Genome Jigsaws (Photo credit: dullhunk)
Sequencing became the household name. In 2000s, it was thought to be the key of the Pandora’s box for cure. Then, after completion of Human Genome Projects showed that there are less number of genes than expected. This outcome induce to originate yet another set of sequencing programs and collaborations around the world, such as Human Protein Project, Human Microorganisms Projects, ENCODE, Transcriptome Sequencing and Consortiums etc.
It is in humankind to believe in magic and illusion. The strength of biological diversity and complex mechanism of expression may chalanges the set up of a simple but informative specific essay. Thus, there is a new developing field to mash rules of biology with mathematical formulas to develop the best bioinformatics or also called computational biology. Predicting transcription start or termination sites, exon boundaries, possible binding sites of transcription regulators for chromatin modification activities, like histone acetylates and enhancer- and insulator-associated factors based on the human genome sequence. Deep in mind, this assumption supports that the sequence contains signatures for chromatin modifications essential for gene regulation and development.
There are three primary colors, red, yellow and blue, however, an artist can create many shades. Recently, scientists combining and organizing more data to make sense of our blueprint of life to transfer info generation to generation with the hope to cure diseases of human kind.
Analyzing genome and transcriptome open the door. These studies suggested that all eukaryotic cells has a rich portfolio of RNAs. Among these long non-coding RNAs has impact on protein coding gene expression, regulating multiple processes even including epigenetic gene expression.
Epigenetics, stemness and non-coding RNAs play a great role to manipulate and correct the gene expression not only at a proper cell type but also location and time within genome without disturbing the host.
Main concern is differentiation of embryonic stem cells under these epigenetics and influencers. The best known post-transcriptional modifications, which include methylation, acetylation, ubiquination, and SUMOylation of lysine residues, methylation of arginine residues, and phosphorylation of serines, occur on histone tails. “Epi” means “top” or
“above” so this mechanism give a new direction to the genetic pathways as long as the organism live sometime and may lead into evolutions. It is critical to show the complexity of
mechanism and relativity of a gene role with a single example for each.
For example, DNA methylation occurs mostly on cytosine residues on the CpG islands usually located on promoter regions that are associated with tissue-specific gene expression. However, there are many other forms of DNA methylations, such as monoallelic methylation in gene imprinting and inactivation of the X chromosome, in repetitive elements, like transposons. There are two main mechanisms but this is not our main topic. Yet, Myc and hypoxia-inducible factor-1α versus certain methyl-CpG-binding proteins, such as MBD1,MBD2, MBD4, MeCP2, and Kaiso works differently.
Stemness is an important factor for an intervention to correct a pathological condition. In terms of epigenetics, regulation and non-coding RNA Vascular endothelial growth factor A (VEGF-A) is an interesting example for differentiation of endothelial cells and morphogenesis of the vascular system during development with several reasons, epigenetics, gene interactions, time and space. Everything has to be just right, because neither less nor too much can fulfill the destiny to become a complete adult cell or an organism. For example, both having only one VEGF-A allele and having two-fold excess of VEGF-A results in death during early embryogenesis, since mice can’t develop proper vascular network. However, explaining diverse mechanisms and functions of VEGF-A is require more information with specific details. VEGF-A plays many roles in many pathological cases, such as cancer, inflammation, retinopathies, and arthritis because VEGF-A has also function in epigenetic reprogramming of the promoter regions of Rex1 and Oct4 genes, that are critical for a stem cell. Preferred mechanism is anti-angiogeneic state but tumor cells prefer hypermethylation to induce pro-angiogeneic state, thus VEGF-A stimulates PIGF in tumour cells among many other factors.
