المؤلفون: Olivia M. de Goede, Pascal M. Lavoie, Wendy P. Robinson

المصدر: Clinical Epigenetics, Vol 9, Iss 1, Pp 1-13 (2017)

مصطلحات موضوعية: DNA methylation, Cord blood, Preterm birth, Illumina 450K array, Epigenetics, Nucleated red blood cells, Medicine, Genetics, QH426-470

الوصف: Abstract Background Premature infants are highly vulnerable to infection. This is partly attributable to the preterm immune system, which differs from that of the term neonate in cell composition and function. Multiple studies have found differential DNA methylation (DNAm) between preterm and term infants’ cord blood; however, interpretation of these studies is limited by the confounding factor of blood cell composition. This study evaluates the epigenetic impact of preterm birth in isolated hematopoietic cell populations, reducing the concern of cell composition differences. Methods Genome-wide DNAm was measured using the Illumina 450K array in T cells, monocytes, granulocytes, and nucleated red blood cells (nRBCs) isolated from cord blood of 5 term and 5 preterm ( 0.10) discovered between preterm and term infants compared to the

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s13148-017-0339-1Test; https://doaj.org/toc/1868-7075Test; https://doaj.org/toc/1868-7083Test

الوصول الحر: https://doaj.org/article/eb70d81720194e98b71257f55798f755Test

المؤلفون: David A. Knowles, Siddhartha Jaiswal, Mauro Pala, Lars Lind, Kevin S. Smith, Nathan S. Abell, Matthew G. Durrant, David Schlessinger, Chiara Sabatti, Erik Ingelsson, Michael J. Gloudemans, Brunilda Balliu, Olivia M. De Goede, Boxiang Liu, Naomi L. Cook, Francesco Cucca, Xin Li, Stephen B. Montgomery

المصدر: Genome Biology, Vol 20, Iss 1, Pp 1-16 (2019)
Genome Biology

مصطلحات موضوعية: Male, Aging, lcsh:QH426-470, Population, Longevity, Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Gene expression, Genetics, Humans, Genetik, education, Gene, lcsh:QH301-705.5, Aged, 030304 developmental biology, Medicinsk genetik, Aged, 80 and over, Regulation of gene expression, 0303 health sciences, education.field_of_study, Research, Alternative splicing, Human genetics, Gene regulation, lcsh:Genetics, Gene Expression Regulation, lcsh:Biology (General), RNA splicing, Female, Medical Genetics, 030217 neurology & neurosurgery

الوصف: Background Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. Results We perform RNA sequencing in whole blood from the same individuals at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging at a population and individual level. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age. We identify 1291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories. Further, we observe a strong correlation of genetic effects on expression and splicing between the two ages, with a small subset of tested genes showing a reduction in genetic associations with expression and splicing in older age. Conclusions These findings demonstrate that, although the transcriptome and its genetic regulation is mostly stable late in life, a small subset of genes is dynamic and is characterized by a reduction in genetic regulation, most likely due to increasing environmental variance with age.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::440f174780131a7164f963c9fe6c5534Test
http://link.springer.com/article/10.1186/s13059-019-1840-yTest

