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Chromosome-Centric Human Proteome Project Allies with Developmental Biology: a Case Study of the Role of Y chromosome Genes in Organ Development

Published on Dec 1, 2017in Journal of Proteome Research3.78
· DOI :10.1021/acs.jproteome.7b00446
Anna Meyfour2
Estimated H-index: 2
,
Paria Pooyan2
Estimated H-index: 2
+ 4 AuthorsGhasem Hosseini Salekdeh36
Estimated H-index: 36
Cite
Abstract
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno’s law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes is to decide the male-specific characteristics including sex, testis formation, and spermatogenesis, which are majorly formed by ampliconic g...
  • References (131)
  • Citations (3)
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References131
Newest
Published on Dec 1, 2017in Journal of Proteome Research3.78
Anna Meyfour2
Estimated H-index: 2
,
Hassan Ansari4
Estimated H-index: 4
+ 5 AuthorsGhasem Hosseini Salekdeh36
Estimated H-index: 36
Despite evidence for sex-specific cardiovascular physiology and pathophysiology, the biological basis for this dimorphism remains to be explored. Apart from hormonal factors, gender-related characteristics may reside in the function of sex chromosomes during cardiac development. In this study, we investigated the differential expression of the male-specific region of the Y chromosome (MSY) genes and their X counterparts during cardiac differentiation of human embryonic stem cells (hESC). We obse...
Published on Jul 1, 2017in Human Reproduction5.51
Yuanlong Yan4
Estimated H-index: 4
(Sichuan University),
Xiling Yang3
Estimated H-index: 3
(Sichuan University)
+ 6 AuthorsYuan Yang15
Estimated H-index: 15
(Sichuan University)
Published on Apr 28, 2017in Circulation Research15.86
Sophie Dal-Pra4
Estimated H-index: 4
(Duke University),
Conrad P. Hodgkinson22
Estimated H-index: 22
(Duke University)
+ 2 AuthorsVictor J. Dzau115
Estimated H-index: 115
(Duke University)
Rationale: Direct reprogramming of cardiac fibroblasts to cardiomyocytes has recently emerged as a novel and promising approach to regenerate the injured myocardium. We have previously demonstrated the feasibility of this approach in vitro and in vivo using a combination of 4 microRNAs (miR-1, miR-133, miR-208, and miR-499) that we named miR combo. However, the mechanism of miR combo mediated direct cardiac reprogramming is currently unknown. Objective: Here, we investigated the possibility that...
Yi Ding3
Estimated H-index: 3
(UCLA: University of California, Los Angeles),
Diego Ploper7
Estimated H-index: 7
(UCLA: University of California, Los Angeles)
+ 6 AuthorsEdward M. De Robertis17
Estimated H-index: 17
(UCLA: University of California, Los Angeles)
The earliest event in Xenopus development is the dorsal accumulation of nuclear β-catenin under the influence of cytoplasmic determinants displaced by fertilization. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of conditions that inhibit or promote formation of the Spemann organizer signaling center. Loss of function of β-catenin with antisense morpholinos reproducibly reduced the expression of ...
Published on Dec 1, 2016in Biology of Sex Differences3.19
Martin Johansson9
Estimated H-index: 9
(Uppsala University),
Elin Lundin3
Estimated H-index: 3
(Science for Life Laboratory)
+ 6 AuthorsElena Jazin35
Estimated H-index: 35
(Uppsala University)
Background Renewed attention has been directed to the functions of the Y chromosome in the central nervous system during early human male development, due to the recent proposed involvement in neurodevelopmental diseases. PCDH11Y and NLGN4Y are of special interest because they belong to gene families involved in cell fate determination and formation of dendrites and axon.