Now, let’s turn around to observe development of a cell with Polycomb repressive complexes (PRCs) because they are important chromatin regulators of embryonic stem (ES) cell function. Originally, RYBP shown to function as transcriptional repressor in reporter assays from both in tissue culture cells and in fruit fly (Drosophila melanogaster ) and as a direct interactor with Ring1A during embryogenesis through methylation. In addition, RYBP in epigenetic resetting during preimplantation development through repression of germ line genes and PcG targets before formation of pluripotent epiblast cells. However, I do believe that the most important element is efficient repression of endogenous retroviruses (murine endogenous retrovirus called MuERV class), preimplantation containing zygotic genome activation stage and germ line specific genes. The selective repressor activity of RYBP is in the ES cell state. When RYBP−/− ES cells were analyzed by measuring gene expression during differentiation as embryo bodies formed from mutant and wild-type cells, the result presented that expression of pluripotency genes Oct4 and Nanog was usually downregulated. However, RYBP is able to bind genomic regions independently of H3K27me3 and there is no relation between altered RYBP binding in Dnmt1-mutant cells to DNA methylation status. In sum, RYBP has a large value in undifferentiated ES cells and may affect or even reset epigenetic landscape during early developmental stages. These are the gaps filled by long non coding RNAs.
We learn more compelling information by comparing and contrasting what is normal and what is abnormal. As a result, pathology is a key learning canvas for basic mechanisms in molecular genetics. Then peppered with functional genomics completes the story for an edible outcome. We generally refer this as a Translational Research. For example, recent foundlings suggest that H19 contributes to cancer, including hepatocellular carcinoma (HCC) after reviewing Oncomine resource. According to these observations, in most HCC cases there is a lower expression of H19 level is compared to the liver. Thus, in vitro and in vivo studies were undertaken with classical genetic analyzes based on loss- and gain-of-function on H19 to characterize two outcomes depend on H19, that are the effects on gene expression and on HCC metastasis. First, the expression of H19 showed gene expression variation since H19 expression was low in tumor cells than peripheral tumor cells. Second, the metastasis of cancer based on alteration of miR-200 pathway contributing mesenchymal-to-epithelial transition by H19. Therefore, H19 and miR-200 are targets to be utilized during molecular diagnostics development and establishing targeted therapies in cancer.
Long story short, there is a circle of life where everything is connected even though they look different. As a result, when we see a sunflower or a baby we remember to smile, because life is still an act to puzzle human.
References and Further Readings:
“Non-coding RNAs as regulators of gene expression and epigenetics” Cardiovascular Res 1 June 2011: 430-440.
“Epigenetic regulation of key vascular genes and growth factors” Cardiovasc Res 1 June 2011: 441-446.
“Epigenetic Regulation by Long Noncoding RNAs” Science 14 December 2012: 1435-1439.
“Epigenetic control of embryonic stem cell fate” JEM 25 October 2010: 2287-2295.
“Transcribed dark matter: meaning or myth?” Hum Mol Genet 15 October 2010: R162-R168.
“Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma” Carcinogenesis 1 March 2013: 577-586.
“Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA” Science 7 January 2011: 76-79.
“Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context” Bioinformatics 1 May 2013: 1199-1205.
Further Readings specific to Embryonic Stem Cell Differentiation and Development :
“BMP Induces Cochlin Expression to Facilitate Self-renewal and Suppress Neural Differentiation of Mouse Embryonic Stem Cells” J. Biol. Chem. 2013 288:8053-8060
“Regulation of DNA Methylation in Rheumatoid Arthritis Synoviocytes” J. Immunol. 2013 190:1297-1303
“DNA methylome signature in rheumatoid arthritis” Ann Rheum Dis 2013 72:110-117
“The histone demethylase Kdm3a is essential to progression through differentiation” Nucleic Acids Res 2012 40:7219-7232
“Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer” Nucleic Acids Res 2012 40:6725-6740
“Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells” Nucleic Acids Res 2012 40:3403-3418
“RYBP Represses Endogenous Retroviruses and Preimplantation- and Germ Line-Specific Genes in Mouse Embryonic Stem Cells” Mol. Cell. Biol. 2012 32:1139-1149
“Polycomb Repressor Complex-2 Is a Novel Target for Mesothelioma Therapy” Clin. Cancer Res. 2012 18:77-90
“OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes” Proc. Natl. Acad. Sci. USA 2011 108:14497-14502
“Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging” Blood 2011 117:e182-e189
“The CHD3 Chromatin Remodeler PICKLE and Polycomb Group Proteins Antagonistically Regulate Meristem Activity in the Arabidopsis” RootPlant Cell 2011 23:1047-1060
“Chromatin structure of pluripotent stem cells and induced pluripotent stem cells” Briefings in Functional Genomics 2011 10:37-49
Abbreviations used:
DNMT DNA methyl transferase
ES embryonic stem
JmjC Jumonji C
lincRNA long ncRNA
ncRNA noncoding RNA
PcG Polycomb group
PRC Polycomb repressive complex
PRE Polycomb repressive element
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Nice article which brings up the point of context when talking about methylation patterns in cancer. You had said, in reference to RYPB (polycomb) the, as a result of data fro the RYPB knockout studies that ES cells lost their pluripotency presumably by losing Oct4 and Nanog expression and that polycomb repressor can bind to methylated DNA which may result through “gaps filled by long noncoding RNA’s”. Are you suggesting there were possibly other factors (the long coding RNA’s) which may regulate transcriptional repression along with polycomb?