المؤلفون: Nancy J. Cox, Sayantan Das, Abhi Rao, Pejman Mohammadi, Alan Kwong, Brandon L. Pierce, Yanyu Liang, Yuxin Zou, Anna M. Smith, Matthew Stephens, Chiara Sabatti, Yuan He, Kasper D. Hansen, Lei Hou, Meritxell Oliva, W. James Kent, Stacey Gabriel, Andrew R. Hame, Tanya Krubit, Gary Walters, Lori E. Brigham, Gao Wang, Kevin S. Smith, Michael J. Gloudemans, Barbara E. Engelhardt, Yongjin Park, Nicole A. Teran, David A. Davis, Thomas Juettemann, Kimberley Ramsey, Fred A. Wright, Lin Chen, Valentin Wucher, Benjamin J. Strober, Duyen T. Nguyen, Eleazar Eskin, Kane Hadley, Deborah C. Mash, Michael Snyder, Sarah Kim-Hellmuth, Laura A. Siminoff, Maghboeba Mosavel, Shin Lin, Richard Hasz, Daniel C. Rohrer, Latarsha J. Carithers, Kevin Myer, Rajinder Kaul, Andrew D. Skol, Bryan Gillard, Dana R. Valley, Philip A. Branton, Stephane E. Castel, Robert E. Handsaker, Debra Bradbury, Meng Wang, Mary Barcus, Xiaoquan Wen, Hua Tang, Daniel J. Cotter, Lihua Jiang, Jason Bridge, Ashis Saha, Gen Li, Susan E. Koester, Qin Li, Mark H. Johnson, Barbara E. Stranger, Jimmie B. Vaught, Hae Kyung Im, Paul Flicek, Marcus Hunter, François Aguet, Elise D. Flynn, Sandra Linder, Nancy Roche, Daniel R. Zerbino, Xiao Li, Barbara A. Foster, Stephen B. Montgomery, Daniel Nachun, Serghei Mangul, Emmanouil T. Dermitzakis, Brian Jo, Simona Volpi, Farzana Jasmine, Scott D. Jewell, Jonah Einson, Tuuli Lappalainen, Farhad Hormozdiari, John M. Rouhana, Ana Viñuela, Daniel G. MacArthur, William F. Leinweber, Gad Getz, Peter Hickey, Eric R. Gamazon, Brunilda Balliu, Jennifer A. Doherty, Christopher D. Brown, Roderic Guigó, Gene Kopen, Rodrigo Bonazzola, Pedro G. Ferreira, Andrew P. Feinberg, Shankara Anand, Helen M. Moore, Paul J. Hoffman, Heather M. Gardiner, Ping Guan, Ferran Reverter, Jin Billy Li, Tiffany Eulalio, Joseph Wheeler, Alvaro N. Barbeira, Jared L. Nedzel, Seva Kashin, Laure Fresard, Lindsay F. Rizzardi, Abhiram Rao, Muhammad G. Kibriya, David Tabor, Leslie H. Sobin, A. Roger Little, Stephen J. Trevanion, Nicole M. Ferraro, Kate R. Rosenbloom, John A. Stamatoyannopoulos, Liqun Qi, Princy Parsana, Ayellet V. Segrè, Dan Sheppard, Nathan S. Abell, Kathryn Demanelis, Manolis Kellis, Silva Kasela, Xin Li, Conner C. Powell, YoSon Park, Michael Washington, Magali Ruffier, Saboor Shad, Christopher Johns, Jeffrey A. Thomas, Andrew Brown, Alisa McDonald, Karna Robinson, Esti Yeger-Lotem, Manuel Muñoz-Aguirre, Kieron Taylor, Marta Melé, Diego Garrido-Martín, Brian Roe, Michael T. Moser, Andrew B. Nobel, Alexis Battle, Maximilian Haeussler, Concepcion R. Nierras, Ellen Karasik, Sam Meier, Anita H. Undale, Ellen Todres, Aaron Graubert, Joshua M. Akey, Jeffrey McLean, Donald F. Conrad, Olivia M. De Goede, Katherine H. Huang, Laura Barker, Kristin G. Ardlie, Christopher Lee

المصدر: Genome Biology, Vol 21, Iss 1, Pp 1-12 (2020)
Genome Biology

مصطلحات موضوعية: animal structures, Future studies, lcsh:QH426-470, Short Report, Gene Expression, Genomics, Computational biology, Biology, eQTL, Polymorphism, Single Nucleotide, ASE, Regulatory variation, 03 medical and health sciences, 0302 clinical medicine, Resource (project management), Humans, SNP, Allele, lcsh:QH301-705.5, Alleles, Allele specific, 030304 developmental biology, 0303 health sciences, Allelic expression, Genome, Human, Sequence Analysis, RNA, Haplotype, Functional genomics, Human genetics, lcsh:Genetics, Haplotypes, lcsh:Biology (General), Expression data, Expression quantitative trait loci, GTEx, 030217 neurology & neurosurgery

