanno Hopp
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Narine Harutyunyan
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Carly Stewart
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - David Cobrinik
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck
School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of
Medicine, University of Southern California, Los Angeles, CA, USA
- USC Roski Eye Institute, Department of Ophthalmology, Keck
School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mark Borchert
- The Vision Center and The Saban Research Institute,
Children’s Hospital Los Angeles, Los Angeles, CA, USA
- USC Roski Eye Institute, Department of Ophthalmology, Keck
School of Medicine, University of Southern California, Los Angeles, CA, USA
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13
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Ramakrishnan A, Wangensteen G, Kim S, Nestler EJ, Shen L. DeepRegFinder: deep learning-based regulatory elements finder. BIOINFORMATICS ADVANCES 2024; 4:vbae007. [PMID: 38343388 PMCID: PMC10858349 DOI: 10.1093/bioadv/vbae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/06/2023] [Accepted: 01/12/2024] [Indexed: 06/15/2024]
Abstract
Summary Enhancers and promoters are important classes of DNA regulatory elements (DREs) that govern gene expression. Identifying them at a genomic scale is a critical task in bioinformatics. The DREs often exhibit unique histone mark binding patterns, which can be captured by high-throughput ChIP-seq experiments. To account for the variations and noises among the binding sites, machine learning models are trained on known enhancer/promoter sites using histone mark ChIP-seq data and predict enhancers/promoters at other genomic regions. To this end, we have developed a highly customizable program named DeepRegFinder, which automates the entire process of data processing, model training, and prediction. We have employed convolutional and recurrent neural networks for model training and prediction. DeepRegFinder further categorizes enhancers and promoters into active and poised states, making it a unique and valuable feature for researchers. Our method demonstrates improved precision and recall in comparison to existing algorithms for enhancer prediction across multiple cell types. Moreover, our pipeline is modular and eliminates the tedious steps involved in preprocessing, making it easier for users to apply on their data quickly. Availability and implementation https://github.com/shenlab-sinai/DeepRegFinder.
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Affiliation(s)
- Aarthi Ramakrishnan
- Friedman Brain Institute and Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - George Wangensteen
- Department of Computer Science, Brown University, Providence, RI 02912, United States
| | - Sarah Kim
- Cancer Program, Broad Institute, Cambridge, MA 02142, United States
| | - Eric J Nestler
- Friedman Brain Institute and Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Li Shen
- Friedman Brain Institute and Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
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14
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Schubach M, Maass T, Nazaretyan L, Röner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res 2024; 52:D1143-D1154. [PMID: 38183205 PMCID: PMC10767851 DOI: 10.1093/nar/gkad989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 01/07/2024] Open
Abstract
Machine Learning-based scoring and classification of genetic variants aids the assessment of clinical findings and is employed to prioritize variants in diverse genetic studies and analyses. Combined Annotation-Dependent Depletion (CADD) is one of the first methods for the genome-wide prioritization of variants across different molecular functions and has been continuously developed and improved since its original publication. Here, we present our most recent release, CADD v1.7. We explored and integrated new annotation features, among them state-of-the-art protein language model scores (Meta ESM-1v), regulatory variant effect predictions (from sequence-based convolutional neural networks) and sequence conservation scores (Zoonomia). We evaluated the new version on data sets derived from ClinVar, ExAC/gnomAD and 1000 Genomes variants. For coding effects, we tested CADD on 31 Deep Mutational Scanning (DMS) data sets from ProteinGym and, for regulatory effect prediction, we used saturation mutagenesis reporter assay data of promoter and enhancer sequences. The inclusion of new features further improved the overall performance of CADD. As with previous releases, all data sets, genome-wide CADD v1.7 scores, scripts for on-site scoring and an easy-to-use webserver are readily provided via https://cadd.bihealth.org/ or https://cadd.gs.washington.edu/ to the community.
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Affiliation(s)
- Max Schubach
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Thorben Maass
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Lusiné Nazaretyan
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Röner
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Kircher
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
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15
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Betti MJ, Aldrich MC, Gamazon ER. Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544507. [PMID: 37398170 PMCID: PMC10312628 DOI: 10.1101/2023.06.11.544507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We introduce CoRE-BED, a framework trained using 19 epigenomic features in 33 major cell and tissue types to predict cell-type-specific regulatory function. CoRE-BED identifies nine functional classes de-novo, capturing both known and new regulatory categories. Notably, we describe a previously undercharacterized class that we term Development Associated Elements (DAEs), which are highly enriched in cell types with elevated regenerative potential and distinguished by the dual presence of either H3K4me2 and H3K9ac (an epigenetic signature associated with kinetochore assembly) or H3K79me3 and H4K20me1 (a signature associated with transcriptional pause release). Unlike bivalent promoters, which represent a transitory state between active and silenced promoters, DAEs transition directly to or from a non-functional state during stem cell differentiation and are proximal to highly expressed genes. CoRE-BED's interpretability facilitates causal inference and functional prioritization. Across 70 complex traits, distal insulators account for the largest mean proportion of SNP heritability (~49%) captured by the GWAS. Collectively, our results demonstrate the value of exploring non-conventional ways of regulatory classification that enrich for trait heritability, to complement existing approaches for cis-regulatory prediction.
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Affiliation(s)
| | | | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN
- Clare Hall, University of Cambridge, Cambridge, England
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16
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Pan JH, Du PF. SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks. Brief Bioinform 2023; 25:bbad494. [PMID: 38168841 PMCID: PMC10782921 DOI: 10.1093/bib/bbad494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/09/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Silencers are repressive cis-regulatory elements that play crucial roles in transcriptional regulation. Experimental methods for identifying silencers are always costly and time-consuming. Computational methods, which relies on genomic sequence features, have been introduced as alternative approaches. However, silencers do not have significant epigenomic signature. Therefore, we explore a new way to computationally identify silencers, by incorporating chromatin structural information. We propose the SilenceREIN method, which focuses on finding silencers on anchors of chromatin loops. By using graph neural networks, we extracted chromatin structural information from a regulatory element interaction network. SilenceREIN integrated the chromatin structural information with linear genomic signatures to find silencers. The predictive performance of SilenceREIN is comparable or better than other states-of-the-art methods. We performed a genome-wide scanning to systematically find silencers in human genome. Results suggest that silencers are widespread on anchors of chromatin loops. In addition, enrichment analysis of transcription factor binding motif support our prediction results. As far as we can tell, this is the first attempt to incorporate chromatin structural information in finding silencers. All datasets and source codes of SilenceREIN have been deposited in a GitHub repository (https://github.com/JianHPan/SilenceREIN).