In addition I find the discussion of H19 interesting since this is altered expression not a complete loss, correct? There seems to be other factors, such as HIF1 which may alter the H19 expression as well as the mir-200. All in you are correct that all expression data always need to be taken into context Therefore the bioinformatics becomes critical if expression analysis is used in the clinical setting for diagnosis and treatment strategy.
Hi Dr. Williams,
Thank you for your comments and insightful points onto the subject. lincRNAs along with other types of ncRNAs function in gene regulation at transcriptional level. I need to back up a little. RYBP controls Ring1A and Ring1B that are Polycomb H2A monoubiquitin ligases. Thus, the assistance of RYPB helps PrC localization to their targets. When RYPB interrupted different types of pathologies arise.
Polycomb repressive complexes (PrCs) are important. RYPB function in undifferentiated ESc independent of methylation since RYPB. Dynamic recruitment of PcG proteins to chromatin during lineage specification and DNMTs are two main influencers of ESc. PrCs is very special since they put out a critical background before anything changes or differentiates. At this stage ncRNAs has a function to insure that correct methylation initiate the target genes for time and tissue specify differentiation. However, before target genes OCT4, NANOG and SOX2 need to know how they are commend these actions. This stage is the very early stage of stem cells “stemness” sometimes it is referred as “undifferentiated stage”. As a result, these ncRNAs modulate the polycomb. Thus studying HOX, or sperm vs. egg that is female vs. male even in sex-linked pathologies or cancer for disrupted cell differentiation has a great importance. However, “Importantly, lincRNAs show dynamic patterns of expression with suggested roles in cell fate choices,
But the mechanisms by which these trans-acting ncRNAs
Recruit PcG complexes to specific sites are not fully understood” as a result there are theories. Bioinformatics must include molecular genetics, developmental biology with evolution, pathologic conditions, and epigenetics for personal genomics as well as mechanism on gene regulation.
HCCs have a great interest since not only we study stem cells but also understand the only regenerating organ “liver” in our body. Also, produces enzymes, coagulation factors, bile mechanism, glicolysis etc, among many physiological roles. Yes, H19 is not a complete loss genetically but altered expression. Indeed, this is a great point since some knock out studies forget about this factor. Usually certain exons, part of promoter are deleted without taking consideration of ncRNAs or introns.
Not to mention, endogenous microorganisms alter these ncRNAs because the introns and ncRNAs are also their close relatives.
In sum, genomics and bioinformatics is not about A, T, C, G or Us require a great deal of synthesis with system biology and development approaches.
Methylation Status of Imprinting Centers for H19/IGF2 and SNURF …
You have full text access to this OnlineOpen article Methylation Status of Imprinting Centers for H19/IGF2 and SNURF/SNRPN in Primate Embryonic Stem Cells
onlinelibrary.wiley.com/doi/10.1634/stemcells.2006-0120/full
Downregulation of H19 Improves the Differentiation Potential of …
NCBI; Skip to main content; Skip to navigation; Resources. All Resources; Chemicals & Bioassays. BioSystems
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328764
More results from ncbi.nlm.nih.gov »
Parthenogenetic embryonic stem cells with H19 siRNA-mediated …
1. Int J Mol Med. 2012 Feb;29(2):257-62. doi: 10.3892/ijmm.2011.838. Epub 2011 Nov 15. Parthenogenetic embryonic stem cells with H19 siRNA-mediated knockdown as a …
http://www.ncbi.nlm.nih.gov/pubmed/22089545
The above articles also a good source to introduce importance of H19 as well as other unknown ncRNAs for stemness.