الوصف: Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::90fddfebf856337cc6189fbe1de49662Test
http://hdl.handle.net/10230/45398Test

المؤلفون: Olivia M. de Goede, Daniel C. Nachun, Nicole M. Ferraro, Michael J. Gloudemans, Abhiram S. Rao, Craig Smail, Tiffany Y. Eulalio, François Aguet, Bernard Ng, Jishu Xu, Alvaro N. Barbeira, Stephane E. Castel, Sarah Kim-Hellmuth, YoSon Park, Alexandra J. Scott, Benjamin J. Strober, Christopher D. Brown, Xiaoquan Wen, Ira M. Hall, Alexis Battle, Tuuli Lappalainen, Hae Kyung Im, Kristin G. Ardlie, Sara Mostafavi, Thomas Quertermous, Karla Kirkegaard, Stephen B. Montgomery, Shankara Anand, Stacey Gabriel, Gad A. Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Xiao Li, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen T. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Rodrigo Bonazzola, Andrew Brown, Donald F. Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Emmanouil T. Dermitzakis, Jonah Einson, Barbara E. Engelhardt, Eleazar Eskin, Elise D. Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Roderic Guigó, Andrew R. Hamel, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Brian Jo, Silva Kasela, Seva Kashin, Manolis Kellis, Alan Kwong, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Manuel Muñoz-Aguirre, Andrew B. Nobel, Meritxell Oliva, Yongjin Park, Princy Parsana, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Matthew Stephens, Barbara E. Stranger, Nicole A. Teran, Ana Viñuela, Gao Wang, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, David E. Tabor, Anita Undale, Jason Bridge, Lori E. Brigham, Barbara A. Foster, Bryan M. Gillard, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Ellen Karasik, Gene Kopen, William F. Leinweber, Alisa McDonald, Michael T. Moser, Kevin Myer, Kimberley D. Ramsey, Brian Roe, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Scott D. Jewell, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Mary E. Barcus, Philip A. Branton, Leslie Sobin, Laura K. Barker, Heather M. Gardiner, Maghboeba Mosavel, Laura A. Siminoff, Paul Flicek, Maximilian Haeussler, Thomas Juettemann, W. James Kent, Christopher M. Lee, Conner C. Powell, Kate R. Rosenbloom, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Nathan S. Abell, Joshua Akey, Lin Chen, Kathryn Demanelis, Jennifer A. Doherty, Andrew P. Feinberg, Kasper D. Hansen, Peter F. Hickey, Farzana Jasmine, Lihua Jiang, Rajinder Kaul, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Shin Lin, Sandra E. Linder, Brandon L. Pierce, Lindsay F. Rizzardi, Andrew D. Skol, Kevin S. Smith, Michael Snyder, John Stamatoyannopoulos, Hua Tang, Meng Wang, Latarsha J. Carithers, Ping Guan, Susan E. Koester, A. Roger Little, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi

المصدر: Cell

مصطلحات موضوعية: Multifactorial Inheritance, Population, Quantitative Trait Loci, Coronary Artery Disease, Disease, Computational biology, Quantitative trait locus, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Humans, education, Gene, 030304 developmental biology, 0303 health sciences, education.field_of_study, Gene Expression Profiling, Genetic Variation, Inflammatory Bowel Diseases, Long non-coding RNA, Diabetes Mellitus, Type 1, Diabetes Mellitus, Type 2, Organ Specificity, Expression quantitative trait loci, Trait, RNA, Long Noncoding, 030217 neurology & neurosurgery

الوصف: Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::557f936307744ad75495f8a544a29ccdTest
https://doi.org/10.1016/j.cell.2021.03.050Test