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Affiliation(s)
- Jian-Hua Pan
- College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
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17
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Hong H, Mocci E, Kamp K, Zhu S, Cain KC, Burr RL, Perry J, Heitkemper MM, Weaver-Toedtman KR, Dorsey SG. Genetic Variations in TrkB.T1 Isoform and Their Association with Somatic and Psychological Symptoms in Individuals with IBS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.14.23295434. [PMID: 37745409 PMCID: PMC10516087 DOI: 10.1101/2023.09.14.23295434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Irritable bowel syndrome (IBS), a disorder of gut-brain interaction, is often comorbid with somatic pain and psychological disorders. Dysregulated signaling of brain-derived neurotrophic factor (BDNF) and its receptor, tropomyosin-related kinase B (TrkB), has been implicated in somatic-psychological symptoms in individuals with IBS. Thus, we investigated the association of 10 single nucleotide polymorphisms (SNPs) in the regulatory 3' untranslated region (UTR) of NTRK2 (TrkB) kinase domain-deficient truncated isoform (TrkB.T1) and the BDNF Val66Met SNP with somatic and psychological symptoms and quality of life in a U.S. cohort (IBS n=464; healthy controls n=156). We found that the homozygous recessive genotype (G/G) of rs2013566 in individuals with IBS is associated with worsened somatic symptoms, including headache, back pain, joint pain, muscle pain, and somatization as well as diminished sleep quality, energy level and overall quality of life. Validation using U.K. BioBank (UKBB) data confirmed the association of rs2013566 with increased likelihood of headache. Several SNPs (rs1627784, rs1624327, rs1147198) showed significant associations with muscle pain in our U.S. cohort. Notably, these SNPs are predominantly located in H3K4Me1-enriched regions, suggesting their enhancer and/or transcription regulation potential. Together, our findings suggest that genetic variation within the 3'UTR region of the TrkB.T1 isoform may contribute to comorbid conditions in individuals with IBS, resulting in a spectrum of somatic and psychological symptoms that may influence their quality of life. These findings advance our understanding of the genetic interaction between BDNF/TrkB pathways and somatic-psychological symptoms in IBS, highlighting the importance of further exploring this interaction for potential clinical applications.
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Affiliation(s)
- H Hong
- Department of Biobehavioral Health Sciences, University of Pennsylvania School of Nursing
| | - E Mocci
- Department of Pain and Translational Symptom Science, University of Maryland School of Nursing
| | - K Kamp
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing
| | - S Zhu
- Department of Organizational Systems and Adult Health, University of Maryland School of Nursing
| | - K C Cain
- Department of Biostatistics, University of Washington School of Nursing
| | - R L Burr
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing
| | - J Perry
- Department of Medicine, University of Maryland School of Medicine
| | - M M Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington School of Nursing
| | - K R Weaver-Toedtman
- Department of Biobehavioral Health and Nursing Science, University of South Carolina College of Nursing
| | - S G Dorsey
- Department of Pain and Translational Symptom Science, University of Maryland School of Nursing
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18
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Borger MJ, Weissing FJ, Boon E. Human genomic data have different statistical properties than the data of randomised controlled trials. Behav Brain Sci 2023; 46:e184. [PMID: 37694897 DOI: 10.1017/s0140525x22002229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Madole & Harden argue that the Mendelian reshuffling of genes and genomes is analogous to randomised controlled trials. We are not convinced by their arguments. First, their recipe for meeting the demands on randomised experiments is inherently inconsistent. Second, disequilibrium across chromosomes conflicts with their assumption of statistical independence. Third, the genome-wide association study (GWAS) method has many pitfalls, including low repeatability.
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Affiliation(s)
- Mirjam J Borger
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands ; ; https://www.marmgroup.eu/
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands ; ; https://www.marmgroup.eu/
| | - Eva Boon
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands ; ; https://www.marmgroup.eu/
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19
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Fan K, Pfister E, Weng Z. Toward a comprehensive catalog of regulatory elements. Hum Genet 2023; 142:1091-1111. [PMID: 36935423 DOI: 10.1007/s00439-023-02519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/03/2023] [Indexed: 03/21/2023]
Abstract
Regulatory elements are the genomic regions that interact with transcription factors to control cell-type-specific gene expression in different cellular environments. A precise and complete catalog of functional elements encoded by the human genome is key to understanding mammalian gene regulation. Here, we review the current state of regulatory element annotation. We first provide an overview of assays for characterizing functional elements, including genome, epigenome, transcriptome, three-dimensional chromatin interaction, and functional validation assays. We then discuss computational methods for defining regulatory elements, including peak-calling and other statistical modeling methods. Finally, we introduce several high-quality lists of regulatory element annotations and suggest potential future directions.
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Affiliation(s)
- Kaili Fan
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Edith Pfister
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, 368 Plantation Street, ASC5-1069, Worcester, MA, 01605, USA.
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20
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Littman R, Cheng M, Wang N, Peng C, Yang X. SCING: Inference of robust, interpretable gene regulatory networks from single cell and spatial transcriptomics. iScience 2023; 26:107124. [PMID: 37434694 PMCID: PMC10331489 DOI: 10.1016/j.isci.2023.107124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/31/2023] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
Gene regulatory network (GRN) inference is an integral part of understanding physiology and disease. Single cell/nuclei RNA-seq (scRNA-seq/snRNA-seq) data has been used to elucidate cell-type GRNs; however, the accuracy and speed of current scRNAseq-based GRN approaches are suboptimal. Here, we present Single Cell INtegrative Gene regulatory network inference (SCING), a gradient boosting and mutual information-based approach for identifying robust GRNs from scRNA-seq, snRNA-seq, and spatial transcriptomics data. Performance evaluation using Perturb-seq datasets, held-out data, and the mouse cell atlas combined with the DisGeNET database demonstrates the improved accuracy and biological interpretability of SCING compared to existing methods. We applied SCING to the entire mouse single cell atlas, human Alzheimer's disease (AD), and mouse AD spatial transcriptomics. SCING GRNs reveal unique disease subnetwork modeling capabilities, have intrinsic capacity to correct for batch effects, retrieve disease relevant genes and pathways, and are informative on spatial specificity of disease pathogenesis.
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Affiliation(s)
- Russell Littman
- Department of Integrative Biology & Physiology, UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Michael Cheng
- Department of Integrative Biology & Physiology, UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - Ning Wang
- Department of Integrative Biology & Physiology, UCLA, Los Angeles, CA, USA
| | - Chao Peng
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Xia Yang
- Department of Integrative Biology & Physiology, UCLA, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences (QCBio), Los Angeles, CA, USA
- Molecular Biology Institute (MBI), Los Angeles, CA, USA
- Brain Research Institute (BRI), Los Angeles, CA, USA
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21
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Dincer TU, Ernst J. Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549056. [PMID: 37503240 PMCID: PMC10369970 DOI: 10.1101/2023.07.14.549056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genomewide predictions of regulatory activity associated with each functional characterization dataset across many cell types based on available epigenomic data. It then for each cell type produces (1) ChromScoreHMM genome annotations based on the combinatorial and spatial patterns within these predictions and (2) ChromScore tracks of overall predicted regulatory activity. ChromActivity provides a resource for analyzing and interpreting the human regulatory genome across diverse cell types.