Published on Dec 1, 2016in Biology of Sex Differences3.19
Samantha D. Praktiknjo2
Estimated H-index: 2
(UdeM: Université de Montréal),
Sylvie Picard12
Estimated H-index: 12
(UdeM: Université de Montréal),
Christian F. Deschepper34
Estimated H-index: 34
(UdeM: Université de Montréal)
Background The C57BL/6J.YA/J mouse strain is a chromosome-substituted line where the original male-specific portion of chromosome Y (MSY) from C57BL/6J mice was substituted for that from A/J mice. In hearts from male C57BL/6J.YA/J and C57BL/6J mice, orchidectomy (ORX) affected in a strictly strain-specific fashion the expression a subset of genes showing enrichment for functional categories, including that of circadian rhythms and cardiac contractility. We further tested whether: (1) there were ...
Published on Sep 1, 2016in Human Mutation4.45
Nina Bögershausen9
Estimated H-index: 9
,
Vincent Gatinois5
Estimated H-index: 5
+ 38 AuthorsDagmar Wieczorek47
Estimated H-index: 47
(HHU: University of Düsseldorf)
Kabuki syndrome (KS) is a rare but recognizable condition that consists of a characteristic face, short stature, various organ malformations, and a variable degree of intellectual disability. Mutations in KMT2D have been identified as the main cause for KS, whereas mutations in KDM6A are a much less frequent cause. Here, we report a mutation screening in a case series of 347 unpublished patients, in which we identified 12 novel KDM6A mutations (KS type 2) and 208 mutations in KMT2D (KS type 1), ...
Published on Jul 18, 2016in Clinical Science5.24
Neza Grgurevic7
Estimated H-index: 7
(University of Ljubljana),
Gregor Majdic21
Estimated H-index: 21
(University of Maribor)
Although considerable progress has been made in our understanding of brain function, many questions remain unanswered. The ultimate goal of studying the brain is to understand the connection between brain structure and function and behavioural outcomes. Since sex differences in brain morphology were first observed, subsequent studies suggest different functional organization of the male and female brains in humans. Sex and gender have been identified as being a significant factor in understandin...
Published on Apr 15, 2016in Circulation Research15.86
Christa L. Blenck2
Estimated H-index: 2
,
Pamela A. Harvey9
Estimated H-index: 9
+ 1 AuthorsLeslie A. Leinwand76
Estimated H-index: 76
Nearly one-third of deaths in the United States are caused by cardiovascular disease (CVD) each year. In the past, CVD was thought to mainly affect men, leading to the exclusion of women and female animals from clinical studies and preclinical research. In light of sexual dimorphisms in CVD, a need exists to examine baseline cardiac differences in humans and the animals used to model CVD. In humans, sex differences are apparent at every level of cardiovascular physiology from action potential du...
Published on Mar 1, 2016in Journal of Cellular Biochemistry3.45
Sizhou Huang1
Estimated H-index: 1
(Chengdu Medical College),
Qian Li1
Estimated H-index: 1
+ 1 AuthorsXiaohong Li3
Estimated H-index: 3
The human protein kinase X gene (PRKX) and cAMP-dependent protein kinase (PKA) are both c-AMP-dependent serine/threonine protein kinases within the protein kinase AGC subgroup. Of all the protein kinases in this group, PRKX is the least studied. PRKX has been isolated from patients with chondrodysplasia punctate and is involved in numerous processes, including sexual differentiation and fertilization, normal kidney development, and autosomal dominant polycystic kidney disease (ADPKD), blood matu...
Cited By3
Newest
Published on Mar 4, 2019in Expert Review of Proteomics2.96
José González-Gomariz (University of Navarra), Elizabeth Guruceaga13
Estimated H-index: 13
(University of Navarra)
+ 1 AuthorsVictor Segura24
Estimated H-index: 24
(University of Navarra)
ABSTRACTIntroduction: The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SR...
Published on Dec 1, 2018in Reproductive Biology and Endocrinology2.59
Stacy Colaco2
Estimated H-index: 2
(National Institute for Research in Reproductive Health),
Deepak Modi22
Estimated H-index: 22
(National Institute for Research in Reproductive Health)
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that ...
Published on Dec 1, 2017in Journal of Proteome Research3.78
Young-Ki Paik41
Estimated H-index: 41
,
Christopher M. Overall73
Estimated H-index: 73
(UBC: University of British Columbia)
+ 2 AuthorsGilbert S. Omenn65
Estimated H-index: 65
This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HP...