المؤلفون: Wendy P. Robinson, Pascal M. Lavoie, Olivia M. de Goede

المصدر: Clinical Epigenetics, Vol 9, Iss 1, Pp 1-13 (2017)
Clinical Epigenetics

مصطلحات موضوعية: Epigenomics, Male, 0301 basic medicine, Epigenetic clock, lcsh:QH426-470, Term Birth, Illumina 450K array, lcsh:Medicine, Biology, Epigenesis, Genetic, Blood cell, 03 medical and health sciences, Nucleated red blood cells, White blood cell, Genetics, medicine, Humans, Molecular Biology, Genetics (clinical), Fetus, DNA methylation, Research, lcsh:R, Infant, Newborn, dNaM, Gestational age, Cord blood, Preterm birth, DNA, Fetal Blood, 3. Good health, Haematopoiesis, lcsh:Genetics, 030104 developmental biology, medicine.anatomical_structure, Immunology, Female, Epigenetics, Bone marrow, Infant, Premature, Developmental Biology

الوصف: Background Premature infants are highly vulnerable to infection. This is partly attributable to the preterm immune system, which differs from that of the term neonate in cell composition and function. Multiple studies have found differential DNA methylation (DNAm) between preterm and term infants’ cord blood; however, interpretation of these studies is limited by the confounding factor of blood cell composition. This study evaluates the epigenetic impact of preterm birth in isolated hematopoietic cell populations, reducing the concern of cell composition differences. Methods Genome-wide DNAm was measured using the Illumina 450K array in T cells, monocytes, granulocytes, and nucleated red blood cells (nRBCs) isolated from cord blood of 5 term and 5 preterm ( 0.10) discovered between preterm and term infants compared to the

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::926f4b97a80179195032dc7bb105ae8fTest
http://link.springer.com/article/10.1186/s13148-017-0339-1Test

المؤلفون: Stephen B. Montgomery, Lars Lind, Mauro Pala, Nathan S. Abell, Siddhartha Jaiswal, Matthew G. Durrant, Olivia M. De Goede, Kevin S. Smith, Chiara Sabatti, Brunilda Balliu, Michael J. Gloudemans, Erik Ingelsson, Francesco Cucca, Boxiang Liu, Naomi L. Cook, Xin Li, David Schlessinger

مصطلحات موضوعية: Genetics, 0303 health sciences, DNA repair, Period (gene), Alternative splicing, RNA, Biology, 03 medical and health sciences, 0302 clinical medicine, Gene expression, RNA splicing, Gene, 030217 neurology & neurosurgery, 030304 developmental biology

الوصف: SummaryMolecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age; 93% of samples cluster with their own measurement at another age, and there is a strong correlation of genetic effects on expression between the two ages (median ρG = 0.96). Despite this, we identify 1,291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories of aging. Further, 7.8% and 9.6% of tested genes show a reduction in genetic associations with expression and alternative splicing in older age, with impacted genes enriched in DNA repair pathways. Together these findings indicate that, although gene expression and alternative splicing and their genetic regulation are mostly stable late in life, a small subset of genes is dynamic and is characterized by changes in expression and splicing and a reduction in genetic regulation.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::91f17c83f21088ec8961f9b9cef9e969Test

المؤلفون: Alexander M. Morin, Michael S. Kobor, Kristina Gervin, Raymond T. Ng, Henriëtte A. Moll, Robert Lyle, Julia L. MacIsaac, Liesbeth Duijts, Olivia M. de Goede, Wendy P. Robinson, Sara Mostafavi, Hamid R. Razzaghian, Louie Dinh, Janine F. Felix, Meaghan J. Jones, Menno C. van Zelm, Devin C. Koestler, Pascal M. Lavoie

مصطلحات موضوعية: 0303 health sciences, Cell type, Cord, Nucleated Red Blood Cell, Biology, Andrology, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Immune system, 030220 oncology & carcinogenesis, White blood cell, Cord blood, DNA methylation, medicine, Cytotoxic T cell, 030304 developmental biology