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Affiliation(s)
- Tevfik Umut Dincer
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, CA, 90095, USA
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, CA, 90095, USA
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22
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Brocal-Ruiz R, Esteve-Serrano A, Mora-Martínez C, Franco-Rivadeneira ML, Swoboda P, Tena JJ, Vilar M, Flames N. Forkhead transcription factor FKH-8 cooperates with RFX in the direct regulation of sensory cilia in Caenorhabditis elegans. eLife 2023; 12:e89702. [PMID: 37449480 PMCID: PMC10393296 DOI: 10.7554/elife.89702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Cilia, either motile or non-motile (a.k.a primary or sensory), are complex evolutionarily conserved eukaryotic structures composed of hundreds of proteins required for their assembly, structure and function that are collectively known as the ciliome. Ciliome gene mutations underlie a group of pleiotropic genetic diseases known as ciliopathies. Proper cilium function requires the tight coregulation of ciliome gene transcription, which is only fragmentarily understood. RFX transcription factors (TF) have an evolutionarily conserved role in the direct activation of ciliome genes both in motile and non-motile cilia cell-types. In vertebrates, FoxJ1 and FoxN4 Forkhead (FKH) TFs work with RFX in the direct activation of ciliome genes, exclusively in motile cilia cell-types. No additional TFs have been described to act together with RFX in primary cilia cell-types in any organism. Here we describe FKH-8, a FKH TF, as a direct regulator of the sensory ciliome genes in Caenorhabditis elegans. FKH-8 is expressed in all ciliated neurons in C. elegans, binds the regulatory regions of ciliome genes, regulates ciliome gene expression, cilium morphology and a wide range of behaviors mediated by sensory ciliated neurons. FKH-8 and DAF-19 (C. elegans RFX) physically interact and synergistically regulate ciliome gene expression. C. elegans FKH-8 function can be replaced by mouse FOXJ1 and FOXN4 but not by other members of other mouse FKH subfamilies. In conclusion, RFX and FKH TF families act jointly as direct regulators of ciliome genes also in sensory ciliated cell types suggesting that this regulatory logic could be an ancient trait predating functional cilia sub-specialization.
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Affiliation(s)
- Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Ainara Esteve-Serrano
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | | | - Peter Swoboda
- Department of Biosciences and Nutrition. Karolinska Institute. Campus FlemingsbergStockholmSweden
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de OlavideSevilleSpain
| | - Marçal Vilar
- Molecular Basis of Neurodegeneration Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSICValenciaSpain
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23
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Li MJ, Kumari P, Lin YS, Yao ML, Zhang BH, Yin B, Duan SJ, Cornell R, Marazita M, Shi B, Jia ZL. A Variant in the IRF6 Promoter Associated with the Risk for Orofacial Clefting. J Dent Res 2023; 102:806-813. [PMID: 37161310 PMCID: PMC10399074 DOI: 10.1177/00220345231165210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
The single-nucleotide polymorphism (SNP) rs2235371 (IRF6 V274I) is associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Han Chinese and other populations but appears to be without a functional effect. To find the common etiologic variant or variants within the haplotype tagged by rs2235371, we carried out targeted sequencing of an interval containing IRF6 in 159 Han Chinese with NSCL/P. This study revealed that the SNP rs12403599, within the IRF6 promoter, is associated with all phenotypes of NSCL/P, especially nonsyndromic cleft lip (NSCLO) and a subphenotype of it, microform cleft lip (MCL). This association was replicated in 2 additional much larger cohorts of cases and controls from the Han Chinese. Conditional logistic analysis indicated that association of rs2235371 with NSCL/P was lost if rs12403599 was excluded. rs12403599 contributes the most risk to MCL: its G allele is responsible for 38.47% of the genetic contribution to MCL, and the odds ratios of G/C and G/G genotypes were 2.91 and 6.58, respectively, for MCL. To test if rs12403599 is functional, we carried out reporter assays in a fetal oral epithelium cells (GMSM-K). Unexpectedly, the risk allele G yielded higher promoter activity in GMSM-K. Consistent with the reporter studies, expression of IRF6 in lip tissues from NSCLO and MCL patients with the G/G phenotype was higher than in those from patients with the C/C phenotype. These results indicate that rs12403599 is tagging the risk haplotype for NSCL/P better than rs2235371 in Han Chinese and supports investigation of the mechanisms by which the allele of rs12403599 affects IRF6 expression and tests of this association in different populations.
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Affiliation(s)
- M.-J. Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - P. Kumari
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - Y.-S. Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M.-L. Yao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - B.-H. Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - B. Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - S.-J. Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - R.A. Cornell
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - M.L. Marazita
- Centre for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - B. Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z.-l. Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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24
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FitzPatrick VD, Leemans C, van Arensbergen J, van Steensel B, Bussemaker H. Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR. Nucleic Acids Res 2023; 51:5499-5511. [PMID: 37013986 PMCID: PMC10287907 DOI: 10.1093/nar/gkad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of recapitulating expression in an ectopic setting is first identified, followed by targeted mutation of putative transcription factor binding sites. Massively parallel reporter assays such as survey of regulatory elements (SuRE) provide an alternative way to study millions of promoter fragments in parallel. Here we show how a generalized linear model (GLM) can be used to transform genome-scale SuRE data into a high-resolution genomic track that quantifies the contribution of local sequence to promoter activity. This coefficient track helps identify regulatory elements and can be used to predict promoter activity of any sub-region in the genome. It thus allows in silico dissection of any promoter in the human genome to be performed. We developed a web application, available at cissector.nki.nl, that lets researchers easily perform this analysis as a starting point for their research into any promoter of interest.
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Affiliation(s)
- Vincent D FitzPatrick
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Christ Leemans
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
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25
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Yen A, Mateusiak C, Sarafinovska S, Gachechiladze MA, Guo J, Chen X, Moudgil A, Cammack AJ, Hoisington-Lopez J, Crosby M, Brent MR, Mitra RD, Dougherty JD. Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544098. [PMID: 37333130 PMCID: PMC10274760 DOI: 10.1101/2023.06.07.544098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next generation sequencing. Compared to other genomic assays, whose readout provides a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon (SRT) "Calling Cards" into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile specific transcription factor binding with custom transcription factor (TF)-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Card reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 1-2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high-performance computing environment and to conduct downstream analyses. Basic Protocol 1: Preparation and delivery of Calling Cards reagentsBasic Protocol 2: Sample preparationBasic Protocol 3: Sequencing library preparationBasic Protocol 4: Library pooling and sequencingBasic Protocol 5: Data analysis.
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Affiliation(s)
- Allen Yen
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110
| | - Chase Mateusiak
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Simona Sarafinovska
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110
| | - Mariam A Gachechiladze
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110
| | - Juanru Guo
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Arnav Moudgil
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Alexander J Cammack
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Jessica Hoisington-Lopez
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - MariaLynn Crosby
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Michael R Brent
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
- Department of Computer Science and Engineering, Washington University, Saint Louis, MO 63130
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO 63110
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, Saint Louis, MO 63110
- Lead contact
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26
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Hussain S, Sadouni N, van Essen D, Dao LTM, Ferré Q, Charbonnier G, Torres M, Gallardo F, Lecellier CH, Sexton T, Saccani S, Spicuglia S. Short tandem repeats are important contributors to silencer elements in T cells. Nucleic Acids Res 2023; 51:4845-4866. [PMID: 36929452 PMCID: PMC10250210 DOI: 10.1093/nar/gkad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/18/2023] Open
Abstract
The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.