Dr. Sag,
Thank you for this creative article, linking genomics with stem cells.
Few comments:
1. Please research HCC on our Journal, work by Dr. Ritu and Dr. Saha, pl.add to references with picture, I love that format, teach me how to do it.
2. Translational medicine is of strong interest to us. Would you consider to join forces with Dr. Williams to edit a new e-Book on that topic?
3. I am interested in the Genomics of Hormones and Enzyme – How is that related to Epigenetics? May be a collaboration with Dr. Saha on this matter can yield a new e-Book.
Great direction of scientific discussion.
Thank you. I will include HCC articles. To be able to generate pictures you need to change the settings of your blog “screen options” so that when you do the search simply it shows the pictures and the articles they posted. All you need to do is copy and paste.
I like to collaborate with Dr. Williams to edit and write the e-book.
Genomics Enzymes and Hormones are important. The key is studying female and male embryonic cell development as well well pregnancy, maternity and sex-linked diseases. Thus epigenetics is the MAIN interest during this procedure. Sperm versus egg acts differently during methylation but there are mechanisms does not controlled in the egg/female compare to sperm. I am looking for a stem cell and epigenetics position in translational medicine. People overlook onto this subject or there are studies but little connection.
Regards Dee
If you have any questions or would like more information, please don’t hesitate to contact me via email demet.sag@gmail.com or phone at 919-259-1204.
I look forward to hearing from you soon.
Sincerely,
Dee Sag, PhD, CRA, GCP Translates science for personalized medicine with passion
http://www.vodinh.pratt.duke.edu/people.
Thank you. I will include HCC articles. To be able to generate pictures you need to change the settings of your blog “screen options” so that when you do the search simply it shows the pictures and the articles they posted. All you need to do is copy and paste.
I like to collaborate with Dr. Williams to edit and write the e-book.
Genomics Enzymes and Hormones are important. The key is studying female and male embryonic cell development as well well pregnancy, maternity and sex-linked diseases. Thus epigenetics is the MAIN interest during this procedure. Sperm versus egg acts differently during methylation but there are mechanisms does not controlled in the egg/female compare to sperm. I am looking for a stem cell and epigenetics position in translational medicine. People overlook onto this subject or there are studies but little connection.
Regards
Dee
I haven’t paid attention to this recently. Frank Dixon, Chairman of Pathology at Pittsburgh, became the first Director of the Scripps Institute. He was young, and he had a great Department at Pittsburgh. He did a lot with hepatomas, and Herschel Sidransky, who left Pittsburgh to become my Chairman before taking the position at George Washington University, did a lot of work with minimal deviation asnd fast growing hepatomas, although his work on induction of kwashiorkor made him famous.
I don’t know whether there has been work since then related to H19 expression and minimum deviation vs fast-growing hepatoma.
I did some work on the hepatomas for which I filed a continuation patent. There was a defect in the cytoplasmic malate dehydrogenase. I could assay for the mitochondrial and cytoplasmic MDH using the differential effect of the abortive ternary complex of MDH, NAD+, and OAA, for which there was differential inhibition. We checked the assay against centrifugation and other methods, which led us to publish on the comparison between different species of animals. In the studies on hepatomas I found that I kept raising the concentration of OAA, but I did not saturate the enzyme. The Km is a fingerprint of the enzyme. I sent my graduate student to work with Johannes Everse, at Texas Tech University. They published the work in the British J Cancer. Now, Matt Grisham has returned to TT as Chairman of Microbiology.
[…] V. By: Demet Sag PhD CRA, GCP. The Magic of the Pandora’s Box : Epigenetics and Stemness with Long non-coding RNAs (lincRNA). https://pharmaceuticalintelligence.com/2013/06/30/the-magic-of-the-pandoras-box-epigenetics-and-stemm… […]