الوصف: BackgroundDNA methylation profiling of peripheral blood leukocytes has many research applications, and characterizing the changes in DNA methylation of specific white blood cell types between newborn and adult could add insight into the maturation of the immune system. As a consequence of developmental changes, DNA methylation profiles derived from adult white blood cells are poor references for prediction of cord blood cell types from DNA methylation data. We thus examined cell-type specific differences in DNA methylation in leukocyte subsets between cord and adult blood, and assessed the impact of these differences on prediction of cell types in cord blood.ResultsThough all cell types showed differences between cord and adult blood, some specific patterns stood out that reflected how the immune system changes after birth. In cord blood, lymphoid cells showed less variability than in adult, potentially demonstrating their naïve status. In fact, cord CD4 and CD8 T cells were so similar that genetic effects on DNA methylation were greater than cell type effects in our analysis, and CD8 T cell frequencies remained difficult to predict, even after optimizing the library used for cord blood composition estimation. Myeloid cells showed fewer changes between cord and adult and also less variability, with monocytes showing the fewest sites of DNA methylation change between cord and adult. Finally, including nucleated red blood cells in the reference library was necessary for accurate cell type predictions in cord blood.ConclusionChanges in DNA methylation with age were highly cell type specific, and those differences paralleled what is known about the maturation of the postnatal immune system.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fa6620064000ee7685c8162540cd5290Test

المؤلفون: Lihua Jiang, Meng Wang, Shin Lin, Ruiqi Jian, Xiao Li, Joanne Chan, Guanlan Dong, Huaying Fang, Aaron E. Robinson, Michael P. Snyder, François Aguet, Shankara Anand, Kristin G. Ardlie, Stacey Gabriel, Gad Getz, Aaron Graubert, Kane Hadley, Robert E. Handsaker, Katherine H. Huang, Seva Kashin, Daniel G. MacArthur, Samuel R. Meier, Jared L. Nedzel, Duyen Y. Nguyen, Ayellet V. Segrè, Ellen Todres, Brunilda Balliu, Alvaro N. Barbeira, Alexis Battle, Rodrigo Bonazzola, Andrew Brown, Christopher D. Brown, Stephane E. Castel, Don Conrad, Daniel J. Cotter, Nancy Cox, Sayantan Das, Olivia M. de Goede, Emmanouil T. Dermitzakis, Barbara E. Engelhardt, Eleazar Eskin, Tiffany Y. Eulalio, Nicole M. Ferraro, Elise Flynn, Laure Fresard, Eric R. Gamazon, Diego Garrido-Martín, Nicole R. Gay, Roderic Guigó, Andrew R. Hamel, Yuan He, Paul J. Hoffman, Farhad Hormozdiari, Lei Hou, Hae Kyung Im, Brian Jo, Silva Kasela, Manolis Kellis, Sarah Kim-Hellmuth, Alan Kwong, Tuuli Lappalainen, Xin Li, Yanyu Liang, Serghei Mangul, Pejman Mohammadi, Stephen B. Montgomery, Manuel Muñoz-Aguirre, Daniel C. Nachun, Andrew B. Nobel, Meritxell Oliva, YoSon Park, Yongjin Park, Princy Parsana, Ferran Reverter, John M. Rouhana, Chiara Sabatti, Ashis Saha, Andrew D. Skol, Matthew Stephens, Barbara E. Stranger, Benjamin J. Strober, Nicole A. Teran, Ana Viñuela, Gao Wang, Xiaoquan Wen, Fred Wright, Valentin Wucher, Yuxin Zou, Pedro G. Ferreira, Gen Li, Marta Melé, Esti Yeger-Lotem, Mary E. Barcus, Debra Bradbury, Tanya Krubit, Jeffrey A. McLean, Liqun Qi, Karna Robinson, Nancy V. Roche, Anna M. Smith, Leslie Sobin, David E. Tabor, Anita Undale, Jason Bridge, Lori E. Brigham, Barbara A. Foster, Bryan M. Gillard, Richard Hasz, Marcus Hunter, Christopher Johns, Mark Johnson, Ellen Karasik, Gene Kopen, William F. Leinweber, Alisa McDonald, Michael T. Moser, Kevin Myer, Kimberley D. Ramsey, Brian Roe, Saboor Shad, Jeffrey A. Thomas, Gary Walters, Michael Washington, Joseph Wheeler, Scott D. Jewell, Daniel C. Rohrer, Dana R. Valley, David A. Davis, Deborah C. Mash, Philip A. Branton, Laura K. Barker, Heather M. Gardiner, Maghboeba Mosavel, Laura A. Siminoff, Paul Flicek, Maximilian Haeussler, Thomas Juettemann, W. James Kent, Christopher M. Lee, Conner C. Powell, Kate R. Rosenbloom, Magali Ruffier, Dan Sheppard, Kieron Taylor, Stephen J. Trevanion, Daniel R. Zerbino, Nathan S. Abell, Joshua Akey, Lin Chen, Kathryn Demanelis, Jennifer A. Doherty, Andrew P. Feinberg, Kasper D. Hansen, Peter F. Hickey, Farzana Jasmine, Rajinder Kaul, Muhammad G. Kibriya, Jin Billy Li, Qin Li, Sandra E. Linder, Brandon L. Pierce, Lindsay F. Rizzardi, Kevin S. Smith, John Stamatoyannopoulos, Hua Tang, Latarsha J. Carithers, Ping Guan, Susan E. Koester, A. Roger Little, Helen M. Moore, Concepcion R. Nierras, Abhi K. Rao, Jimmie B. Vaught, Simona Volpi

