Editing Genomics (section)

== Research areas ==

=== Functional genomics ===
{{Main|Functional genomics}}
Functional genomics is a field of [[molecular biology]] that attempts to make use of the vast wealth of data produced by genomic projects (such as [[genome project|genome sequencing projects]]) to describe [[gene]] (and [[protein]]) functions and interactions. Functional genomics focuses on the dynamic aspects such as gene [[transcription (genetics)|transcription]], [[translation (biology)|translation]], and [[protein–protein interaction]]s, as opposed to the static aspects of the genomic information such as [[DNA sequence]] or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "gene-by-gene" approach.

A major branch of genomics is still concerned with [[sequencing]] the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of [[functional genomics]], mainly concerned with patterns of [[gene expression]] during various conditions. The most important tools here are [[microarray]]s and [[bioinformatics]].

=== Structural genomics ===
{{Main|Structural genomics}}
[[File:Argonne's Midwest Center for Structural Genomics deposits 1,000th protein structure.jpg|An example of a protein structure determined by the Midwest Center for Structural Genomics|thumb|300px]]
Structural genomics seeks to describe the [[Protein Structure|3-dimensional structure]] of every protein encoded by a given [[genome]].<ref name = "Marsden_2007"/><ref name = "Brenner_2000"/> This genome-based approach allows for a high-throughput method of structure determination by a combination of [[protein structure prediction|experimental and modeling approaches]]. The principal difference between structural genomics and [[protein structure prediction|traditional structural prediction]] is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved homologs. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or [[homology modeling|structural homology]] to a protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure. As opposed to traditional [[structural biology]], the determination of a [[protein structure]] through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in [[structural bioinformatics]], i.e. determining protein function from its [[Three-dimensional space|3D]] structure.<ref name = "Brenner_2001"/>

=== Epigenomics ===
{{Main|Epigenomics}}
Epigenomics is the study of the complete set of [[epigenetic]] modifications on the genetic material of a cell, known as the [[epigenome]].<ref name = "Francis_2011"/>   Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p.&nbsp;475).  Two of the most characterized epigenetic modifications are [[DNA methylation]] and [[Epigenetics#DNA methylation and chromatin remodeling|histone modification]].<ref>{{cite journal |last1=Gallego |first1=L.D |last2=Schneider |first2=M |last3=Mittal |first3=C |last4=Romanuska |first4=Anete |last5=Gudino Carrillo |first5=R.M |last6=Schubert |first6=T |last7=Pugh |first7=B.F |last8=Kohler |first8=A |title=Phase separation directs ubiquitination of gene-body nucleosomes |journal=Nature |date=March 2020 |volume=579 |issue=7800 |pages=592–597 |doi=10.1038/s41586-020-2097-z |pmid=32214243 |pmc=7481934 |bibcode=2020Natur.579..592G }}</ref>  Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in [[Epigenetics#Development|differentiation/development]]<ref>{{cite journal |last1=Sams |first1=K.L |last2=Mukai |first2=C |last3=Marks |first3=B.A |last4=Mittal |first4=C |last5=Demeter |first5=E.A |last6=Nelissen |first6=S |last7=Grenier |first7=J.K |last8=Tate |first8=A.E |last9=Ahmed |first9=F |last10=Coonrod |first10=S.A |title=Delayed puberty, gonadotropin abnormalities and subfertility in male Padi2/Padi4 double knockout mice |journal=Reprod Biol Endocrinol |date=October 2022 |volume=20 |issue=1 |page=150 |doi=10.1186/s12958-022-01018-w |pmid=36224627 |pmc=9555066 |doi-access=free }}</ref> and [[Epigenetics#Cancer|tumorigenesis]].<ref name = "Francis_2011"/>  The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.<ref name = "Laird_2010"/>

=== Metagenomics ===
[[File:Environmental shotgun sequencing.png|thumb|right|upright|Environmental Shotgun Sequencing (ESS) is a key technique in metagenomics. (A) Sampling from habitat; (B) filtering particles, typically by size; (C) Lysis and DNA extraction; (D) cloning and library construction; (E) sequencing the clones; (F) sequence assembly into contigs and scaffolds.]]

{{Main|Metagenomics}}
Metagenomics is the study of ''metagenomes'', [[genetics|genetic]] material recovered directly from [[Natural environment|environmental]] samples.  The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional [[microbiology]] and microbial [[genome sequencing]] rely upon cultivated [[clone (genetics)|clonal]] [[microbiological culture|cultures]], early environmental gene sequencing cloned specific genes (often the [[16S ribosomal RNA|16S rRNA]] gene) to produce a [[microbial ecology|profile of diversity]] in a natural sample.  Such work revealed that the vast majority of [[biodiversity|microbial biodiversity]] had been missed by [[Microbiological culture|cultivation-based]] methods.<ref name = "Hugenholz_1998"/> Recent studies use "shotgun" [[chain termination method|Sanger sequencing]] or massively parallel [[pyrosequencing]] to get largely unbiased samples of all genes from all the members of the sampled communities.<ref name = "Eisen_2007"/> Because of its power to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.<ref name = "Marco_2010"/><ref name = "Marco_2011"/>

=== Model  systems ===

==== Viruses and bacteriophages ====
[[Bacteriophage]]s have played and continue to play a key role in bacterial [[genetics]] and [[molecular biology]]. Historically, they were used to define [[gene]] structure and gene regulation. Also the first [[genome]] to be sequenced was a [[bacteriophage]]. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying [[phage]] evolution.  Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of [[prophage]] sequences and prophage-like elements.<ref name = "Canchaya_2003"/> A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome: Overall, this method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.<ref name = "McGrath_2007"/><ref name = "Fouts_2005"/>

==== Cyanobacteria ====
At present there are 24 [[cyanobacteria]] for which a total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six ''[[Prochlorococcus]]'' strains, seven marine ''[[Synechococcus]]'' strains, ''[[Trichodesmium erythraeum]]'' IMS101 and ''[[Crocosphaera watsonii]]'' [[WH8501]]. Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further ''[[Prochlorococcus]]'' and marine ''[[Synechococcus]]'' isolates, ''[[Acaryochloris]]'' and ''[[Prochloron]]'', the N<sub>2</sub>-fixing filamentous cyanobacteria ''[[Nodularia]] spumigena'', ''[[Lyngbya aestuarii]]'' and ''[[Lyngbya majuscula]]'', as well as [[bacteriophage]]s infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into the evolutionary origin of [[photosynthesis]], or estimation of the contribution of [[horizontal gene transfer]] to the genomes that have been analyzed.<ref name = "Herrero_2008"/>