FAQs about our Project



       Frequently asked questions (FAQs) on Synthetic Chromatin

<!-- /* Font Definitions */ @font-face {font-family:"Times New Roman"; panose-1:0 2 2 6 3 5 4 5 2 3; mso-font-charset:0; mso-generic-font-family:auto; mso-font-pitch:variable; mso-font-signature:50331648 0 0 0 1 0;} @font-face {font-family:Arial; panose-1:0 2 11 6 4 2 2 2 2 2; mso-font-charset:0; mso-generic-font-family:auto; mso-font-pitch:variable; mso-font-signature:50331648 0 0 0 1 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman";} p.MsoListBullet2, li.MsoListBullet2, div.MsoListBullet2 {mso-style-update:auto; margin-top:0in; margin-right:0in; margin-bottom:0in; margin-left:.5in; margin-bottom:.0001pt; text-indent:-.25in; mso-pagination:widow-orphan; mso-list:l0 level1 lfo3; tab-stops:list .5in; font-size:12.0pt; font-family:"Times New Roman";} table.MsoNormalTable {mso-style-parent:""; font-size:10.0pt; font-family:"Times New Roman";} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} /* List Definitions */ @list l0	{mso-list-id:-125; mso-list-type:simple; mso-list-template-ids:-1508585756;} @list l0:level1 {mso-level-number-format:bullet; mso-level-style-link:"List Bullet 2"; mso-level-text:\F0B7; mso-level-tab-stop:.5in; mso-level-number-position:left; text-indent:-.25in; font-family:Symbol;} @list l1	{mso-list-id:52774932; mso-list-type:hybrid; mso-list-template-ids:989912902 67698703 67698689 67698689 67698703 67698713 67698715 67698703 67698713 67698715;} @list l1:level2 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:1.0in; mso-level-number-position:left; text-indent:-.25in; font-family:Symbol;} @list l1:level3 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:117.0pt; mso-level-number-position:left; margin-left:117.0pt; text-indent:-.25in; font-family:Symbol;} @list l2	{mso-list-id:524756907; mso-list-type:hybrid; mso-list-template-ids:273606660 67698715 67698689 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} @list l2:level1 {mso-level-number-format:roman-lower; mso-level-tab-stop:.75in; mso-level-number-position:right; margin-left:.75in; text-indent:-.25in;} @list l2:level2 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:1.0in; mso-level-number-position:left; text-indent:-.25in; font-family:Symbol;} @list l3	{mso-list-id:1669675019; mso-list-type:hybrid; mso-list-template-ids:1454386800 67698689 67698713 67698715 67698703 67698713 67698715 67698703 67698713 67698715;} @list l3:level1 {mso-level-number-format:bullet; mso-level-text:\F0B7; mso-level-tab-stop:1.0in; mso-level-number-position:left; margin-left:1.0in; text-indent:-.25in; font-family:Symbol;} ol {margin-bottom:0in;} ul {margin-bottom:0in;} -->



Q. How is control of gene expression by chromatin different from control by transcription factors (and what are its advantages)?

<span style='font-size:11.0pt;font-family:Arial'><![if !supportEmptyParas]> <![endif]></o:p>

<p class=MsoNormal> A. Chromatin is a completely different level of gene expression control.</o:p></b>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> Dominant over transcription factors (resistant to noise).</o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> Regional &#8211; silences domains, not individual genes (reduces the engineering required for regulation of complex multi-gene systems).</o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> Memory&#8211;Alteration in gene expression lasts for multiple generations (epigenetic control).</o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> Intrinsically bistable, i.e. all-or-none expression (increases parameter space over which circuits are predicted to be stable).</o:p>

<p class=MsoNormal> <![if !supportEmptyParas]> <![endif]></o:p>

<p class=MsoNormal> <![if !supportEmptyParas]> <![endif]></o:p>

<p class=MsoNormal style='margin-left:.5in;text-indent:-.5in'><span style='font-size:11.0pt;font-family:Arial'>Q. What applications could this type of synthetic chromatin control system be used for?</o:p></b>

<p class=MsoNormal> <![if !supportEmptyParas]> <![endif]></o:p>

<p class=MsoNormal> A. To stably and permanently switch cells between different states characterized by significant differences in gene expression (i.e. cellular differentiation).</o:p></b>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l2 level2 lfo7; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> In bio-production&#8211;for coordinated switching between a growth phase and a production phase.</o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l3 level1 lfo9; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> In bio-production&#8211;to differentiate a clonal population of cells into a distribution of subtypes that function cooperatively (“factory” with different specialized “workers”).</o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> To reprogram cell fate in a highly specific manner (e.g. stem cell engineering, correction of epigenetic abnormalities in cancer cells).<o:p></o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> To create cells with highly digital computational capabilities.<o:p></o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> To study chromatin spreading mechanism in a quantitative and controlled way.<o:p></o:p>

<p class=MsoNormal style='margin-left:.25in'><span style='font-size:11.0pt; font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p>

<p class=MsoNormal style='margin-left:.25in'><span style='font-size:11.0pt; font-family:Arial'><![if !supportEmptyParas]> <![endif]><o:p></o:p>

<p class=MsoNormal> <b>Q. Could this type of yeast synthetic chromatin control system be utilized in other cell types, including mammalian cells?<o:p></o:p></b>

<p class=MsoNormal> <![if !supportEmptyParas]> <![endif]><o:p></o:p>

<p class=MsoNormal> <b>A. Yes, the approach should be transferable.<o:p></o:p></b>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> Core elements of this system are: initiator, covalent mark, spreading (polymerization).<o:p></o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> In S. cerevisiae <span style='font-size:11.0pt'>, covalent mark is deacetylation&#8211;we use an initiator (LexA-Sir2) that when localized deacetylates adjacent histones.<span style="mso-spacerun: yes"> This leads to further recruitment of Sir2, which propagates the mark outward. Deacetylated chromatin adopts a “closed” conformation. <o:p></o:p>

<p class=MsoListBullet2 style='margin-left:1.0in;mso-list:l1 level2 lfo5; tab-stops:list 1.0in'><![if !supportLists]><span style='font-size:11.0pt; font-family:Symbol'>· <![endif]> For higher eukaryotes, from S. pombe to human, the covalent mark is methylation, initiator is a histone methyltransferase. But in principle, a similar system should work. Same logical design, with different catalytic functions propagating spread.<o:p></o:p>

<p class=MsoNormal> <span style="mso-spacerun: yes"> <o:p></o:p>