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Affiliation(s)
- Saadat Hussain
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Nori Sadouni
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Dominic van Essen
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Lan T M Dao
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Quentin Ferré
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Magali Torres
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Charles-Henri Lecellier
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- LIRMM, University of Montpellier, CNRS, Montpellier, France
| | - Tom Sexton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire – IGBMC (CNRS UMR 7104, INSERM U1258, Université de Strasbourg), 67404 Illkirch, France
| | - Simona Saccani
- Institute for Research on Cancer and Ageing, IRCAN, 06107 Nice, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Marseille, France
- Equipe Labélisée Ligue Contre le Cancer, Marseille, France
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27
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Georgakopoulos-Soares I, Deng C, Agarwal V, Chan CSY, Zhao J, Inoue F, Ahituv N. Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nat Commun 2023; 14:2333. [PMID: 37087538 PMCID: PMC10122648 DOI: 10.1038/s41467-023-37960-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/06/2023] [Indexed: 04/24/2023] Open
Abstract
The gene regulatory code and grammar remain largely unknown, precluding our ability to link phenotype to genotype in regulatory sequences. Here, using a massively parallel reporter assay (MPRA) of 209,440 sequences, we examine all possible pair and triplet combinations, permutations and orientations of eighteen liver-associated transcription factor binding sites (TFBS). We find that TFBS orientation and order have a major effect on gene regulatory activity. Corroborating these results with genomic analyses, we find clear human promoter TFBS orientation biases and similar TFBS orientation and order transcriptional effects in an MPRA that tested 164,307 liver candidate regulatory elements. Additionally, by adding TFBS orientation to a model that predicts expression from sequence we improve performance by 7.7%. Collectively, our results show that TFBS orientation and order have a significant effect on gene regulatory activity and need to be considered when analyzing the functional effect of variants on the activity of these sequences.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA
| | - Candace S Y Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
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28
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Ushiki A, Sheng RR, Zhang Y, Zhao J, Nobuhara M, Murray E, Ruan X, Rios JJ, Wise CA, Ahituv N. Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536497. [PMID: 37090618 PMCID: PMC10120660 DOI: 10.1101/2023.04.12.536497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Adolescent idiopathic scoliosis (AIS), a sideways curvature of the spine, is sexually dimorphic, with increased incidence in females. A GWAS identified a female-specific AIS susceptibility locus near the PAX1 gene. Here, we used mouse enhancer assays, three mouse enhancer knockouts and subsequent phenotypic analyses to characterize this region. Using mouse enhancer assays, we characterized a sequence, PEC7, that overlaps the AIS-associated variant, and found it to be active in the tail tip and intervertebral disc. Removal of PEC7 or Xe1, a known sclerotome enhancer nearby, and deletion of both sequences led to a kinky phenotype only in the Xe1 and combined (Xe1+PEC7) knockouts, with only the latter showing a female sex dimorphic phenotype. Extensive phenotypic characterization of these mouse lines implicated several differentially expressed genes and estrogen signaling in the sex dimorphic bias. In summary, our work functionally characterizes an AIS-associated locus and dissects the mechanism for its sexual dimorphism.
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Affiliation(s)
- Aki Ushiki
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rory R. Sheng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yichi Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingjing Zhao
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mai Nobuhara
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Murray
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Xin Ruan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jonathan J. Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A. Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
- Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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29
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Agarwal V, Inoue F, Schubach M, Martin BK, Dash PM, Zhang Z, Sohota A, Noble WS, Yardimci GG, Kircher M, Shendure J, Ahituv N. Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531189. [PMID: 36945371 PMCID: PMC10028905 DOI: 10.1101/2023.03.05.531189] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The human genome contains millions of candidate cis-regulatory elements (CREs) with cell-type-specific activities that shape both health and myriad disease states. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these CREs. Here, we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of over 680,000 sequences, representing a nearly comprehensive set of all annotated CREs among three cell types (HepG2, K562, and WTC11), finding 41.7% to be functional. By testing sequences in both orientations, we find promoters to have significant strand orientation effects. We also observe that their 200 nucleotide cores function as non-cell-type-specific 'on switches' providing similar expression levels to their associated gene. In contrast, enhancers have weaker orientation effects, but increased tissue-specific characteristics. Utilizing our lentiMPRA data, we develop sequence-based models to predict CRE function with high accuracy and delineate regulatory motifs. Testing an additional lentiMPRA library encompassing 60,000 CREs in all three cell types, we further identified factors that determine cell-type specificity. Collectively, our work provides an exhaustive catalog of functional CREs in three widely used cell lines, and showcases how large-scale functional measurements can be used to dissect regulatory grammar.
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Affiliation(s)
- Vikram Agarwal
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- mRNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA 02451, USA
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Max Schubach
- Berlin Institute of Health of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pyaree Mohan Dash
- Berlin Institute of Health of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
| | - Zicong Zhang
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Ajuni Sohota
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Galip Gürkan Yardimci
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Martin Kircher
- Berlin Institute of Health of Health at Charité - Universitätsmedizin Berlin, 10178, Berlin, Germany
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Center for Cell Lineage Tracing, University of Washington, Seattle, WA 98195, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA
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30
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Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS. Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528663. [PMID: 36824845 PMCID: PMC9949039 DOI: 10.1101/2023.02.15.528663] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and disease. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 sequences, including differentially accessible cell-type specific regions in the developing cortex and single-nucleotide variants associated with psychiatric disorders. In primary cells, we identified 46,802 active enhancer sequences and 164 disorder-associated variants that significantly alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning, we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
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Affiliation(s)
- Chengyu Deng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Sean Whalen
- Gladstone Institutes; San Francisco, CA, USA
| | - Marilyn Steyert
- Department of Anatomy, University of California, San Francisco; San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco; San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco; San Francisco, CA, USA
| | - Ryan Ziffra
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
| | | | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University; Kyoto, Japan
| | - Daniela A. Pereira
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
- Graduate Program of Genetics, Institute of Biological Sciences, Federal University of Minas Gerais; Belo Horizonte, Minas Gerais, Brazil
| | | | - Scott Norton
- Child Study Center, Yale University; New Haven, CT, USA
| | - Flora M. Vaccarino
- Child Study Center, Yale University; New Haven, CT, USA
- Department of Neuroscience, Yale University; New Haven, CT, USA
| | - Alex Pollen
- Department of Neurology, University of California, San Francisco; San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco; San Francisco, CA, USA
| | - Tomasz J. Nowakowski
- Department of Anatomy, University of California, San Francisco; San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco; San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco; San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco; San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco; San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco; San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
| | - Katherine S. Pollard
- Institute for Human Genetics, University of California, San Francisco; San Francisco, CA, USA
- Gladstone Institutes; San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco; San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco; San Francisco, CA, USA
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31
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Аpplication of massive parallel reporter analysis in biotechnology and medicine. КЛИНИЧЕСКАЯ ПРАКТИКА 2023. [DOI: 10.17816/clinpract115063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The development and functioning of an organism relies on tissue-specific gene programs. Genome regulatory elements play a key role in the regulation of such programs, and disruptions in their function can lead to the development of various pathologies, including cancers, malformations and autoimmune diseases. The emergence of high-throughput genomic studies has led to massively parallel reporter analysis (MPRA) methods, which allow the functional verification and identification of regulatory elements on a genome-wide scale. Initially MPRA was used as a tool to investigate fundamental aspects of epigenetics, but the approach also has great potential for clinical and practical biotechnology. Currently, MPRA is used for validation of clinically significant mutations, identification of tissue-specific regulatory elements, search for the most promising loci for transgene integration, and is an indispensable tool for creating highly efficient expression systems, the range of application of which extends from approaches for protein development and design of next-generation therapeutic antibody superproducers to gene therapy. In this review, the main principles and areas of practical application of high-throughput reporter assays will be discussed.
