Genomics research and related news I found interesting...
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Genomics research and related news I found interesting...
A totally biased and personal choice of interesting papers and web news/comments about genomics (in different fields of research)...  and the reasons why I did like them (if I have time to write it ;-)
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▶ Epigenome: The symphony in your cells - YouTube

Published on Feb 18, 2015

Almost every cell in your body has the same DNA sequence. So how come a heart cell is different from a brain cell? Cells use their DNA code in different ways, depending on their jobs. Just like orchestras can perform one piece of music in many different ways. A cell’s combined set of changes in gene expression is called its epigenome. This week Nature publishes a slew of new data on the epigenomic landscape in lots of different cells. Learn how epigenomics works in this video.

Read the latest research on epigenetics at http://www.nature.com/epigenomeroadmap

steva.travaggio's insight:

A very original approach to explain gene expression regulation through epigenetic mechanisms!

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Single-cell genome sequencing gets better and better

Single-cell genome sequencing gets better and better | Genomics research and related news I found interesting... | Scoop.it

Researchers led by bioengineers at the University of California, San Diego have generated the most complete genome sequences from single E. coli cells and individual neurons from the human brain. The breakthrough comes from a new single-cell genome sequencing technique that confines genome amplification to fluid-filled wells with a volume of just 12 nanoliters. "Our preliminary data suggest that individual neurons from the same brain have different genetic compositions. This is a relatively new idea, and our approach will enable researchers to look at genomic differences between single cells with much finer detail," said Kun Zhang, a professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering and the corresponding author on the paper.

 

The researchers report that the genome sequences of single cells generated using the new approach exhibited comparatively little "amplification bias," which has been the most significant technological obstacle facing single-cell genome sequencing in the past decade. This bias refers to the fact that the amplification step is uneven, with different regions of a genome being copied different numbers of times. This imbalance complicates many downstream genomic analyses, including assembly of genomes from scratch and identifying DNA content variations among cells from the same individual.

 

Sequencing the genomes of single cells is of great interest to researchers working in many different fields. For example, probing the genetic make-up of individual cells would help researchers identify and understand a wide range of organisms that cannot be easily grown in the lab from the bacteria that live within our digestive tracts and on our skin, to the microscopic organisms that live in ocean water. Single-cell genetic studies are also being used to study cancer cells, stem cells and the human brain, which is made up of cells that increasingly appear to have significant genomic diversity.


Via Dr. Stefan Gruenwald, Alberto Goldoni
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Eduardo Camina Paniagua's curator insight, November 19, 2013 1:55 AM
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases in a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as diagnostic, and biological systemathics. The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbiall species.

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Genomic organization of human transcription initiation complexes [Nature 502, 53–58 (03 October 2013)]

The human genome is pervasively transcribed, yet only a small fraction is coding. Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcription factor IIB (TFIIB) and RNA polymerase (Pol) II. Using ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing), we identify approximately 160,000 transcription initiation complexes across the human K562 genome, and more in other cancer genomes. Only about 5% associate with messenger RNA genes. The remainder associates with non-polyadenylated non-coding transcription. Regardless, Pol II moves into a transcriptionally paused state, and TBP and TFIIB remain at the promoter. Remarkably, the vast majority of locations contain the four core promoter elements— upstream TFIIB recognition element (BREu), TATA, downstream TFIIB recognition element (BREd), and initiator element (INR)—in constrained positions. All but the INR also reside at Pol III promoters, where TBP makes similar contacts. This comprehensive and high-resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events from yeast to humans at Pol II/III TATA-containing/TATA-less coding and non-coding genes.

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Nature Special: Mouse ENCODE

Nature Special: Mouse ENCODE | Genomics research and related news I found interesting... | Scoop.it
steva.travaggio's insight:
After the human genome ENCODE here comes the mouse... a great follow-up project and resources!
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DNA: Celebrate the unknowns : Nature : Nature Publishing Group

DNA: Celebrate the unknowns : Nature : Nature Publishing Group | Genomics research and related news I found interesting... | Scoop.it
On the 60th anniversary of the double helix, we should admit that we don't fully understand how evolution works at the molecular level, suggests Philip Ball.
steva.travaggio's insight:

A very interesting commentary... after all doing science is moving forward from unknown to unknown :-) I agree with the author that, even if not easy to do for some of us, we might have to "admit that we are not so close to understand ourselves as we thought".

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An integrated encyclopedia of DNA elements in the human genome [Nature 489, 57–74 (06 September 2012)]

An integrated encyclopedia of DNA elements in the human genome [Nature 489, 57–74 (06 September 2012)] | Genomics research and related news I found interesting... | Scoop.it

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

steva.travaggio's insight:

A key publication with very interesting results and several important data analysis tools that are now available to a larger community of genomics researchers.

To note that this paper shows that "it is possible to correlate quantitatively RNA sequence production and processing with both chromatin marks and transcription factor binding at promoters, indicating that promoter functionality can explain most of the variation in RNA expression." I found this conclusion quite important, as I feel that sometimes in recent days with the discovery of other regulators of gene expression, we might forget the central role of promoters in transcriptional regulation.

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