Here is a set of conditions that does not require $a$, $b$ or $f$ to be $\mathcal C^1$.
Assume for simplicity that $f$ is defined on $\mathbb R^2$ and that the functions $a,b$ are defined on $\mathbb R$. Then, the function $F$ defined by
$$F(x)=\int_{a(x)}^{b(x)} f(x,t)\, dt $$ will be differentiable with derivative given by the above formula provided that
(1) the functions $a$ and $b$ are differentiable;
(2) $f(x,t)$ is continuous with respect to $t$;
(3) $\frac{\partial f}{\partial x}(x,t)$ exists at all points;
(4) for any compact intervals $I,J\subset\mathbb R$, there exists an integrable function $g:J\to\mathbb R^+$ such that
$$\left\vert \frac{\partial f}{\partial x}(x,t)\right\vert\leq g(t)\quad {\rm on}\quad I\times J $$
As you know, the idea is to consider the function of 3 variables defined by
$$\Phi(u,v,x)=\int_u^v f(x,t)dt\, .$$
By condition (2) and the fundamental theorem of calculus, $\frac{\partial\Phi}{\partial v}$ exists at all points and is given by $\frac{\partial\Phi}{\partial v}(u,v,x)=f(x,v)$. Likewise, $\frac{\partial\Phi}{\partial u}$ exists at all points and is given by $\frac{\partial\Phi}{\partial u}=-f(x,u)$. Finally, conditions (3) and (4) imply (by the "standard" theorem on differentiating under the integral sign) that $\frac{\partial\Phi}{\partial x}$ also exists at each point and is given by $\frac{\partial\Phi}{\partial x}(u,v,x)=\int_u^v \frac{\partial f}{\partial x}(x,t)\, dt$.
Now, let us show that in fact the function $\Phi$ is differentiable. If we can do this, then, we'll get the required result by (1) since $F(x)=\Phi(a(x),b(x),x)$.
Let us fix $(u,v,x)\in\mathbb R^3$. We have to check that
$$\Phi(u+\delta u, v+\delta v, x+\delta x)-\Phi(u,v,x)=L(\delta u,\delta v,\delta x)+o(\Vert (\delta u,\delta v,\delta x)\Vert) $$
as $(\delta u,\delta v,\delta x)\to (0,0,0)$, where
$$L(\delta u,\delta v,\delta x)=-f(x,u)\,\delta u +f(x,v)\, \delta v+\left(\int_u^v \frac{\partial f}{\partial x}(x,t)\, dt\right) \delta x\, .$$
Without loss of generality, we may assume that $u,v$ $u+\delta$, $v+\delta v$ belong to some fixed compact interval $J$, and that $x, x+\delta x$ belong to some fixed compact interval $I$. So we may use the integrable function $g$ from (4).
Write $$\alpha(\delta u,\delta v,\delta x):=\Phi(u+\delta u,v+\delta v,x+\delta x)-\Phi(u,v,x)-L(\delta u,\delta v,\delta x)\, .$$
We have
\begin{eqnarray}
\alpha(\delta u,\delta v,\delta x)&=&-\left(\int_u^{u+\delta u} f(x+\delta x, t)\, dt -f(x,u)\, \delta u\right)\\& &+\int_v^{v+\delta v} f(x+\delta x, t)\, dt -f(x,v)\, \delta v\\
& &+\int_u^v \left( f(x+\delta x,t)-f(x,t)-\delta x\,\frac{\partial f}{\partial x}(x,t)\right) dt\\
&:=& \varepsilon_1 +\varepsilon_2 +\eta\, .
\end{eqnarray}
We may write
\begin{eqnarray}-\varepsilon_1&=& \int_u^{u+\delta u} \left(f(x+\delta x,t)-f(x,t)\right)dt+\int_u^{u+\delta u}f(x,t)\, dt-f(x,u)\, \delta u\\
&=&\int_u^{u+\delta u} \delta x\, \frac{\partial f}{\partial x}(z(\delta x,t), t)\, dt+\int_u^{u+\delta u} f(x,t)\, dt -f(x,u)\, \delta u\, ,
\end{eqnarray}
where $z(\delta x,t)$ lies between $u$ and $u+\delta u$, and hence belongs to $I$. Using (4), (1) and the fundamental theorem of calculus, it follows that
$$ \varepsilon_1=O(\delta u\delta x)+o(\delta u)=o(\Vert(\delta u,\delta v, \delta x)\Vert)\, .$$
In the same way, we get $$\varepsilon_2=o(\Vert(\delta u,\delta v,\delta x)\Vert\, .$$
Finally, using (4) and the dominated convergence theorem we obtain that
$$\eta =o(\delta x)=o(\Vert (\delta u,\delta v,\delta x)\Vert)\, .$$
Altogether, the map $\Phi$ is indeed differentiable, and the proof is complete.