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Hnf1b renal expression directed by a distal enhancer responsive to Pax8. Sci Rep 2022; 12:19921. [PMID: 36402859 PMCID: PMC9675860 DOI: 10.1038/s41598-022-21171-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Xenopus provides a simple and efficient model system to study nephrogenesis and explore the mechanisms causing renal developmental defects in human. Hnf1b (hepatocyte nuclear factor 1 homeobox b), a gene whose mutations are the most commonly identified genetic cause of developmental kidney disease, is required for the acquisition of a proximo-intermediate nephron segment in Xenopus as well as in mouse. Genetic networks involved in Hnf1b expression during kidney development remain poorly understood. We decided to explore the transcriptional regulation of Hnf1b in the developing Xenopus pronephros and mammalian renal cells. Using phylogenetic footprinting, we identified an evolutionary conserved sequence (CNS1) located several kilobases (kb) upstream the Hnf1b transcription start and harboring epigenomic marks characteristics of a distal enhancer in embryonic and adult renal cells in mammals. By means of functional expression assays in Xenopus and mammalian renal cell lines we showed that CNS1 displays enhancer activity in renal tissue. Using CRISPR/cas9 editing in Xenopus tropicalis, we demonstrated the in vivo functional relevance of CNS1 in driving hnf1b expression in the pronephros. We further showed the importance of Pax8-CNS1 interaction for CNS1 enhancer activity allowing us to conclude that Hnf1b is a direct target of Pax8. Our work identified for the first time a Hnf1b renal specific enhancer and may open important perspectives into the diagnosis for congenital kidney anomalies in human, as well as modeling HNF1B-related diseases.
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Zeng W, Liu Q, Yin Q, Jiang R, Wong WH. HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Res 2022; 51:D159-D166. [PMID: 36215037 PMCID: PMC9825415 DOI: 10.1093/nar/gkac859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/19/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains ∼262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.
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Affiliation(s)
| | | | | | - Rui Jiang
- Correspondence may also be addressed to Rui Jiang. Tel: +86 10 6279 5578;
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34
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Garda S, Lenihan-Geels F, Proft S, Hochmuth S, Schülke M, Seelow D, Leser U. RegEl corpus: identifying DNA regulatory elements in the scientific literature. Database (Oxford) 2022; 2022:6618549. [PMID: 35758881 PMCID: PMC9235371 DOI: 10.1093/database/baac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022]
Abstract
High-throughput technologies led to the generation of a wealth of data on regulatory DNA elements in the human genome. However, results from disease-driven studies are primarily shared in textual form as scientific articles. Information extraction (IE) algorithms allow this information to be (semi-)automatically accessed. Their development, however, is dependent on the availability of annotated corpora. Therefore, we introduce RegEl (Regulatory Elements), the first freely available corpus annotated with regulatory DNA elements comprising 305 PubMed abstracts for a total of 2690 sentences. We focus on enhancers, promoters and transcription factor binding sites. Three annotators worked in two stages, achieving an overall 0.73 F1 inter-annotator agreement and 0.46 for regulatory elements. Depending on the entity type, IE baselines reach F1-scores of 0.48–0.91 for entity detection and 0.71–0.88 for entity normalization. Next, we apply our entity detection models to the entire PubMed collection and extract co-occurrences of genes or diseases with regulatory elements. This generates large collections of regulatory elements associated with 137 870 unique genes and 7420 diseases, which we make openly available. Database URL: https://zenodo.org/record/6418451#.YqcLHvexVqg
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Affiliation(s)
- Samuele Garda
- Humboldt-Universitält zu Berlin Computer Science, , Rudower Chaussee 25, 12489, Berlin, Germany
| | - Freyda Lenihan-Geels
- Charité-Universitätsmedizin Berlin Klinik für Pädiatrie m.S. Neurologie, , Augustenburger Platz 1, 13353, Berlin, Germany
| | - Sebastian Proft
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin Bioinformatics and Translational Genetics, , Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
- Charité-Universitätsmedizin Berlin Institut für Medizinische Genetik und Humangenetik, , Augustenburger Platz 1, 13353, Berlin, Germany
| | - Stefanie Hochmuth
- Charité-Universitätsmedizin Berlin Klinik für Pädiatrie m.S. Neurologie, , Augustenburger Platz 1, 13353, Berlin, Germany
| | - Markus Schülke
- Charité-Universitätsmedizin Berlin Klinik für Pädiatrie m.S. Neurologie, , Augustenburger Platz 1, 13353, Berlin, Germany
| | - Dominik Seelow
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin Bioinformatics and Translational Genetics, , Anna-Louisa-Karsch-Straße 2, 10178, Berlin, Germany
| | - Ulf Leser
- Humboldt-Universitält zu Berlin Computer Science, , Rudower Chaussee 25, 12489, Berlin, Germany
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Feng Y, Cai L, Hong W, Zhang C, Tan N, Wang M, Wang C, Liu F, Wang X, Ma J, Gao C, Kumar M, Mo Y, Geng Q, Luo C, Lin Y, Chen H, Wang SY, Watson MJ, Jegga AG, Pedersen RA, Fu JD, Wang ZV, Fan GC, Sadayappan S, Wang Y, Pauklin S, Huang F, Huang W, Jiang L. Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy. Circulation 2022; 145:1663-1683. [PMID: 35400201 PMCID: PMC9251830 DOI: 10.1161/circulationaha.121.055781] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Transcriptional reconfiguration is central to heart failure, the most common cause of which is dilated cardiomyopathy (DCM). The effect of 3-dimensional chromatin topology on transcriptional dysregulation and pathogenesis in human DCM remains elusive. METHODS We generated a compendium of 3-dimensional epigenome and transcriptome maps from 101 biobanked human DCM and nonfailing heart tissues through highly integrative chromatin immunoprecipitation (H3K27ac [acetylation of lysine 27 on histone H3]), in situ high-throughput chromosome conformation capture, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin using sequencing, and RNA sequencing. We used human induced pluripotent stem cell-derived cardiomyocytes and mouse models to interrogate the key transcription factor implicated in 3-dimensional chromatin organization and transcriptional regulation in DCM pathogenesis. RESULTS We discovered that the active regulatory elements (H3K27ac peaks) and their connectome (H3K27ac loops) were extensively reprogrammed in DCM hearts and contributed to transcriptional dysregulation implicated in DCM development. For example, we identified that nontranscribing NPPA-AS1 (natriuretic peptide A antisense RNA 1) promoter functions as an enhancer and physically interacts with the NPPA (natriuretic peptide A) and NPPB (natriuretic peptide B) promoters, leading to the cotranscription of NPPA and NPPB in DCM hearts. We revealed that DCM-enriched H3K27ac loops largely resided in conserved high-order chromatin architectures (compartments, topologically associating domains) and their anchors unexpectedly had equivalent chromatin accessibility. We discovered that the DCM-enriched H3K27ac loop anchors exhibited a strong enrichment for HAND1 (heart and neural crest derivatives expressed 1), a key transcription factor involved in early cardiogenesis. In line with this, its protein expression was upregulated in human DCM and mouse failing hearts. To further validate whether HAND1 is a causal driver for the reprogramming of enhancer-promoter connectome in DCM hearts, we performed comprehensive 3-dimensional epigenome mappings in human induced pluripotent stem cell-derived cardiomyocytes. We found that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced a distinct gain of enhancer-promoter connectivity and correspondingly increased the expression of their connected genes implicated in DCM pathogenesis, thus recapitulating the transcriptional signature in human DCM hearts. Electrophysiology analysis demonstrated that forced overexpression of HAND1 in human induced pluripotent stem cell-derived cardiomyocytes induced abnormal calcium handling. Furthermore, cardiomyocyte-specific overexpression of Hand1 in the mouse hearts resulted in dilated cardiac remodeling with impaired contractility/Ca2+ handling in cardiomyocytes, increased ratio of heart weight/body weight, and compromised cardiac function, which were ascribed to recapitulation of transcriptional reprogramming in DCM. CONCLUSIONS This study provided novel chromatin topology insights into DCM pathogenesis and illustrated a model whereby a single transcription factor (HAND1) reprograms the genome-wide enhancer-promoter connectome to drive DCM pathogenesis.
