Flatten a List of Lists in R

How to flatten a list of lists in R

Coefficient of Variation as a Measure for Transcriptional Stability

"To measure transcriptional stability, we computed the coefficient of variation for gene expression over 12 developmental time points."

Mini Review "Cohesin Loading and Sliding"

Cohesin Loading and Sliding

MS2 Tagging

Cited from In Vivo RNA Visualization in Plants Using MS2 Tagging

"This technique involves the tagging of the RNA of interest with repeats of an RNA stem-loop (SL) that is derived from the origin of assembly of the bacteriophage MS2 and recruits the MS2 coat protein (MCP). Thus, expression of MCP fused to a fluorescent marker allows the specific visualization of the SL-carrying RNA."

Condensins, Topoisomerases and Cohesion

Cited from the review "Chromosome  Condensation and Cohesion"

"Early research on chromosome structure demonstrated the
existence of a nonhistone protein scaffold that runs along the chromatids. This scaffold  is composed mainly of two proteins topoisomerase IIa  and the condensin subunit SMC2."

"Topoisomerases modify the topology of DNA by transiently introducing nicks in a single strand to allow relaxation of supercoils (topoisomerases I and III) or breaking a  double strand to allow passage of another DNA duplex  through the opening (topoisomerase II). The latter  reaction allows the catenation or decatenation of two DNA molecules and is essential for chromosome individualisation and condensation, as well as for sister-chromatid  resolution and segregation."

"Condensins contain two Structural Maintenance of Chromosomes (SMC) proteins, SMC2 and SMC4. They form long coiled-coil rods joined by a hinge region and containing an adenosine triphosphatase (ATPase) head at the free end."

"Eukaryotic SMCs are found in  three types of complexes. Condensins consisting of the SMC2/4 heterodimer are involved in chromosome condensation. The cohesin complex containing SMC1/3  mediates sister-chromatid cohesion. The SMC5/6 complex is involved in DNA repair and telomere maintenance."

"Two forms of condensin complexes exist: condensins I and II. Both complexes are pentamers that contain SMC2 and SMC4, but differ in their non-SMC subunits. Condensin I contains the non-SMC subunits CAP-D2, CAP-G and CAP-H, whereas condensin II contains CAP-D3, CAP-G2 and CAP-H2."

"These two complexes might play  different roles in the condensation process, since depletion  of non-SMC subunits of condensin I results in ‘puffed’  chromosomes while depletion of those in condensin II leads  to ‘curly’ chromosomes."

"It is generally accepted that both condensin and topoisomerase IIa (Topo IIa) are important for chromosome condensation."

"Both Topo IIa and condensin associate with chromosomes in late G2 primarily at centromeres.Topo IIa decorates the chromosome scaffold during prophase, but condensin enrichment occurs later, in prometaphase."

"Condensin II is present in the nucleus during interphase
while condensin I is cytoplasmic and comes into contact
with chromosomes only after nuclear envelope breakdown.
Selective depletion of condensin II, but not condensin I,
by depleting their non-SMC subunits showed delayed
chromosome condensation in prophase."

"Interestingly, cells depleted of both condensins  I and II were still able to condense their chromosomes."

"Maintenance of chromosome condensation, therefore, seems to rely more on condensin."

"Cohesin binds to chromatin during early G1 and before  DNA replication, however, suggesting that cohesin binding to chromatin does not equal sister-chromatid cohesion."

"Approximately 90% of cohesin can be depleted  from human cells without substantial defects in sister chromatid cohesion."

"In higher eukaryotes, cohesin removal occurs  through two pathways. In the prophase pathway, Plk1- mediated phosphorylation of SA1/2 triggers its removal by  the Wapl–Pds5 complex. This pathway removes most cohesin from the chromosome arms. Centromeric cohesin is protected from  the prophase pathway by the Sgo1–PP2A complex. In the metaphase pathway, the Scc1 subunit  of the centromeric pool of cohesin is cleaved by separase  to allow anaphase onset."

"Centromeric cohesion is actively protected  during mitosis by two mechanisms: protection against  cohesin removal by the Sgo1–PP2A complex and inhibition of separase activation by the spindle checkpoint."

"Thus, Topo IIa is  required not only for chromosome individualisation and  condensation during early mitosis, but also for sister chromatid separation during anaphase."

"Cleavage of centromeric cohesin by separase  promotes DNA decatenation by Topo IIa, presumably  because cohesin removal increases the access of Topo IIa to  catenated DNA."

Mitosis-specific Histone Modifications

Cited from the review "Chromosome  Condensation and Cohesion"

"H3-S10 phosphorylation is mediated by the Aurora B kinase.It initiates at centromeres in late G2 and extends to the whole chromosome by early mitosis."

"Phosphorylation of H3-S10 dissociates chromatin-bound proteins such as heterochromatin protein 1 (HP1) and splicing factors SRp20 and ASF/SF2 during mitosis, suggesting that this phosphorylation event might contribute to chromosome condensation by removing chromatin-bound proteins ."

"In addition to histone H3, the linker histone H1 is also
heavily phosphorylated during mitosis, which has been
implicated in chromosome condensation."