Additional file of Imprinted genes show unique patterns of sequence conservation

Additional file 1:Imprinted genes according to RefSeq annotation. This Excel spreadsheet gives information about the imprinted genes analyzed in this study, their parental expression, and their imprinting status in human and mouse. (XLS 12 KB)

Additional file 1:Imprinted genes according to RefSeq annotation. This Excel spreadsheet gives information about the imprinted genes analyzed in this study, their parental expression, and their imprinting status in human and mouse. (XLS 12 KB)

In mammalian cells, one-third of all polypeptides is transported into or through the ER-membrane via the Sec61-channel. While the Sec61-complex facilitates the transport of all polypeptides with amino-terminal signal peptides (SP) or SP-equivalent transmembrane helices (TMH), the translocating chain-associated membrane protein (now termed TRAM1) was proposed to support transport of a subset of precursors. To identify possible determinants of TRAM1 substrate specificity, we systematically identified TRAM1-dependent precursors by analyzing cellular protein abundance changes upon TRAM1 depletion in HeLa cells using quantitative label-free proteomics. In contrast to previous analysis after TRAP depletion, SP and TMH analysis of TRAM1 clients did not reveal any distinguishing features that could explain its putative substrate specificity. To further address the TRAM1 mechanism, live-cell calcium imaging was carried out after TRAM1 depletion in HeLa cells. In additional contrast to previous analysis after TRAP depletion, TRAM1 depletion did not affect calcium leakage from the ER. Thus, TRAM1 does not appear to act as SP- or TMH-receptor on the ER-membrane’s cytosolic face and does not appear to affect the open probability of the Sec61-channel. It may rather play a supportive role in protein transport, such as making the phospholipid bilayer conducive for accepting SP and TMH in the vicinity of the lateral gate of the Sec61-channel. Abbreviations: ER, endoplasmic reticulum; OST, oligosaccharyltransferase; RAMP, ribosome-associated membrane protein; SP, signal peptide; SR, SRP-receptor; SRP, signal recognition particle; TMH, signal peptide-equivalent transmembrane helix; TRAM, translocating chain-associated membrane protein; TRAP, translocon-associated protein.

In mammalian cells, one-third of all polypeptides is transported into or through the ER-membrane via the Sec61-channel. While the Sec61-complex facilitates the transport of all polypeptides with amino-terminal signal peptides (SP) or SP-equivalent transmembrane helices (TMH), the translocating chain-associated membrane protein (now termed TRAM1) was proposed to support transport of a subset of precursors. To identify possible determinants of TRAM1 substrate specificity, we systematically identified TRAM1-dependent precursors by analyzing cellular protein abundance changes upon TRAM1 depletion in HeLa cells using quantitative label-free proteomics. In contrast to previous analysis after TRAP depletion, SP and TMH analysis of TRAM1 clients did not reveal any distinguishing features that could explain its putative substrate specificity. To further address the TRAM1 mechanism, live-cell calcium imaging was carried out after TRAM1 depletion in HeLa cells. In additional contrast to previous analysis after TRAP depletion, TRAM1 depletion did not affect calcium leakage from the ER. Thus, TRAM1 does not appear to act as SP- or TMH-receptor on the ER-membrane’s cytosolic face and does not appear to affect the open probability of the Sec61-channel. It may rather play a supportive role in protein transport, such as making the phospholipid bilayer conducive for accepting SP and TMH in the vicinity of the lateral gate of the Sec61-channel. Abbreviations: ER, endoplasmic reticulum; OST, oligosaccharyltransferase; RAMP, ribosome-associated membrane protein; SP, signal peptide; SR, SRP-receptor; SRP, signal recognition particle; TMH, signal peptide-equivalent transmembrane helix; TRAM, translocating chain-associated membrane protein; TRAP, translocon-associated protein.

Table S2. Occurrence of each considered type of transcriptomic alteration per transition. Shown are the number of rewiring events for all observed types of transcriptomic alterations when only exclusive causes were considered. (XLSX 9.79 kb)

Table S3. Pathway enrichment analysis of rewiring events controlled by different types of regulation. Listed are pathways for which annotated interactions could be associated with rewiring events across all transitions that were caused by a certain type of regulation. The exact methodology is described in the â Methodsâ section. In all tables, significantly enriched pathway terms (adj.p<0.05) were marked in green. Very small p-values were reported as 0.0 due to numerical reasons (computed in Python using SciPy version 0.17 [114]). (XLSX 168 kb)

Table S4. Association of rewiring events with protein complexes. Listed are all rewiring events that affected at least one human CORUM complex [56] separated by transition, type of regulation, and direction. (XLSX 193 kb)

Table S5. Pathway enrichment analysis of rewiring events controlled by different types of regulation separated by transition and direction. Listed are pathways for which annotated interactions could be associated with rewiring events that were caused in a certain transition in a certain direction by a certain type of regulation. The exact methodology is described in the â Methodsâ section. Significantly enriched pathway terms (adj.p<0.05) were marked in green. Very small p-values were reported as 0.0 due to numerical reasons (computed in Python using SciPy version 0.17 [114]). (XLSX 455 kb)

Table S6. Sizes of resulting small sets of likely changes in the transcriptome that explain the rewiring in each transition. Listed are the sizes of the resulting small sets of likely changes in the transcriptome that explain the rewiring in each transition, the overall number of rewired interactions for comparison, as well as the number of proteins that are affected by the rewiring. (XLSX 455 kb)