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Affiliation(s)
- Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
- These authors contributed equally to this work
| | - Liuyang Cai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR 999077, China
- These authors contributed equally to this work
| | - Wanzi Hong
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- These authors contributed equally to this work
| | - Chunxiang Zhang
- Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000, China
- These authors contributed equally to this work
| | - Ning Tan
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Mingyang Wang
- College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Cheng Wang
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland D02 VF25
| | - Feng Liu
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Xiaohong Wang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jianyong Ma
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chen Gao
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mohit Kumar
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yuanxi Mo
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Qingshan Geng
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Changjun Luo
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Yan Lin
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Haiyang Chen
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shuang-Yin Wang
- Department of Immunology, Weizmann Institute of Science, Rehovot WR35+R8, Israel
| | - Michael J. Watson
- Department of Surgery, Cardiovascular & Thoracic, Duke University, Durham, NC 27710, USA
| | - Anil G. Jegga
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Department of Computer Science, University of Cincinnati College of Engineering, Cincinnati, OH 45221, USA
| | - Roger A. Pedersen
- Department of OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research, Stanford University, Stanford, California, USA
| | - Ji-dong Fu
- Departments of Physiology and Cell Biology, the Dorothy M. Davis Heart and Lung Research Institute, Frick Center for Heart Failure and Arrhythmia, the Ohio State University, Columbus, OH 43210, USA
| | - Zhao V. Wang
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA, 75390-8573
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Sakthivel Sadayappan
- Heart, Lung and Vascular Institute, Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45236, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Old Road, Headington, Oxford, OX3 7LD, UK
| | - Feng Huang
- Institute of Cardiovascular Diseases, the First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Lei Jiang
- Guangdong Provincial Geriatrics Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
- Lead contact
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Spurna Z, Capkova P, Srovnal J, Duchoslavova J, Punova L, Aleksijevic D, Vrtel R. Clinical impact of variants in non-coding regions of SHOX - Current knowledge. Gene 2022; 818:146238. [PMID: 35074420 DOI: 10.1016/j.gene.2022.146238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 01/21/2023]
Abstract
The short stature homeobox-containing (SHOX) is the most frequently analysed gene in patients classified as short stature patients (ISS) or diagnosed with Leri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia (LMD), or Madelung deformity (MD). However, clinical testing of this gene focuses primarily on single nucleotide variants (SNV) in its coding sequences and copy number variants (CNV) overlapping SHOX gene. This review summarizes the clinical impact of variants in noncoding regions of SHOX. RECENT FINDINGS: CNV extending exclusively into the regulatory elements (i.e., not interrupting the coding sequence) are found more frequently in downstream regulatory elements of SHOX. Further, duplications are more frequent than deletions. Interestingly, downstream duplications are more common than deletions in patients with ISS or LWD but no such differences exist for upstream CNV. Moreover, the presence of specific CNVs in the patient population suggests the involvement of additional unknown factors. Some of its intronic variants, notably NM_000451.3(SHOX):c.-9delG and c.-65C>A in the 5'UTR, have unclear clinical roles. However, these intronic SNV may increase the probability that other CNV will arise de novo in the SHOX gene based on homologous recombination or incorrect splicing of mRNA. SUMMARY: This review highlights the clinical impact of noncoding changes in the SHOX gene and the need to apply new technologies and genotype-phenotype correlation in their analysis.
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Affiliation(s)
- Zuzana Spurna
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic.
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jana Duchoslavova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Lucia Punova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
| | - Darina Aleksijevic
- Department of Paediatrics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic; Department of Medical Genetics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czech Republic
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Austin-Tse CA, Jobanputra V, Perry DL, Bick D, Taft RJ, Venner E, Gibbs RA, Young T, Barnett S, Belmont JW, Boczek N, Chowdhury S, Ellsworth KA, Guha S, Kulkarni S, Marcou C, Meng L, Murdock DR, Rehman AU, Spiteri E, Thomas-Wilson A, Kearney HM, Rehm HL. Best practices for the interpretation and reporting of clinical whole genome sequencing. NPJ Genom Med 2022; 7:27. [PMID: 35395838 PMCID: PMC8993917 DOI: 10.1038/s41525-022-00295-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/17/2022] [Indexed: 01/19/2023] Open
Abstract
Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.
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Affiliation(s)
- Christina A Austin-Tse
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Vaidehi Jobanputra
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ted Young
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Nicole Boczek
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Saurav Guha
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Shashikant Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cherisse Marcou
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linyan Meng
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Atteeq U Rehman
- Molecular Diagnostics Laboratory, New York Genome Center, New York, NY, USA
| | - Elizabeth Spiteri
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, CA, USA
| | | | - Hutton M Kearney
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Heidi L Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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38
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Spielmann M, Kircher M. Computational and experimental methods for classifying variants of unknown clinical significance. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006196. [PMID: 35483875 PMCID: PMC9059783 DOI: 10.1101/mcs.a006196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The increase in sequencing capacity, reduction in costs, and national and international coordinated efforts have led to the widespread introduction of next-generation sequencing (NGS) technologies in patient care. More generally, human genetics and genomic medicine are gaining importance for more and more patients. Some communities are already discussing the prospect of sequencing each individual's genome at time of birth. Together with digital health records, this shall enable individualized treatments and preventive measures, so-called precision medicine. A central step in this process is the identification of disease causal mutations or variant combinations that make us more susceptible for diseases. Although various technological advances have improved the identification of genetic alterations, the interpretation and ranking of the identified variants remains a major challenge. Based on our knowledge of molecular processes or previously identified disease variants, we can identify potentially functional genetic variants and, using different lines of evidence, we are sometimes able to demonstrate their pathogenicity directly. However, the vast majority of variants are classified as variants of uncertain clinical significance (VUSs) with not enough experimental evidence to determine their pathogenicity. In these cases, computational methods may be used to improve the prioritization and an increasing toolbox of experimental methods is emerging that can be used to assay the molecular effects of VUSs. Here, we discuss how computational and experimental methods can be used to create catalogs of variant effects for a variety of molecular and cellular phenotypes. We discuss the prospects of integrating large-scale functional data with machine learning and clinical knowledge for the development of accurate pathogenicity predictions for clinical applications.