المصدر: Cell
PMC

مصطلحات موضوعية: Proteomics, Cell signaling, Proteome, Quantitative proteomics, Gene Expression, Disease, Computational biology, Biology, ENCODE, Article, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Humans, Secretion, RNA, Messenger, Gene, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, RNA, Metabolism, Phenotype, Secretory protein, 030217 neurology & neurosurgery

الوصف: Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from 12,627 genes across 32 normal human tissue types prepared by the GTEx project. Known and new tissue specific or enriched proteins (5,499) were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode highly tissue specific proteins. Discordance in the sites of RNA expression and protein detection also revealed potential sites of synthesis and action of protein signaling molecules. Overall, these results provide an extraordinary resource, and demonstrate that understanding protein levels can provide insights into metabolism, regulation, secretome, and human diseases.SummaryQuantitative proteome study of 32 human tissues and integrated analysis with transcriptome data revealed that understanding protein levels could provide in-depth knowledge to post transcriptional or translational regulations, human metabolism, secretome, and diseases.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::62fecfd381ad58880ff2fe2b28799a97Test
https://doi.org/10.1016/j.cell.2020.08.036Test

المؤلفون: Wendy P. Robinson, Pascal M. Lavoie, Olivia M. de Goede

المصدر: Epigenomics. 8(11)

مصطلحات موضوعية: 0301 basic medicine, Male, Cancer Research, Erythroblasts, Placenta, Population, Biology, Epigenesis, Genetic, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Genetics, Cytotoxic T cell, Humans, education, education.field_of_study, 030219 obstetrics & reproductive medicine, Infant, Newborn, dNaM, Nucleated Red Blood Cell, DNA Methylation, Fetal Blood, Molecular biology, Haematopoiesis, 030104 developmental biology, Cord blood, DNA methylation, Erythropoiesis, Female

الوصف: Aim: To provide insight into fetal nucleated red blood cell (nRBC) development using genome-wide DNA methylation (DNAm) profiling. Materials & methods: The DNAm profile (Illumina 450K array) of cord blood (n = 7) derived nRBCs was compared with B cells, CD4 and CD8 T cells, natural killer cells, granulocytes, monocytes and placenta (n = 5). Results: nRBCs and placenta had similarly low array-wide DNAm compared with white blood cells, but their patterns of hypomethylation differed at biologically relevant subsets of the array. High interindividual variability in nRBC DNAm was driven by a negative association between DNAm and nRBC count. Conclusion: nRBC hypomethylation is likely an epigenetic signature of erythropoiesis rather than of early development. Variability in nRBC DNAm may stem from differences in the cell population's maturity or hematopoietic source.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0f00b4c7ba28c2929eb9f091331f5875Test
https://pubmed.ncbi.nlm.nih.gov/27687885Test