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Affiliation(s)
- Malte Spielmann
- Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany;,Institute of Human Genetics, Christian-Albrechts-Universität, 24105 Kiel, Germany;,Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;,DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, 23562 Lübeck, Germany
| | - Martin Kircher
- Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany;,Berlin Institute of Health at Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;,DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10115 Berlin, Germany
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39
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Lorber D, Volk T. Evaluation of chromatin mesoscale organization. APL Bioeng 2022; 6:010902. [PMID: 35071965 PMCID: PMC8758204 DOI: 10.1063/5.0069286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
Chromatin organization in the nucleus represents an important aspect of transcription regulation. Most of the studies so far focused on the chromatin structure in cultured cells or in fixed tissue preparations. Here, we discuss the various approaches for deciphering chromatin 3D organization with an emphasis on the advantages of live imaging approaches.
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Affiliation(s)
- Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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40
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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41
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Orozco G. Fine mapping with epigenetic information and 3D structure. Semin Immunopathol 2022; 44:115-125. [PMID: 35022890 PMCID: PMC8837508 DOI: 10.1007/s00281-021-00906-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022]
Abstract
Since 2005, thousands of genome-wide association studies (GWAS) have been published, identifying hundreds of thousands of genetic variants that increase risk of complex traits such as autoimmune diseases. This wealth of data has the potential to improve patient care, through personalized medicine and the identification of novel drug targets. However, the potential of GWAS for clinical translation has not been fully achieved yet, due to the fact that the functional interpretation of risk variants and the identification of causal variants and genes are challenging. The past decade has seen the development of great advances that are facilitating the overcoming of these limitations, by utilizing a plethora of genomics and epigenomics tools to map and characterize regulatory elements and chromatin interactions, which can be used to fine map GWAS loci, and advance our understanding of the biological mechanisms that cause disease.
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Affiliation(s)
- Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9LJ, UK. .,NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
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42
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Choi S, Kim GS, Yang J, Cho H, Kang CY, Wang G. Controllable SiO x Nanorod Memristive Neuron for Probabilistic Bayesian Inference. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2104598. [PMID: 34618384 DOI: 10.1002/adma.202104598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Modern artificial neural network technology using a deterministic computing framework is faced with a critical challenge in dealing with massive data that are largely unstructured and ambiguous. This challenge demands the advances of an elementary physical device for tackling these uncertainties. Here, we designed and fabricated a SiOx nanorod memristive device by employing the glancing angle deposition (GLAD) technique, suggesting a controllable stochastic artificial neuron that can mimic the fundamental integrate-and-fire signaling and stochastic dynamics of a biological neuron. The nanorod structure provides the random distribution of multiple nanopores all across the active area, capable of forming a multitude of Si filaments at many SiOx nanorod edges after the electromigration process, leading to a stochastic switching event with very high dynamic range (≈5.15 × 1010 ) and low energy (≈4.06 pJ). Different probabilistic activation (ProbAct) functions in a sigmoid form are implemented, showing its controllability with low variation by manufacturing and electrical programming schemes. Furthermore, as an application prospect, based on the suggested memristive neuron, we demonstrated the self-resting neural operation with the local circuit configuration and revealed probabilistic Bayesian inferences for genetic regulatory networks with low normalized mean squared errors (≈2.41 × 10-2 ) and its robustness to the ProbAct variation.
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Affiliation(s)
- Sanghyeon Choi
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Gwang Su Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Electronic Materials Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jehyeon Yang
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Haein Cho
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Chong-Yun Kang
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Electronic Materials Research Center, Korea Institute of Science and Technology (KIST), 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Gunuk Wang
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department of Integrative Energy Engineering, College of Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
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Farrell CM, Goldfarb T, Rangwala SH, Astashyn A, Ermolaeva OD, Hem V, Katz KS, Kodali VK, Ludwig F, Wallin CL, Pruitt KD, Murphy TD. RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. Genome Res 2022; 32:175-188. [PMID: 34876495 PMCID: PMC8744684 DOI: 10.1101/gr.275819.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022]
Abstract
Eukaryotic genomes contain many nongenic elements that function in gene regulation, chromosome organization, recombination, repair, or replication, and mutation of those elements can affect genome function and cause disease. Although numerous epigenomic studies provide high coverage of gene regulatory regions, those data are not usually exposed in traditional genome annotation and can be difficult to access and interpret without field-specific expertise. The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature. The curated data set is comprised of richly annotated sequence records, descriptive records in the NCBI Gene database, reference genome feature annotation, and activity-based interactions between nongenic regions, target genes, and each other. The data set provides succinct functional details and transparent experimental evidence, leverages data from multiple experimental sources, is readily accessible and adaptable, and uses a flexible data model. The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation; as known positive controls for epigenomic data evaluation; and as reference standards for functional interactions. Comparisons to other gene regulatory data sets show that the RefSeqFE data set includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data selection biases. RefSeqFEs thus provide an alternative and complementary resource for experimentally assayed functional elements, with future data set growth expected.
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Affiliation(s)
- Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Alexander Astashyn
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Olga D Ermolaeva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Vichet Hem
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kenneth S Katz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Frank Ludwig
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Craig L Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Romanov SE, Kalashnikova DA, Laktionov PP. Methods of massive parallel reporter assays for investigation of enhancers. Vavilovskii Zhurnal Genet Selektsii 2021; 25:344-355. [PMID: 34901731 PMCID: PMC8627875 DOI: 10.18699/vj21.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/19/2022] Open
Abstract
The correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory elements play an exceptional role in this process. There are few types of gene regulatory elements, including promoters, enhancers, insulators and silencers. Alterations of gene regulatory elements may cause various pathologies, including cancer, congenital disorders and autoimmune diseases. The development of high-throughput genomic assays has made it possible to significantly accelerate the accumulation of information about the characteristic epigenetic properties of regulatory elements. In combination with high-throughput studies focused on the genome-wide distribution of epigenetic marks, regulatory proteins and the spatial structure of chromatin, this significantly expands the understanding of the principles of epigenetic regulation of genes and allows potential regulatory elements to be searched for in silico. However, common experimental approaches used to study the local characteristics of chromatin have a number of technical limitations that may reduce the reliability of computational identification of genomic regulatory sequences. Taking into account the variability of the functions of epigenetic determinants and complex multicomponent regulation of genomic elements activity, their functional verification is often required. A plethora of methods have been developed to study the functional role of regulatory elements on the genome scale. Common experimental approaches for in silico identification of regulatory elements and their inherent technical limitations will be described. The present review is focused on original high-throughput methods of enhancer activity reporter analysis that are currently used to validate predicted regulatory elements and to perform de novo searches. The methods described allow assessing the functional role of the nucleotide sequence of a regulatory element, to determine its exact boundaries and to assess the influence of the local state of chromatin on the activity of enhancers and gene expression. These approaches have contributed substantially to the understanding of the fundamental principles of gene regulation.
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Affiliation(s)
- S E Romanov
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
| | - D A Kalashnikova
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
| | - P P Laktionov
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
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Polymorphic Variants in the GRK5 Gene Promoter Are Associated With Diastolic Dysfunction in Coronary Artery Bypass Graft Surgery Patients. Anesth Analg 2021; 134:858-868. [PMID: 34871184 DOI: 10.1213/ane.0000000000005809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The G-protein-coupled receptor kinase 5 (GRK5) is a mediator of cardiovascular homeostasis and participates in inflammation and cardiac fibrosis, both being involved in the development of diastolic dysfunction (DD). While mechanisms of transcriptional regulation of the GRK5 promoter are unclear, we tested the hypotheses, that (1) GRK5 expression varies depending on functional single nucleotide polymorphisms (SNPs) in the GRK5 promoter and (2) this is associated with DD in patients undergoing coronary artery bypass graft (CABG) surgery. METHODS We amplified and sequenced the GRK5 promoter followed by cloning, reporter assays, and electrophoretic mobility shift assays (EMSA). GRK5 messenger ribonucleic acid (mRNA) expression was determined in right atrial tissue sampled from 50 patients undergoing CABG surgery. In another prospective study, GRK5 genotypes were associated with determinants of diastolic function using transesophageal echocardiography in 255 patients with CABG with normal systolic left ventricular (LV) function. Specifically, we measured ejection fraction (EF), transmitral Doppler early filling velocity (E), tissue Doppler early diastolic lateral mitral annular velocity (E' lateral), and calculated E/E', E' norm and the difference of E' lateral and E' norm to account for age-related changes in diastolic function. RESULTS We identified 6 SNPs creating 3 novel haplotypes with the greatest promoter activation in haplotype tagging (ht) SNP T(-678)C T-allele constructs (P < .001). EMSAs showed allele-specific transcription factor binding proving functional activity. GRK5 mRNA expression was greatest in TT genotypes (TT: 131 fg/µg [95% CI, 108-154]; CT: 109 [95% confidence interval {CI}, 93-124]; CC: 83 [95% CI, 54-112]; P = .012). Moreover, GRK5 genotypes were significantly associated with determinants of diastolic function. Grading of DD revealed more grade 3 patients in TT compared to CT and CC genotypes (58% vs 38% vs 4%; P = .023). E´ lateral was lowest in TT genotypes (P = .007) and corresponding E/E' measurements showed 1.27-fold increased values in TT versus CC genotypes (P = .01), respectively. While E' norm values were not different between genotypes (P = .182), the difference between E' lateral and E' norm was significantly higher in TT genotypes compared to CC and CT genotypes (-1.2 [interquartile range {IQR}, 2.7], -0.5 [IQR, 3.4], and -0.4 [IQR, 4.2; P = .035], respectively). CONCLUSIONS A functional GRK5 SNP results in allele-dependent differences in GRK5 promoter activity and mRNA expression. This is associated with altered echocardiographic determinants of diastolic function. Thus, SNPs in the GRK5 promoter are associated with altered perioperative diastolic cardiac function. In the future, preoperative testing for these and other SNPs might allow to initiate more specific diagnostic and perioperative pathways to benefit patients at risk.
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Chatterjee S, Karasaki KM, Fries LE, Kapoor A, Chakravarti A. A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease. Genome Res 2021; 31:2199-2208. [PMID: 34782358 PMCID: PMC8647834 DOI: 10.1101/gr.275667.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/05/2021] [Indexed: 01/25/2023]
Abstract
The major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk variants attenuate binding of the transcription factors RARB, GATA2, and SOX10 to their cognate CREs, reduce RET gene expression, and dysregulate other ENS and HSCR genes in the RET-EDNRB gene regulatory network (GRN). Here, we use siRNA, ChIP, and CRISPR-Cas9 deletion analyses in the SK-N-SH cell line to ask how many additional HSCR-associated risk variants reside in RET CREs that affect its gene expression. We identify 22 HSCR-associated variants in candidate RET CREs, of which seven have differential allele-specific in vitro enhancer activity, and four of these seven affect RET gene expression; of these, two enhancers are bound by the transcription factor PAX3. We also show that deleting multiple variant-containing enhancers leads to synergistic effects on RET gene expression. These, coupled with our prior results, show that common sequence variants in at least 10 RET enhancers affect HSCR risk, seven with experimental evidence of affecting RET gene expression, extending the known RET-EDNRB GRN to reveal an extensive regulatory code modulating disease risk at a single gene.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Kameko M Karasaki
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
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47
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Tian P, Zhong M, Wei GH. Mechanistic insights into genetic susceptibility to prostate cancer. Cancer Lett 2021; 522:155-163. [PMID: 34560228 DOI: 10.1016/j.canlet.2021.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the second most common cancer in men and is a highly heritable disease that affects millions of individuals worldwide. Genome-wide association studies have to date discovered nearly 270 genetic loci harboring hundreds of single nucleotide polymorphisms (SNPs) that are associated with PCa susceptibility. In contrast, the functional characterization of the mechanisms underlying PCa risk association is still growing. Given that PCa risk-associated SNPs are highly enriched in noncoding cis-regulatory genomic regions, accumulating evidence suggests a widespread modulation of transcription factor chromatin binding and allelic enhancer activity by these noncoding SNPs, thereby dysregulating gene expression. Emerging studies have shown that a proportion of noncoding variants can modulate the formation of transcription factor complexes at enhancers and CTCF-mediated 3D genome architecture. Interestingly, DNA methylation-regulated CTCF binding could orchestrate a long-range chromatin interaction between PCa risk enhancer and causative genes. Additionally, one-causal-variant-two-risk genes or multiple-risk-variant-multiple-genes are prevalent in some PCa risk-associated loci. In this review, we will discuss the current understanding of the general principles of SNP-mediated gene regulation, experimental advances, and functional evidence supporting the mechanistic roles of several PCa genetic loci with potential clinical impact on disease prevention and treatment.
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Affiliation(s)
- Pan Tian
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Mengjie Zhong
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Gong-Hong Wei
- Fudan University Shanghai Cancer Center; Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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Bhatia S, Kleinjan DJ, Uttley K, Mann A, Dellepiane N, Bickmore WA. Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. eLife 2021; 10:65601. [PMID: 34796872 PMCID: PMC8604437 DOI: 10.7554/elife.65601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan Kleinjan
- Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty Uttley
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anita Mann
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Nefeli Dellepiane
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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Santiago-Algarra D, Souaid C, Singh H, Dao LTM, Hussain S, Medina-Rivera A, Ramirez-Navarro L, Castro-Mondragon JA, Sadouni N, Charbonnier G, Spicuglia S. Epromoters function as a hub to recruit key transcription factors required for the inflammatory response. Nat Commun 2021; 12:6660. [PMID: 34795220 PMCID: PMC8602369 DOI: 10.1038/s41467-021-26861-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Our previous results demonstrated that a subset of gene promoters, termed Epromoters, work as bona fide enhancers and regulate distal gene expression. Here, we hypothesized that Epromoters play a key role in the coordination of rapid gene induction during the inflammatory response. Using a high-throughput reporter assay we explored the function of Epromoters in response to type I interferon. We find that clusters of IFNa-induced genes are frequently associated with Epromoters and that these regulatory elements preferentially recruit the STAT1/2 and IRF transcription factors and distally regulate the activation of interferon-response genes. Consistently, we identified and validated the involvement of Epromoter-containing clusters in the regulation of LPS-stimulated macrophages. Our findings suggest that Epromoters function as a local hub recruiting the key TFs required for coordinated regulation of gene clusters during the inflammatory response.
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Affiliation(s)
- David Santiago-Algarra
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Charbel Souaid
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Himanshu Singh
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Lan T M Dao
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Vinmec Research Institute of Stem cell and Gene technology, Vinmec Healthcare System, Hanoi, Vietnam
| | - Saadat Hussain
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Lucia Ramirez-Navarro
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Jaime A Castro-Mondragon
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway
| | - Nori Sadouni
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France.
- Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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